Starting phenix.real_space_refine on Wed Apr 10 04:01:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/04_2024/8e57_27905_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/04_2024/8e57_27905.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/04_2024/8e57_27905_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/04_2024/8e57_27905_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/04_2024/8e57_27905_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/04_2024/8e57_27905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/04_2024/8e57_27905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/04_2024/8e57_27905_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e57_27905/04_2024/8e57_27905_updated.pdb" } resolution = 2.8 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= -0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians I 2 10.91 5 Ca 2 9.91 5 P 1 5.49 5 S 109 5.16 5 C 11967 2.51 5 N 2983 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ASP 465": "OD1" <-> "OD2" Residue "A ASP 598": "OD1" <-> "OD2" Residue "A ASP 662": "OD1" <-> "OD2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1151": "OD1" <-> "OD2" Residue "A ASP 1196": "OD1" <-> "OD2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1296": "OD1" <-> "OD2" Residue "A GLU 1327": "OE1" <-> "OE2" Residue "A GLU 1341": "OE1" <-> "OE2" Residue "A PHE 1384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F ASP 59": "OD1" <-> "OD2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F ASP 430": "OD1" <-> "OD2" Residue "F ASP 493": "OD1" <-> "OD2" Residue "F GLU 497": "OE1" <-> "OE2" Residue "F GLU 575": "OE1" <-> "OE2" Residue "F GLU 587": "OE1" <-> "OE2" Residue "F ASP 603": "OD1" <-> "OD2" Residue "F ASP 654": "OD1" <-> "OD2" Residue "F GLU 688": "OE1" <-> "OE2" Residue "F PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 711": "OD1" <-> "OD2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 740": "OD1" <-> "OD2" Residue "F ASP 820": "OD1" <-> "OD2" Residue "F ASP 849": "OD1" <-> "OD2" Residue "F GLU 980": "OE1" <-> "OE2" Residue "F PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1038": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18449 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8919 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 1068} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "B" 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: "C" 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: "D" 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: "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: 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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {' CA': 1, 'BBI': 1, 'WFR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {' CA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.56, per 1000 atoms: 0.79 Number of scatterers: 18449 At special positions: 0 Unit cell: (147.048, 137.022, 160.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) I 2 52.95 Ca 2 19.99 S 109 16.00 P 1 15.00 O 3385 8.00 N 2983 7.00 C 11967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.04 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.03 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.03 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 1 " - " ASN F 350 " " NAG C 1 " - " ASN F 615 " " NAG D 1 " - " ASN F 898 " " NAG F1203 " - " ASN F 891 " " NAG F1204 " - " ASN F 92 " " NAG F1205 " - " ASN F 606 " " NAG F1206 " - " ASN F 784 " " NAG F1207 " - " ASN F1001 " " NAG F1208 " - " ASN F 988 " " NAG H 1 " - " ASN F 827 " " NAG I 1 " - " ASN F 186 " " NAG J 1 " - " ASN F 470 " Time building additional restraints: 10.26 Conformation dependent library (CDL) restraints added in 4.7 seconds 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 11 sheets defined 51.2% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 53 through 70 Processing helix chain 'A' and resid 81 through 107 removed outlier: 3.963A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 142 removed outlier: 3.634A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 178 removed outlier: 3.516A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 180 through 191 Processing helix chain 'A' and resid 194 through 217 removed outlier: 4.145A pdb=" N HIS A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 323 through 345 Processing helix chain 'A' and resid 434 through 450 Processing helix chain 'A' and resid 458 through 485 removed outlier: 3.909A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 4.001A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 527 Processing helix chain 'A' and resid 530 through 541 removed outlier: 3.896A pdb=" N ARG A 534 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 537 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 540 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 554 removed outlier: 3.611A pdb=" N SER A 551 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 581 Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 635 through 672 removed outlier: 3.623A pdb=" N CYS A 647 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 648 " --> pdb=" O PHE A 645 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 