Starting phenix.real_space_refine on Sun Mar 17 17:35:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e56_27904/03_2024/8e56_27904_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e56_27904/03_2024/8e56_27904.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e56_27904/03_2024/8e56_27904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e56_27904/03_2024/8e56_27904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e56_27904/03_2024/8e56_27904_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e56_27904/03_2024/8e56_27904_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 11982 2.51 5 N 2981 2.21 5 O 3384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 126": "OD1" <-> "OD2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1180": "OD1" <-> "OD2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1327": "OE1" <-> "OE2" Residue "A ASP 1382": "OD1" <-> "OD2" Residue "A ASP 1385": "OD1" <-> "OD2" Residue "A PHE 1402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 227": "OD1" <-> "OD2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F GLU 649": "OE1" <-> "OE2" Residue "F ASP 677": "OD1" <-> "OD2" Residue "F PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 717": "OE1" <-> "OE2" Residue "F TYR 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 774": "OD1" <-> "OD2" Residue "F ASP 852": "OD1" <-> "OD2" Residue "F ASP 868": "OD1" <-> "OD2" Residue "F ASP 869": "OD1" <-> "OD2" Residue "F ASP 998": "OD1" <-> "OD2" Residue "F PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18461 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: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {' CA': 1, '3PE': 1, 'BBI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 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: 12.53, per 1000 atoms: 0.68 Number of scatterers: 18461 At special positions: 0 Unit cell: (144.82, 138.136, 158.188, 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 3384 8.00 N 2981 7.00 C 11982 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=2.04 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 F1202 " - " ASN F 326 " " 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: 8.07 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 14 sheets defined 51.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 47 through 50 No H-bonds generated for 'chain 'A' and resid 47 through 50' Processing helix chain 'A' and resid 53 through 70 Processing helix chain 'A' and resid 81 through 107 removed outlier: 3.587A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 140 removed outlier: 3.761A pdb=" N GLU A 140 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 178 removed outlier: 3.529A pdb=" N ARG A 165 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.509A 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 218 removed outlier: 3.523A pdb=" N MET A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Proline residue: A 195 - end of helix removed outlier: 5.202A pdb=" N HIS A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE A 199 " --> 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 removed outlier: 3.564A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 345 Processing helix chain 'A' and resid 434 through 450 removed outlier: 3.703A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 486 removed outlier: 3.840A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 493 removed outlier: 3.526A pdb=" N MET A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 490 through 493' Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.895A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 541 removed outlier: 3.804A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 581 removed outlier: 4.044A pdb=" N LEU A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N SER A 551 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 632 through 672 removed outlier: 4.283A pdb=" N LEU A 636 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N CYS A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 817 Processing helix chain 'A' and resid 829 through 851 removed outlier: 3.900A pdb=" N VAL A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 848 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 850 " --> pdb=" O GLU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 881 Processing helix chain 'A' and resid 894 through 897 Processing helix chain 'A' and resid 899 through 910 removed outlier: 3.662A pdb=" N LEU A 902 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 903 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Proline residue: A 904 - end of helix Processing helix chain 'A' and resid 912 through 927 Processing helix chain 'A' and resid 932 through 950 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 removed outlier: 4.064A pdb=" N ILE A1047 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR A1048 " --> pdb=" O PHE A1045 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1051 " --> pdb=" O TYR A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1071 removed outlier: 3.662A pdb=" N PHE A1060 " --> pdb=" O MET A1056 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A1071 " --> pdb=" O THR A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1093 Processing helix chain 'A' and resid 1106 through 1116 removed outlier: 4.194A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1136 Processing helix chain 'A' and resid 1149 through 1172 Processing helix chain 'A' and resid 1181 through 1205 Processing helix chain 'A' and resid 1235 through 1237 No H-bonds generated for 'chain 'A' and resid 1235 through 1237' Processing helix chain 'A' and resid 1240 through 1248 removed outlier: 3.747A pdb=" N LEU A1243 " --> pdb=" O VAL A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1266 removed outlier: 3.662A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1288 removed outlier: 3.792A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1321 Processing helix chain 'A' and resid 1325 through 1330 Processing helix chain 'A' and resid 1355 through 1387 removed outlier: 3.982A pdb=" N PHE A1361 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A1362 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A1363 " --> pdb=" O TYR A1360 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A1365 " --> pdb=" O ILE A1362 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A1371 " --> pdb=" O CYS A1368 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A1372 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A1378 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A1379 " --> pdb=" O PHE A1376 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A1382 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP A1385 " --> pdb=" O ASP A1382 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1387 " --> pdb=" O PHE A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1409 Processing helix chain 'A' and resid 1419 through 1428 removed outlier: 3.703A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 5 No H-bonds generated for 'chain 'E' and resid 2 through 5' Processing helix chain 'E' and resid 7 through 28 removed outlier: 3.701A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 129 removed outlier: 3.774A pdb=" N PHE E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 162 Proline residue: E 139 - end of helix 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: 3.907A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 110 removed outlier: 3.588A pdb=" N ARG F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 201 removed outlier: 3.741A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.405A 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: 3.533A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.807A 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: 4.753A pdb=" N ARG F 422 " --> pdb=" O GLY F 419 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE F 423 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 removed outlier: 3.579A pdb=" N LEU F 432 " --> pdb=" O LEU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 443 removed outlier: 3.804A pdb=" N GLY F 440 " --> pdb=" O MET F 436 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASP F 441 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LYS F 442 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 502 removed outlier: 3.691A 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 571 through 581 Processing helix chain 'F' and resid 628 through 630 No H-bonds generated for 'chain 'F' and resid 628 through 630' Processing helix chain 'F' and resid 641 through 649 Processing helix chain 'F' and resid 653 through 659 removed outlier: 5.333A pdb=" N GLU F 657 " --> pdb=" O ASP F 654 " (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 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 870 through 872 No H-bonds generated for 'chain 'F' and resid 870 through 872' 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 'E' and resid 34 through 36 Processing sheet with id= E, first strand: chain 'E' and resid 48 through 50 Processing sheet with id= F, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= G, first strand: chain 'F' and resid 152 through 154 removed outlier: 3.961A pdb=" N ASP F 154 " --> pdb=" O ARG F 159 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG F 159 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.892A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 411 through 415 removed outlier: 6.295A pdb=" N ASP F 255 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET F 361 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU F 257 " --> pdb=" O MET F 361 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE F 363 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU F 259 " --> pdb=" O PHE F 363 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE F 290 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE F 258 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN F 292 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL F 260 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA F 294 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 513 through 517 Processing sheet with id= K, first strand: chain 'F' and resid 661 through 664 removed outlier: 4.045A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS F 818 " --> pdb=" O LYS F 733 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG F 735 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY F 816 " --> pdb=" O ARG F 735 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL F 737 " --> pdb=" O VAL F 814 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL F 814 " --> pdb=" O VAL F 737 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA F 813 " --> pdb=" O VAL F 801 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 851 through 857 removed outlier: 6.027A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 896 through 902 removed outlier: 4.360A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 905 through 907 866 hydrogen bonds defined for protein. 2264 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: 6.86 Time building geometry restraints manager: 8.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 5782 1.36 - 1.52: 6900 1.52 - 1.67: 6028 1.67 - 1.83: 168 1.83 - 1.99: 2 Bond restraints: 18880 Sorted by residual: bond pdb=" CAR BBI A1902 " pdb=" IAS BBI A1902 " ideal model delta sigma weight residual 2.098 1.988 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" CBC BBI A1902 " pdb=" IBD BBI A1902 " ideal model delta sigma weight residual 2.097 1.988 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CAV BBI A1902 " pdb=" CAW BBI A1902 " ideal model delta sigma weight residual 1.510 1.616 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CAW BBI A1902 " pdb=" NAX BBI A1902 " ideal model delta sigma weight residual 1.449 1.534 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CAD BBI A1902 " pdb=" CAE BBI A1902 " ideal model delta sigma weight residual 1.481 1.545 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 18875 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.93: 372 105.93 - 113.86: 10811 113.86 - 121.79: 10658 121.79 - 129.71: 3648 129.71 - 137.64: 112 Bond angle restraints: 25601 Sorted by residual: angle pdb=" CAM BBI A1902 " pdb=" CAN BBI A1902 " pdb=" CAP BBI A1902 " ideal model delta sigma weight residual 118.51 131.82 -13.31 3.00e+00 1.11e-01 1.97e+01 angle pdb=" CAC BBI A1902 " pdb=" CAD BBI A1902 " pdb=" CAE BBI A1902 " ideal model delta sigma weight residual 112.57 124.92 -12.35 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N LEU A 527 " pdb=" CA LEU A 527 " pdb=" C LEU A 527 " ideal model delta sigma weight residual 111.36 107.11 4.25 1.09e+00 8.42e-01 1.52e+01 angle pdb=" N GLN F 806 " pdb=" CA GLN F 806 " pdb=" CB GLN F 806 " ideal model delta sigma weight residual 110.49 116.97 -6.48 1.69e+00 3.50e-01 1.47e+01 angle pdb=" CA TYR F1071 " pdb=" CB TYR F1071 " pdb=" CG TYR F1071 " ideal model delta sigma weight residual 113.90 120.33 -6.43 1.80e+00 3.09e-01 1.27e+01 ... (remaining 25596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 10676 24.88 - 49.75: 720 49.75 - 74.63: 86 74.63 - 99.51: 32 99.51 - 124.38: 25 Dihedral angle restraints: 11539 sinusoidal: 4952 harmonic: 6587 Sorted by residual: dihedral pdb=" CB CYS F 999 " pdb=" SG CYS F 999 " pdb=" SG CYS F1029 " pdb=" CB CYS F1029 " ideal model delta sinusoidal sigma weight residual 93.00 7.99 85.01 1 1.00e+01 1.00e-02 8.76e+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 93.00 159.30 -66.30 1 1.00e+01 1.00e-02 5.74e+01 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 -143.24 57.24 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 11536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 2922 0.133 - 0.266: 19 0.266 - 0.399: 4 0.399 - 0.532: 1 0.532 - 0.665: 2 Chirality restraints: 2948 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN F 898 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+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 -1.76 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN F 350 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 2945 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 51 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO A 52 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 653 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C LEU A 653 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A 653 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN A 654 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 868 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" CG ASP F 868 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP F 868 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 868 " -0.014 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.75: 2342 2.75 - 3.30: 19058 3.30 - 3.86: 31750 3.86 - 4.41: 39251 4.41 - 4.96: 65318 Nonbonded interactions: 157719 Sorted by model distance: nonbonded pdb=" OD2 ASP F 154 " pdb=" OH TYR F 163 " model vdw 2.201 2.440 nonbonded pdb=" N GLN A 830 " pdb=" OE1 GLN A 830 " model vdw 2.211 2.520 nonbonded pdb=" O GLN F 720 " pdb=" OG SER F 724 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR F 513 " pdb=" OE2 GLU F 567 " model vdw 2.232 2.440 nonbonded pdb=" O TYR A1359 " pdb=" OG SER A1363 " model vdw 2.248 2.440 ... (remaining 157714 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: 1.250 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: 0.020 Extract box with map and model: 5.700 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 56.580 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.004 0.110 18880 Z= 0.249 Angle : 0.624 13.312 25601 Z= 0.308 Chirality : 0.047 0.665 2948 Planarity : 0.004 0.063 3191 Dihedral : 17.184 124.385 7246 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.06 % Allowed : 11.84 % Favored : 87.10 % 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: -0.15 (0.18), residues: 2212 helix: 0.81 (0.16), residues: 1110 sheet: -0.22 (0.33), residues: 219 loop : -1.18 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.003 0.001 HIS F 169 PHE 0.021 0.001 PHE F 689 TYR 0.016 0.001 TYR F 609 ARG 0.003 0.000 ARG A 174 *********************** 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 255 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 234 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 932 VAL cc_start: 0.7420 (t) cc_final: 0.7158 (p) REVERT: F 1045 ASP cc_start: 0.8530 (t0) cc_final: 0.8189 (t0) outliers start: 21 outliers final: 14 residues processed: 248 average time/residue: 1.0815 time to fit residues: 307.5458 Evaluate side-chains 243 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 229 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1382 ASP Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 855 ILE Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 996 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.4980 chunk 169 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 174 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 GLN F 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18880 Z= 0.171 Angle : 0.550 9.411 25601 Z= 0.275 Chirality : 0.044 0.542 2948 Planarity : 0.004 0.062 3191 Dihedral : 11.564 107.126 3022 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.92 % Allowed : 13.21 % Favored : 84.88 % 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: -0.01 (0.18), residues: 2212 helix: 0.95 (0.16), residues: 1118 sheet: -0.21 (0.33), residues: 219 loop : -1.17 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.002 0.001 HIS F 169 PHE 0.020 0.001 PHE A1060 TYR 0.015 0.001 TYR F 609 ARG 0.003 0.000 ARG F 199 *********************** 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 279 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 241 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: A 479 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.5412 (tpp) REVERT: A 536 PHE cc_start: 0.7278 (m-10) cc_final: 0.6883 (m-80) REVERT: A 666 GLU cc_start: 0.5675 (mm-30) cc_final: 0.5137 (mm-30) REVERT: A 932 VAL cc_start: 0.7379 (t) cc_final: 0.7094 (p) REVERT: A 1098 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7169 (pp) REVERT: A 1124 MET cc_start: 0.7617 (mmp) cc_final: 0.7340 (mmm) REVERT: A 1198 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7797 (mp) REVERT: A 1419 HIS cc_start: 0.2513 (OUTLIER) cc_final: 0.1781 (t-90) REVERT: F 1013 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7419 (m110) REVERT: F 1045 ASP cc_start: 0.8526 (t0) cc_final: 0.8179 (t0) outliers start: 38 outliers final: 19 residues processed: 255 average time/residue: 1.0409 time to fit residues: 305.0542 Evaluate side-chains 248 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1234 PHE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1419 HIS Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 55 optimal weight: 0.0040 chunk 202 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 180 optimal weight: 0.2980 chunk 201 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1398 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18880 Z= 0.206 Angle : 0.559 9.708 25601 Z= 0.280 Chirality : 0.045 0.521 2948 Planarity : 0.004 0.063 3191 Dihedral : 10.460 108.454 3001 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.02 % Allowed : 14.31 % Favored : 83.67 % 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: 0.00 (0.18), residues: 2212 helix: 0.98 (0.16), residues: 1117 sheet: -0.22 (0.33), residues: 219 loop : -1.19 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 187 HIS 0.003 0.001 HIS F 169 PHE 0.040 0.001 PHE A1384 TYR 0.016 0.001 TYR F 609 ARG 0.002 0.000 ARG A1249 *********************** 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 274 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 234 time to evaluate : 2.080 Fit side-chains REVERT: A 479 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5272 (tpp) REVERT: A 536 PHE cc_start: 0.7303 (m-10) cc_final: 0.6859 (m-80) REVERT: A 625 MET cc_start: 0.9264 (mmm) cc_final: 0.9041 (mmp) REVERT: A 666 GLU cc_start: 0.6011 (mm-30) cc_final: 0.5516 (tp30) REVERT: A 894 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.5980 (pptt) REVERT: A 932 VAL cc_start: 0.7458 (t) cc_final: 0.7156 (p) REVERT: A 1056 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7057 (mtt) REVERT: A 1098 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7258 (pp) REVERT: A 1124 MET cc_start: 0.7684 (mmp) cc_final: 0.7341 (mmm) REVERT: F 674 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7213 (mtpp) REVERT: F 846 ARG cc_start: 0.7958 (mmm-85) cc_final: 0.7698 (mmm-85) REVERT: F 1013 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7418 (m110) outliers start: 40 outliers final: 18 residues processed: 248 average time/residue: 1.0556 time to fit residues: 301.7427 Evaluate side-chains 242 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 218 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1234 PHE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1068 LEU 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: 0.7980 chunk 105 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 464 GLN A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 GLN F 570 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18880 Z= 0.197 Angle : 0.553 10.265 25601 Z= 0.278 Chirality : 0.045 0.503 2948 Planarity : 0.004 0.061 3191 Dihedral : 9.715 117.754 2999 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.32 % Allowed : 14.87 % Favored : 82.81 % 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: -0.00 (0.18), residues: 2212 helix: 0.98 (0.16), residues: 1118 sheet: -0.22 (0.33), residues: 221 loop : -1.20 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 187 HIS 0.003 0.001 HIS F 169 PHE 0.023 0.001 PHE A1384 TYR 0.015 0.001 TYR F 609 ARG 0.007 0.000 ARG F 199 *********************** 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 274 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 228 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 536 PHE cc_start: 0.7330 (m-10) cc_final: 0.6913 (m-80) REVERT: A 625 MET cc_start: 0.9257 (mmm) cc_final: 0.8964 (mmp) REVERT: A 666 GLU cc_start: 0.5879 (mm-30) cc_final: 0.5357 (mm-30) REVERT: A 894 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6001 (pptt) REVERT: A 932 VAL cc_start: 0.7479 (t) cc_final: 0.7164 (p) REVERT: A 1098 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7260 (pp) REVERT: A 1124 MET cc_start: 0.7863 (mmp) cc_final: 0.7406 (mmm) REVERT: A 1198 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7774 (mp) REVERT: F 42 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: F 674 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7205 (mtpp) REVERT: F 846 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7702 (mmm-85) REVERT: F 1013 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7580 (m110) outliers start: 46 outliers final: 25 residues processed: 251 average time/residue: 1.0625 time to fit residues: 306.9609 Evaluate side-chains 245 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 214 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1234 PHE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 597 GLN Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 855 ILE Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 0.6980 chunk 193 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 GLN F 872 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18880 Z= 0.345 Angle : 0.638 12.432 25601 Z= 0.322 Chirality : 0.049 0.491 2948 Planarity : 0.005 0.060 3191 Dihedral : 9.510 121.617 2999 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.77 % Allowed : 15.47 % Favored : 81.75 % 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: -0.23 (0.18), residues: 2212 helix: 0.76 (0.16), residues: 1123 sheet: -0.18 (0.33), residues: 229 loop : -1.34 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 187 HIS 0.005 0.001 HIS A1397 PHE 0.022 0.002 PHE A1060 TYR 0.020 0.002 TYR F1071 ARG 0.006 0.000 ARG F 199 *********************** 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 280 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 225 time to evaluate : 2.086 Fit side-chains revert: symmetry clash REVERT: A 536 PHE cc_start: 0.7531 (m-10) cc_final: 0.7195 (m-80) REVERT: A 625 MET cc_start: 0.9322 (mmm) cc_final: 