656 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 657 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 662 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 663 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 670 " --> pdb=" O ALA A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 817 Processing helix chain 'A' and resid 827 through 853 removed outlier: 3.589A pdb=" N ILE A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 848 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 849 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 882 removed outlier: 3.935A pdb=" N SER A 882 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 910 removed outlier: 3.906A pdb=" N ARG A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A 902 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ARG A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) Proline residue: A 904 - end of helix removed outlier: 4.615A pdb=" N ALA A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE A 908 " --> pdb=" O PRO A 904 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG A 910 " --> pdb=" O ARG A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 927 Processing helix chain 'A' and resid 930 through 949 Processing helix chain 'A' and resid 976 through 978 No H-bonds generated for 'chain 'A' and resid 976 through 978' Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1016 through 1024 Processing helix chain 'A' and resid 1039 through 1051 Processing helix chain 'A' and resid 1055 through 1070 Processing helix chain 'A' and resid 1084 through 1094 Processing helix chain 'A' and resid 1106 through 1116 removed outlier: 3.957A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1137 removed outlier: 3.545A pdb=" N MET A1137 " --> pdb=" O ILE A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1172 Processing helix chain 'A' and resid 1181 through 1205 Processing helix chain 'A' and resid 1234 through 1249 removed outlier: 3.573A pdb=" N LEU A1243 " --> pdb=" O VAL A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1266 Processing helix chain 'A' and resid 1268 through 1289 removed outlier: 3.662A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 Processing helix chain 'A' and resid 1325 through 1330 Processing helix chain 'A' and resid 1355 through 1387 removed outlier: 3.519A pdb=" N TYR A1358 " --> pdb=" O ASN A1355 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A1363 " --> pdb=" O TYR A1360 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP A1385 " --> pdb=" O ASP A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1409 Processing helix chain 'A' and resid 1419 through 1428 removed outlier: 3.959A pdb=" N VAL A1423 " --> pdb=" O HIS A1419 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1419 through 1428' Processing helix chain 'E' and resid 7 through 27 Processing helix chain 'E' and resid 105 through 132 removed outlier: 3.627A pdb=" N PHE E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LYS E 131 " --> pdb=" O MET E 127 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 164 removed outlier: 3.705A pdb=" N LEU E 137 " --> pdb=" O ASP E 134 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG E 138 " --> pdb=" O TYR E 135 " (cutoff:3.500A) Proline residue: E 139 - end of helix removed outlier: 3.519A pdb=" N ARG E 164 " --> pdb=" O SER E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 203 Processing helix chain 'F' and resid 30 through 52 Processing helix chain 'F' and resid 54 through 64 removed outlier: 3.788A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 110 removed outlier: 4.019A pdb=" N VAL F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 179 through 201 removed outlier: 3.617A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.552A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 4.058A pdb=" N ASN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 346 Processing helix chain 'F' and resid 372 through 378 Processing helix chain 'F' and resid 399 through 405 Processing helix chain 'F' and resid 418 through 424 removed outlier: 4.662A pdb=" N ARG F 422 " --> pdb=" O GLY F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 removed outlier: 3.662A pdb=" N LEU F 432 " --> pdb=" O LEU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 443 removed outlier: 3.867A pdb=" N GLY F 440 " --> pdb=" O MET F 436 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASP F 441 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LYS F 442 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALA F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 484 No H-bonds generated for 'chain 'F' and resid 482 through 484' Processing helix chain 'F' and resid 496 through 502 removed outlier: 3.652A pdb=" N LEU F 502 " --> pdb=" O ASP F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 563 through 566 No H-bonds generated for 'chain 'F' and resid 563 through 566' Processing helix chain 'F' and resid 571 through 581 Processing helix chain 'F' and resid 641 through 650 Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.539A pdb=" N PHE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLU F 657 " --> pdb=" O ASP F 654 