0.9045 (mmp) REVERT: A 666 GLU cc_start: 0.6175 (mm-30) cc_final: 0.5525 (mt-10) REVERT: A 894 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6057 (pptt) REVERT: A 932 VAL cc_start: 0.7493 (t) cc_final: 0.7169 (p) REVERT: A 1098 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7191 (pp) REVERT: A 1124 MET cc_start: 0.7935 (mmp) cc_final: 0.7502 (mmm) REVERT: A 1419 HIS cc_start: 0.2357 (OUTLIER) cc_final: 0.1747 (t-90) REVERT: A 1426 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5786 (tm) REVERT: E 142 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7069 (mpp) REVERT: F 42 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: F 649 GLU cc_start: 0.8390 (pp20) cc_final: 0.7797 (pp20) REVERT: F 674 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7211 (mtpp) REVERT: F 846 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7723 (mmm-85) REVERT: F 1013 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7392 (m110) outliers start: 55 outliers final: 29 residues processed: 260 average time/residue: 1.0882 time to fit residues: 326.0023 Evaluate side-chains 266 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 229 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1234 PHE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1419 HIS Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 855 ILE Chi-restraints excluded: chain F residue 868 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 99 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 GLN E 79 ASN F 872 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18880 Z= 0.208 Angle : 0.569 12.493 25601 Z= 0.287 Chirality : 0.045 0.484 2948 Planarity : 0.004 0.061 3191 Dihedral : 9.049 119.023 2999 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.82 % Allowed : 15.83 % Favored : 81.35 % 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: -0.08 (0.18), residues: 2212 helix: 0.91 (0.16), residues: 1115 sheet: -0.12 (0.33), residues: 227 loop : -1.28 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 187 HIS 0.002 0.001 HIS F 169 PHE 0.019 0.001 PHE F 689 TYR 0.015 0.001 TYR F1071 ARG 0.008 0.000 ARG F 199 *********************** 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 284 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 228 time to evaluate : 2.392 Fit side-chains revert: symmetry clash REVERT: A 536 PHE cc_start: 0.7397 (m-10) cc_final: 0.6912 (m-80) REVERT: A 625 MET cc_start: 0.9299 (mmm) cc_final: 0.9002 (mmp) REVERT: A 666 GLU cc_start: 0.6163 (mm-30) cc_final: 0.5504 (mt-10) REVERT: A 894 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6018 (pptt) REVERT: A 932 VAL cc_start: 0.7407 (t) cc_final: 0.7104 (p) REVERT: A 1098 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7225 (pp) REVERT: A 1124 MET cc_start: 0.7886 (mmp) cc_final: 0.7530 (mmm) REVERT: A 1198 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7799 (mp) REVERT: A 1419 HIS cc_start: 0.2354 (OUTLIER) cc_final: 0.1774 (t-90) REVERT: A 1426 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.5783 (tm) REVERT: E 142 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7193 (mpp) REVERT: F 42 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: F 846 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7709 (mmm-85) REVERT: F 1013 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7635 (m110) REVERT: F 1045 ASP cc_start: 0.8463 (t0) cc_final: 0.8122 (t0) outliers start: 56 outliers final: 28 residues processed: 261 average time/residue: 1.0768 time to fit residues: 323.0634 Evaluate side-chains 256 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1234 PHE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1419 HIS Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 845 LYS Chi-restraints excluded: chain F residue 855 ILE Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 122 optimal weight: 0.6980 chunk 157 optimal weight: 0.0980 chunk 181 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN F 556 GLN F 872 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 18880 Z= 0.148 Angle : 0.532 10.338 25601 Z= 0.270 Chirality : 0.045 0.541 2948 Planarity : 0.004 0.062 3191 Dihedral : 8.373 115.182 2999 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.17 % Allowed : 17.04 % Favored : 80.80 % 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: 0.09 (0.18), residues: 2212 helix: 1.04 (0.16), residues: 1112 sheet: -0.09 (0.32), residues: 229 loop : -1.15 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 187 HIS 0.002 0.000 HIS F 308 PHE 0.021 0.001 PHE F 689 TYR 0.012 0.001 TYR F1071 ARG 0.007 0.000 ARG F 199 *********************** 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 281 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 238 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7436 (mtt-85) REVERT: A 536 PHE cc_start: 0.7341 (m-10) cc_final: 0.6931 (m-80) REVERT: A 