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER F 659 " --> pdb=" O PHE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 692 Processing helix chain 'F' and resid 702 through 721 Processing helix chain 'F' and resid 723 through 725 No H-bonds generated for 'chain 'F' and resid 723 through 725' Processing helix chain 'F' and resid 749 through 752 No H-bonds generated for 'chain 'F' and resid 749 through 752' Processing helix chain 'F' and resid 761 through 763 No H-bonds generated for 'chain 'F' and resid 761 through 763' Processing helix chain 'F' and resid 765 through 772 Processing helix chain 'F' and resid 821 through 829 Processing helix chain 'F' and resid 878 through 880 No H-bonds generated for 'chain 'F' and resid 878 through 880' Processing helix chain 'F' and resid 883 through 891 Processing helix chain 'F' and resid 1046 through 1049 No H-bonds generated for 'chain 'F' and resid 1046 through 1049' Processing sheet with id= A, first strand: chain 'A' and resid 225 through 228 Processing sheet with id= B, first strand: chain 'A' and resid 955 through 957 Processing sheet with id= C, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= D, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= E, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.656A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 411 through 415 removed outlier: 3.707A pdb=" N TYR F 411 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP F 255 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N MET F 361 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU F 257 " --> pdb=" O MET F 361 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE F 363 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU F 259 " --> pdb=" O PHE F 363 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE F 290 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE F 258 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASN F 292 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL F 260 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA F 294 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 513 through 517 Processing sheet with id= H, first strand: chain 'F' and resid 661 through 664 removed outlier: 4.212A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS F 818 " --> pdb=" O LYS F 733 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG F 735 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY F 816 " --> pdb=" O ARG F 735 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL F 737 " --> pdb=" O VAL F 814 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL F 814 " --> pdb=" O VAL F 737 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA F 813 " --> pdb=" O VAL F 801 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 851 through 857 removed outlier: 6.828A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 895 through 902 removed outlier: 3.565A pdb=" N ASN F 898 " --> pdb=" O GLN F 983 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN F 983 " --> pdb=" O ASN F 898 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 905 through 907 removed outlier: 3.637A pdb=" N SER F 905 " --> pdb=" O CYS F 977 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2141 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: 6.13 Time building geometry restraints manager: 10.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 5830 1.37 - 1.52: 8820 1.52 - 1.68: 4047 1.68 - 1.83: 172 1.83 - 1.99: 2 Bond restraints: 18871 Sorted by residual: bond pdb=" C03 WFR A1903 " pdb=" C04 WFR A1903 " ideal model delta sigma weight residual 1.278 1.506 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C05 WFR A1903 " pdb=" N06 WFR A1903 " ideal model delta sigma weight residual 1.337 1.520 -0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb=" C31 WFR A1903 " pdb=" C36 WFR A1903 " ideal model delta sigma weight residual 1.381 1.525 -0.144 2.00e-02 2.50e+03 5.22e+01 bond pdb=" C02 WFR A1903 " pdb=" O01 WFR A1903 " ideal model delta sigma weight residual 1.286 1.429 -0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" O18 WFR A1903 " pdb=" P19 WFR A1903 " ideal model delta sigma weight residual 1.672 1.798 -0.126 2.00e-02 2.50e+03 4.00e+01 ... (remaining 18866 not shown) Histogram of bond angle deviations from ideal: 98.75 - 114.96: 11792 114.96 - 131.17: 13759 131.17 - 147.38: 53 147.38 - 163.59: 0 163.59 - 179.80: 1 Bond angle restraints: 25605 Sorted by residual: angle pdb=" CAM BBI A1902 " pdb=" CAN BBI A1902 " pdb=" CAP BBI A1902 " ideal model delta sigma weight residual 118.51 131.07 -12.56 3.00e+00 1.11e-01 1.75e+01 angle pdb=" CAC BBI A1902 " pdb=" CAD BBI A1902 " pdb=" CAE BBI A1902 " ideal model delta sigma weight residual 112.57 124.19 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CAW BBI A1902 " pdb=" CAV BBI A1902 " pdb=" OAU BBI A1902 " ideal model delta sigma weight residual 108.05 117.87 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CB GLU A 336 " pdb=" CG GLU A 336 " pdb=" CD GLU A 336 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.70e+00 3.46e-01 1.06e+01 angle pdb=" CB MET A 941 " pdb=" CG MET A 941 " pdb=" SD MET A 941 " ideal model delta sigma weight residual 112.70 102.99 9.71 3.00e+00 1.11e-01 1.05e+01 ... (remaining 25600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 10472 22.10 - 44.20: 858 44.20 - 66.29: 123 66.29 - 88.39: 36 88.39 - 110.49: 12 Dihedral angle restraints: 11501 sinusoidal: 4914 harmonic: 6587 Sorted by residual: dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual -86.00 -146.94 60.94 1 1.00e+01 1.00e-02 4.94e+01 dihedral pdb=" CB CYS A 226 " pdb=" SG CYS A 226 " pdb=" SG CYS A 254 " pdb=" CB CYS A 254 " ideal model delta sinusoidal sigma weight residual 93.00 39.08 53.92 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS F 406 " pdb=" SG CYS F 406 " pdb=" SG CYS F1074 " pdb=" CB CYS F1074 " ideal model delta sinusoidal sigma weight residual 93.00 46.68 46.32 1 1.00e+01 1.00e-02 2.97e+01 ... (remaining 11498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.203: 2951 1.203 - 2.407: 0 2.407 - 3.610: 0 3.610 - 4.814: 0 4.814 - 6.017: 1 Chirality restraints: 2952 Sorted by residual: chirality pdb=" C04 WFR A1903 " pdb=" C03 WFR A1903 " pdb=" C05 WFR A1903 " pdb=" C10 WFR A1903 " both_signs ideal model delta sigma weight residual False 2.63 -3.38 6.02 2.00e-01 2.50e+01 9.05e+02 chirality pdb=" P19 WFR A1903 " pdb=" O18 WFR A1903 " pdb=" O20 WFR A1903 " pdb=" O21 WFR A1903 " both_signs ideal model delta sigma weight residual True 3.12 -3.83 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN F 827 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.31e+00 ... (remaining 2949 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 51 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 52 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1112 " -0.011 2.00e-02 2.50e+03 1.23e-02 3.81e+00 pdb=" CG TRP A1112 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A1112 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A1112 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1112 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1112 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1112 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1112 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1112 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A1112 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 131 " -0.009 2.00e-02 2.50e+03 1.40e-02 3.41e+00 pdb=" CG PHE A 131 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 131 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 131 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 131 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 131 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 131 " 0.000 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.76: 3110 2.76 - 3.31: 18517 3.31 - 3.86: 31537 3.86 - 4.41: 38342 4.41 - 4.96: 64500 Nonbonded interactions: 156006 Sorted by model distance: nonbonded pdb=" OH TYR F 513 " pdb=" OE2 GLU F 567 " model vdw 2.214 2.440 nonbonded pdb=" O MET F 281 " pdb=" OG1 THR F 284 " model vdw 2.226 2.440 nonbonded pdb=" O TYR F 647 " pdb=" OG1 THR F 650 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR F 694 " pdb=" OD1 ASN F 696 " model vdw 2.238 2.440 nonbonded pdb=" O ILE A 289 " pdb=" OG SER A 322 " model vdw 2.246 2.440 ... (remaining 156001 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) } 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=0.00 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: 1.280 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: 5.950 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 60.590 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.150 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:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 18871 Z= 0.321 Angle : 0.602 12.562 25605 Z= 0.289 Chirality : 0.121 6.017 2952 Planarity : 0.004 0.054 3192 Dihedral : 16.196 110.488 7208 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.66 % Allowed : 13.61 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2212 helix: 1.57 (0.15), residues: 1122 sheet: 0.18 (0.36), residues: 204 loop : -1.20 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1112 HIS 0.003 0.001 HIS A1397 PHE 0.032 0.001 PHE A 131 TYR 0.010 0.001 TYR A1360 ARG 0.004 0.000 ARG A 906 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 246 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 MET cc_start: 0.6778 (ttp) cc_final: 0.6457 (ttm) REVERT: A 668 GLU cc_start: 0.6406 (tm-30) cc_final: 0.6109 (tm-30) REVERT: F 673 LEU cc_start: 0.8161 (pp) cc_final: 0.7953 (pt) REVERT: F 826 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: F 868 ASP cc_start: 0.6818 (t70) cc_final: 0.6564 (m-30) outliers start: 13 outliers final: 9 residues processed: 257 average time/residue: 1.0814 time to fit residues: 320.3602 Evaluate side-chains 247 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 237 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 575 GLU Chi-restraints excluded: chain F residue 826 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 114 optimal weight: 0.0000 chunk 90 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN A1105 ASN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN F 685 ASN F1013 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18871 Z= 0.222 Angle : 0.622 29.380 25605 