625 MET cc_start: 0.9239 (mmm) cc_final: 0.8997 (mmp) REVERT: A 654 ASN cc_start: 0.7751 (t0) cc_final: 0.7520 (t0) REVERT: A 659 ILE cc_start: 0.7934 (mt) cc_final: 0.7597 (mp) REVERT: A 666 GLU cc_start: 0.6103 (mm-30) cc_final: 0.5409 (mt-10) REVERT: A 932 VAL cc_start: 0.7416 (t) cc_final: 0.7120 (p) REVERT: A 1098 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7215 (pp) REVERT: A 1124 MET cc_start: 0.7915 (mmp) cc_final: 0.7615 (mmm) REVERT: A 1198 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7740 (mp) REVERT: A 1419 HIS cc_start: 0.2292 (OUTLIER) cc_final: 0.1686 (t-90) REVERT: A 1426 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.5760 (tm) REVERT: F 42 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: F 753 GLU cc_start: 0.8298 (mp0) cc_final: 0.8076 (mm-30) outliers start: 43 outliers final: 20 residues processed: 267 average time/residue: 1.0939 time to fit residues: 336.4697 Evaluate side-chains 256 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 230 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1419 HIS Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 845 LYS Chi-restraints excluded: chain F residue 855 ILE Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN E 79 ASN F 556 GLN ** F 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 872 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18880 Z= 0.296 Angle : 0.610 11.247 25601 Z= 0.311 Chirality : 0.048 0.531 2948 Planarity : 0.005 0.061 3191 Dihedral : 8.313 107.550 2999 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.52 % Allowed : 17.24 % Favored : 80.24 % 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: -0.12 (0.18), residues: 2212 helix: 0.88 (0.16), residues: 1117 sheet: -0.19 (0.32), residues: 229 loop : -1.29 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 32 HIS 0.004 0.001 HIS A1397 PHE 0.029 0.002 PHE A1060 TYR 0.018 0.001 TYR F1071 ARG 0.006 0.000 ARG F 646 *********************** 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 286 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 236 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.7903 (tp) cc_final: 0.7635 (tt) REVERT: A 171 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7424 (mtt-85) REVERT: A 345 LYS cc_start: 0.5148 (ttmt) cc_final: 0.4621 (ptmt) REVERT: A 497 ASN cc_start: 0.7297 (m-40) cc_final: 0.6739 (t0) REVERT: A 536 PHE cc_start: 0.7437 (m-10) cc_final: 0.6952 (m-80) REVERT: A 625 MET cc_start: 0.9273 (mmm) cc_final: 0.9048 (mmp) REVERT: A 666 GLU cc_start: 0.6222 (mm-30) cc_final: 0.5466 (mt-10) REVERT: A 932 VAL cc_start: 0.7555 (t) cc_final: 0.7240 (p) REVERT: A 1098 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7253 (pp) REVERT: A 1124 MET cc_start: 0.7980 (mmp) cc_final: 0.7622 (mmm) REVERT: A 1419 HIS cc_start: 0.2475 (OUTLIER) cc_final: 0.1812 (t-90) REVERT: A 1426 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.5805 (tm) REVERT: F 42 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: F 311 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.7780 (tp40) REVERT: F 674 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7208 (mtpp) REVERT: F 753 GLU cc_start: 0.8309 (mp0) cc_final: 0.8087 (mm-30) REVERT: F 1013 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7668 (m110) outliers start: 50 outliers final: 24 residues processed: 268 average time/residue: 1.0665 time to fit residues: 328.2856 Evaluate side-chains 260 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1419 HIS Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 248 GLN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 855 ILE Chi-restraints excluded: chain F residue 977 CYS Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1013 ASN Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 199 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 77 GLN F 872 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18880 Z= 0.198 Angle : 0.564 11.357 25601 Z= 0.287 Chirality : 0.046 0.506 2948 Planarity : 0.004 0.062 3191 Dihedral : 7.913 96.294 2999 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.86 % Allowed : 18.30 % Favored : 79.84 % 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: -0.05 (0.18), residues: 2212 helix: 0.95 (0.16), residues: 1117 sheet: -0.12 (0.32), residues: 229 loop : -1.28 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 187 HIS 0.002 0.001 HIS F 169 PHE 0.027 0.001 PHE F 689 TYR 0.014 0.001 TYR F1071 ARG 0.006 0.000 ARG F 199 *********************** 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 267 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 230 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.7895 (tp) cc_final: 0.7614 (tt) REVERT: A 171 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7404 (mtt-85) REVERT: A 536 PHE cc_start: 0.7411 (m-10) cc_final: 0.6969 (m-80) REVERT: A 625 MET cc_start: 0.9257 (mmm) cc_final: 