Z= 0.300 Chirality : 0.057 1.958 2952 Planarity : 0.005 0.057 3192 Dihedral : 8.707 80.497 2977 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.97 % Allowed : 13.71 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2212 helix: 1.39 (0.16), residues: 1110 sheet: 0.22 (0.35), residues: 214 loop : -1.17 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1112 HIS 0.004 0.001 HIS F1007 PHE 0.020 0.001 PHE A 131 TYR 0.012 0.001 TYR F 609 ARG 0.003 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 250 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 MET cc_start: 0.6709 (ttp) cc_final: 0.6402 (ttm) REVERT: A 493 MET cc_start: 0.4972 (mtt) cc_final: 0.4642 (mtt) REVERT: A 668 GLU cc_start: 0.5969 (tm-30) cc_final: 0.5589 (tm-30) REVERT: A 906 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7012 (mtm110) REVERT: A 941 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7665 (mtp) REVERT: A 983 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8526 (mtm) REVERT: A 984 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: F 868 ASP cc_start: 0.6849 (t70) cc_final: 0.6474 (m-30) outliers start: 39 outliers final: 18 residues processed: 266 average time/residue: 1.0679 time to fit residues: 329.0935 Evaluate side-chains 257 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 235 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 864 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 219 optimal weight: 0.4980 chunk 180 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1105 ASN F 65 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 ASN F1013 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18871 Z= 0.209 Angle : 0.604 28.203 25605 Z= 0.289 Chirality : 0.058 2.092 2952 Planarity : 0.005 0.054 3192 Dihedral : 7.521 77.853 2965 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.92 % Allowed : 14.06 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 2212 helix: 1.28 (0.16), residues: 1111 sheet: 0.21 (0.35), residues: 214 loop : -1.22 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1112 HIS 0.003 0.001 HIS A1397 PHE 0.014 0.001 PHE A 53 TYR 0.011 0.001 TYR F 609 ARG 0.003 0.000 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 257 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 480 LEU cc_start: 0.4580 (mt) cc_final: 0.4266 (pp) REVERT: A 906 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6966 (mtm110) REVERT: A 941 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7624 (mtp) REVERT: A 983 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8519 (mtm) REVERT: A 984 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: A 1124 MET cc_start: 0.8188 (mmm) cc_final: 0.7964 (mmm) REVERT: E 209 GLN cc_start: 0.7808 (tt0) cc_final: 0.7525 (mt0) REVERT: F 868 ASP cc_start: 0.6865 (OUTLIER) cc_final: 0.6481 (m-30) REVERT: F 1020 MET cc_start: 0.8105 (ttt) cc_final: 0.7796 (tmm) outliers start: 58 outliers final: 23 residues processed: 287 average time/residue: 1.0167 time to fit residues: 339.4275 Evaluate side-chains 269 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 241 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 670 CYS Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 868 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 136 optimal weight: 0.0010 chunk 203 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 192 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 277 ASN A1105 ASN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN F 326 ASN F 685 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18871 Z= 0.171 Angle : 0.586 28.339 25605 Z= 0.278 Chirality : 0.057 2.066 2952 Planarity : 0.004 0.054 3192 Dihedral : 6.827 75.878 2965 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.52 % Allowed : 15.02 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.18), residues: 2212 helix: 1.28 (0.16), residues: 1110 sheet: 0.21 (0.35), residues: 214 loop : -1.18 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1112 HIS 0.003 0.001 HIS A1397 PHE 0.025 0.001 PHE A 131 TYR 0.011 0.001 TYR A 313 ARG 0.002 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 254 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8011 (tp30) cc_final: 0.7658 (mm-30) REVERT: A 130 VAL cc_start: 0.7241 (p) cc_final: 0.6848 (m) REVERT: A 216 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7977 (mt-10) REVERT: A 480 LEU cc_start: 0.4923 (mt) cc_final: 0.4626 (pp) REVERT: A 906 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7107 (mtm110) REVERT: A 941 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7626 (mtp) REVERT: A 983 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8466 (mtm) REVERT: A 984 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: F 42 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6973 (tm-30) REVERT: F 819 ILE cc_start: 0.8109 (pt) cc_final: 0.7834 (pp) REVERT: F 851 MET cc_start: 0.7226 (mmp) cc_final: 0.6460 (mmm) REVERT: F 868 ASP cc_start: 0.6770 (t70) cc_final: 0.6398 (m-30) REVERT: F 882 ASP cc_start: 0.8521 (t0) cc_final: 0.8062 (t0) outliers start: 50 outliers final: 21 residues processed: 280 average time/residue: 1.0246 time to fit residues: 335.3513 Evaluate side-chains 272 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 247 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 668 ASP Chi-restraints excluded: chain F residue 670 CYS Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 1013 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN A1105 ASN A1265 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN F 326 ASN F 685 ASN F 697 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18871 Z= 0.208 Angle : 0.600 28.415 25605 Z= 0.286 Chirality : 0.057 2.063 2952 Planarity : 0.004 0.053 3192 Dihedral : 6.580 73.854 2965 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.97 % Allowed : 15.93 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2212 helix: 1.20 (0.16), residues: 1116 sheet: 0.11 (0.35), residues: 204 loop : -1.20 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1112 HIS 0.003 0.001 HIS A1397 PHE 0.024 0.001 PHE F 689 TYR 0.011 0.001 TYR A 435 ARG 0.002 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 259 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7999 (tp30) cc_final: 0.7642 (mm-30) REVERT: A 130 VAL cc_start: 0.7208 (p) cc_final: 0.6809 (m) REVERT: A 480 LEU cc_start: 0.5010 (mt) cc_final: 0.4712 (pp) REVERT: A 653 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7991 (mt) REVERT: A 906 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.6968 (mtm110) REVERT: A 941 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7616 (mtp) REVERT: A 983 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8476 (mtm) REVERT: A 984 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: A 1154 ASN cc_start: 0.7885 (t0) cc_final: 0.7610 (t0) REVERT: A 1202 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7136 (tt) REVERT: A 1234 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7836 (p90) REVERT: A 1245 LYS cc_start: 0.7561 (ptpt) cc_final: 0.7258 (mtmm) REVERT: F 59 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: F 819 ILE cc_start: 0.8162 (pt) cc_final: 0.7856 (pp) REVERT: F 868 ASP cc_start: 0.6866 (t70) cc_final: 0.6536 (m-30) REVERT: F 1020 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7834 (tmm) outliers start: 59 outliers final: 35 residues processed: 286 average time/residue: 1.0262 time to fit residues: 342.6054 Evaluate side-chains 295 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 251 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1234 PHE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 668 ASP Chi-restraints excluded: chain F residue 670 CYS Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1020 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1105 ASN F 108 GLN F 325 ASN F 326 ASN F 445 GLN F 685 ASN F 697 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18871 Z= 0.172 Angle : 0.586 28.368 25605 Z= 0.279 Chirality : 0.057 2.059 2952 Planarity : 0.004 0.053 3192 Dihedral : 6.369 72.577 2965 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.87 % Allowed : 16.43 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2212 helix: 1.23 (0.16), residues: 1116 sheet: 0.13 (0.35), residues: 204 loop : -1.20 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1112 HIS 0.002 0.001 HIS A1397 PHE 0.025 0.001 PHE F 689 TYR 0.011 0.001 TYR A 313 ARG 0.002 0.000 ARG A 906 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 252 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7986 (tp30) cc_final: 0.7637 (mm-30) REVERT: A 130 VAL cc_start: 0.7225 (p) cc_final: 0.6845 (m) REVERT: A 216 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8001 (mt-10) REVERT: A 480 LEU cc_start: 0.5003 (mt) cc_final: 0.4716 (pp) REVERT: A 653 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7887 (mt) REVERT: A 906 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7035 (mtm110) REVERT: A 941 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7605 (mtp) REVERT: A 983 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8446 (mtm) REVERT: A 984 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: A 1154 ASN cc_start: 0.7842 (t0) cc_final: 0.7581 (t0) REVERT: A 1202 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7137 (tt) REVERT: A 1234 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7806 (p90) REVERT: F 819 ILE cc_start: 0.8255 (pt) cc_final: 0.7952 (pp) REVERT: F 868 ASP cc_start: 0.6726 (t70) cc_final: 0.6335 (m-30) REVERT: F 882 ASP cc_start: 0.8516 (t0) cc_final: 0.8037 (t0) REVERT: F 1009 GLU cc_start: 0.7996 (tp30) cc_final: 0.7767 (tp30) REVERT: F 1020 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7807 (tmm) outliers start: 57 outliers final: 34 residues processed: 281 average time/residue: 1.0443 time to fit residues: 344.2783 Evaluate side-chains 287 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 245 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1234 PHE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 668 ASP Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 977 CYS Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1020 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 181 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1105 ASN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN F 326 ASN F 445 GLN F 685 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18871 