0.9026 (mmp) REVERT: A 666 GLU cc_start: 0.6132 (mm-30) cc_final: 0.5376 (mt-10) REVERT: A 932 VAL cc_start: 0.7498 (t) cc_final: 0.7194 (p) REVERT: A 1098 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7258 (pp) REVERT: A 1124 MET cc_start: 0.8002 (mmp) cc_final: 0.7748 (mmm) REVERT: A 1198 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7786 (mp) REVERT: A 1426 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.5803 (tm) REVERT: E 54 TRP cc_start: 0.4720 (OUTLIER) cc_final: 0.3934 (m100) REVERT: F 42 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: F 591 ARG cc_start: 0.8113 (ttt180) cc_final: 0.7911 (ttt180) REVERT: F 753 GLU cc_start: 0.8303 (mp0) cc_final: 0.8088 (mm-30) outliers start: 37 outliers final: 23 residues processed: 258 average time/residue: 1.0701 time to fit residues: 316.9142 Evaluate side-chains 259 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 230 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1419 HIS Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 248 GLN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 855 ILE Chi-restraints excluded: chain F residue 977 CYS Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 6.9990 chunk 129 optimal weight: 0.0370 chunk 100 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 136 optimal weight: 0.1980 chunk 108 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 ASN E 79 ASN F 74 ASN ** F 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 872 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18880 Z= 0.189 Angle : 0.556 12.033 25601 Z= 0.284 Chirality : 0.045 0.503 2948 Planarity : 0.004 0.061 3191 Dihedral : 7.048 71.568 2999 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.76 % Allowed : 18.55 % Favored : 79.69 % 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: -0.02 (0.18), residues: 2212 helix: 0.97 (0.16), residues: 1117 sheet: -0.10 (0.32), residues: 231 loop : -1.27 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 187 HIS 0.002 0.001 HIS F 308 PHE 0.032 0.001 PHE A1060 TYR 0.013 0.001 TYR F1071 ARG 0.006 0.000 ARG F 199 ********************** 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 272 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8862 (p0) REVERT: A 139 LEU cc_start: 0.7815 (tp) cc_final: 0.7548 (tt) REVERT: A 171 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7411 (mtt-85) REVERT: A 536 PHE cc_start: 0.7368 (m-10) cc_final: 0.7008 (m-80) REVERT: A 625 MET cc_start: 0.9259 (mmm) cc_final: 0.9021 (mmp) REVERT: A 659 ILE cc_start: 0.7853 (mt) cc_final: 0.7537 (mp) REVERT: A 666 GLU cc_start: 0.6164 (mm-30) cc_final: 0.5428 (mt-10) REVERT: A 932 VAL cc_start: 0.7520 (t) cc_final: 0.7213 (p) REVERT: A 1098 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7251 (pp) REVERT: A 1124 MET cc_start: 0.8004 (mmp) cc_final: 0.7738 (mmm) REVERT: A 1198 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7772 (mp) REVERT: A 1426 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.5805 (tm) REVERT: E 54 TRP cc_start: 0.4718 (OUTLIER) cc_final: 0.3951 (m100) REVERT: F 42 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6536 (mp0) REVERT: F 753 GLU cc_start: 0.8300 (mp0) cc_final: 0.8090 (mm-30) REVERT: F 1045 ASP cc_start: 0.8495 (t0) cc_final: 0.8131 (t0) outliers start: 35 outliers final: 23 residues processed: 263 average time/residue: 1.0478 time to fit residues: 319.6115 Evaluate side-chains 259 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 229 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1419 HIS Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 248 GLN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 855 ILE Chi-restraints excluded: chain F residue 977 CYS Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 177 optimal weight: 0.0670 chunk 74 optimal weight: 0.0170 chunk 181 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 77 GLN F 556 GLN F 697 ASN ** F 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 872 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122594 restraints weight = 36483.200| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.93 r_work: 0.3128 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18880 Z= 0.145 Angle : 0.528 12.277 25601 Z= 0.270 Chirality : 0.044 0.483 2948 Planarity : 0.004 0.063 3191 Dihedral : 6.825 70.532 2999 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.66 % Allowed : 18.85 % Favored : 79.49 % 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: 0.09 (0.18), residues: 2212 helix: 1.06 (0.16), residues: 1118 sheet: -0.05 (0.32), residues: 233 loop : -1.21 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 187 HIS 0.002 0.000 HIS F 169 PHE 0.028 0.001 PHE A1060 TYR 0.011 0.001 TYR F1071 ARG 0.006 0.000 ARG F 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6303.15 seconds wall clock time: 112 minutes 29.27 seconds (6749.27 seconds total)