Z= 0.158 Angle : 0.580 28.331 25605 Z= 0.275 Chirality : 0.056 2.058 2952 Planarity : 0.004 0.052 3192 Dihedral : 6.052 72.431 2965 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.67 % Allowed : 16.78 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 2212 helix: 1.28 (0.16), residues: 1115 sheet: 0.16 (0.35), residues: 204 loop : -1.19 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1112 HIS 0.002 0.001 HIS A1397 PHE 0.025 0.001 PHE F 689 TYR 0.011 0.001 TYR A 313 ARG 0.002 0.000 ARG A 906 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 261 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 VAL cc_start: 0.7200 (p) cc_final: 0.6831 (m) REVERT: A 216 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7991 (mt-10) REVERT: A 480 LEU cc_start: 0.5012 (mt) cc_final: 0.4699 (pp) REVERT: A 653 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7859 (mt) REVERT: A 668 GLU cc_start: 0.5704 (tm-30) cc_final: 0.5465 (pp20) REVERT: A 906 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6592 (mtm110) REVERT: A 941 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7618 (mtp) REVERT: A 984 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: A 1154 ASN cc_start: 0.7660 (t0) cc_final: 0.7391 (t0) REVERT: A 1202 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7140 (tt) REVERT: F 819 ILE cc_start: 0.8210 (pt) cc_final: 0.7889 (pp) REVERT: F 868 ASP cc_start: 0.6771 (t70) cc_final: 0.6360 (m-30) REVERT: F 882 ASP cc_start: 0.8501 (t0) cc_final: 0.8015 (t0) REVERT: F 1020 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7910 (tmm) outliers start: 53 outliers final: 27 residues processed: 288 average time/residue: 0.9900 time to fit residues: 332.3058 Evaluate side-chains 278 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 245 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1234 PHE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 668 ASP Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 977 CYS Chi-restraints excluded: chain F residue 1020 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 136 optimal weight: 0.0770 chunk 146 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 20 optimal weight: 0.0060 chunk 168 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 overall best weight: 0.5754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1105 ASN F 326 ASN F 445 GLN F 685 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18871 Z= 0.144 Angle : 0.588 28.299 25605 Z= 0.276 Chirality : 0.056 2.057 2952 Planarity : 0.004 0.077 3192 Dihedral : 5.914 72.110 2965 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.22 % Allowed : 17.74 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.18), residues: 2212 helix: 1.29 (0.16), residues: 1116 sheet: 0.19 (0.35), residues: 204 loop : -1.16 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1112 HIS 0.002 0.000 HIS A1397 PHE 0.026 0.001 PHE F 689 TYR 0.015 0.001 TYR A1091 ARG 0.002 0.000 ARG A 906 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 259 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6479 (tt0) cc_final: 0.6084 (tp30) REVERT: A 130 VAL cc_start: 0.7186 (p) cc_final: 0.6834 (m) REVERT: A 216 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7988 (mt-10) REVERT: A 480 LEU cc_start: 0.5042 (mt) cc_final: 0.4726 (pp) REVERT: A 653 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7852 (mt) REVERT: A 906 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7081 (mtm110) REVERT: A 941 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7632 (mtp) REVERT: A 984 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: A 1154 ASN cc_start: 0.7660 (t0) cc_final: 0.7378 (t0) REVERT: F 819 ILE cc_start: 0.8059 (pt) cc_final: 0.7741 (pp) REVERT: F 868 ASP cc_start: 0.6675 (t70) cc_final: 0.6243 (m-30) REVERT: F 882 ASP cc_start: 0.8485 (t0) cc_final: 0.8001 (t0) REVERT: F 1020 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7855 (tmm) outliers start: 44 outliers final: 26 residues processed: 286 average time/residue: 0.9916 time to fit residues: 331.4289 Evaluate side-chains 281 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 250 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1234 PHE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 668 ASP Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 977 CYS Chi-restraints excluded: chain F residue 1020 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 157 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 189 optimal weight: 0.3980 chunk 199 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1105 ASN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN F 445 GLN F 685 ASN F 697 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18871 Z= 0.158 Angle : 0.590 28.320 25605 Z= 0.279 Chirality : 0.057 2.059 2952 Planarity : 0.004 0.068 3192 Dihedral : 5.830 72.100 2964 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.92 % Allowed : 17.99 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.18), residues: 2212 helix: 1.25 (0.16), residues: 1120 sheet: 0.22 (0.36), residues: 204 loop : -1.16 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1112 HIS 0.002 0.001 HIS A1397 PHE 0.027 0.001 PHE F 689 TYR 0.012 0.001 TYR A1091 ARG 0.002 0.000 ARG A 906 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6471 (tt0) cc_final: 0.6092 (tp30) REVERT: A 103 MET cc_start: 0.7323 (ttm) cc_final: 0.6910 (tpt) REVERT: A 130 VAL cc_start: 0.7246 (p) cc_final: 0.6930 (m) REVERT: A 216 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7964 (mt-10) REVERT: A 480 LEU cc_start: 0.5251 (mt) cc_final: 0.4914 (pp) REVERT: A 653 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7861 (mt) REVERT: A 668 GLU cc_start: 0.5737 (tm-30) cc_final: 0.5474 (pp20) REVERT: A 906 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7089 (mtm110) REVERT: A 941 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7608 (mtp) REVERT: A 984 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: A 1154 ASN cc_start: 0.7581 (t0) cc_final: 0.7109 (t0) REVERT: A 1202 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7145 (tt) REVERT: E 158 MET cc_start: 0.5000 (mmp) cc_final: 0.4337 (mmm) REVERT: F 59 ASP cc_start: 0.8362 (m-30) cc_final: 0.7926 (m-30) REVERT: F 819 ILE cc_start: 0.8063 (pt) cc_final: 0.7741 (pp) REVERT: F 868 ASP cc_start: 0.6698 (t70) cc_final: 0.6259 (m-30) REVERT: F 882 ASP cc_start: 0.8485 (t0) cc_final: 0.7999 (t0) REVERT: F 1020 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7868 (tmm) outliers start: 38 outliers final: 24 residues processed: 275 average time/residue: 1.0551 time to fit residues: 337.2591 Evaluate side-chains 277 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 247 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1234 PHE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 977 CYS Chi-restraints excluded: chain F residue 1020 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 108 optimal weight: 0.0000 chunk 140 optimal weight: 0.3980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1105 ASN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 GLN F 685 ASN F 697 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18871 Z= 0.162 Angle : 0.595 28.335 25605 Z= 0.282 Chirality : 0.057 2.060 2952 Planarity : 0.004 0.061 3192 Dihedral : 5.772 72.119 2964 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.76 % Allowed : 18.30 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 2212 helix: 1.23 (0.16), residues: 1120 sheet: 0.23 (0.35), residues: 204 loop : -1.17 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1112 HIS 0.002 0.001 HIS A1397 PHE 0.027 0.001 PHE F 689 TYR 0.012 0.001 TYR A1091 ARG 0.009 0.000 ARG A1239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6469 (tt0) cc_final: 0.6100 (tp30) REVERT: A 130 VAL cc_start: 0.7194 (p) cc_final: 0.6862 (m) REVERT: A 216 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7948 (mt-10) REVERT: A 480 LEU cc_start: 0.5218 (mt) cc_final: 0.4890 (pp) REVERT: A 653 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7856 (mt) REVERT: A 668 GLU cc_start: 0.5760 (tm-30) cc_final: 0.5485 (pp20) REVERT: A 906 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7057 (mtm110) REVERT: A 941 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7608 (mtp) REVERT: A 984 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: A 1202 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7148 (tt) REVERT: E 158 MET cc_start: 0.5102 (mmp) cc_final: 0.4478 (mmm) REVERT: F 59 ASP cc_start: 0.8361 (m-30) cc_final: 0.7907 (m-30) REVERT: F 819 ILE cc_start: 0.8072 (pt) cc_final: 0.7769 (pp) REVERT: F 868 ASP cc_start: 0.6702 (t70) cc_final: 0.6264 (m-30) REVERT: F 882 ASP cc_start: 0.8482 (t0) cc_final: 0.7987 (t0) REVERT: F 1020 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7905 (tmm) REVERT: F 1052 GLN cc_start: 0.8028 (tp40) cc_final: 0.7571 (pm20) outliers start: 35 outliers final: 24 residues processed: 271 average time/residue: 1.0362 time to fit residues: 327.4245 Evaluate side-chains 275 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1234 PHE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 977 CYS Chi-restraints excluded: chain F residue 1020 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 163 optimal weight: 0.0070 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 177 optimal weight: 0.3980 chunk 74 optimal weight: 0.0870 chunk 181 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1105 ASN A1154 ASN F 445 GLN F 685 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.174083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127331 restraints weight = 38908.800| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.96 r_work: 0.3109 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 18871 Z= 0.136 Angle : 0.580 28.289 25605 Z= 0.273 Chirality : 0.056 2.058 2952 Planarity : 0.004 0.058 3192 Dihedral : 5.624 71.449 2964 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.36 % Allowed : 18.75 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2212 helix: 1.39 (0.16), residues: 1103 sheet: 0.27 (0.36), residues: 204 loop : -1.09 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1112 HIS 0.002 0.000 HIS F 888 PHE 0.027 0.001 PHE F 689 TYR 0.012 0.001 TYR A1091 ARG 0.004 0.000 ARG A1239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6299.55 seconds wall clock time: 114 minutes 17.96 seconds (6857.96 seconds total)