Starting phenix.real_space_refine on Fri Mar 6 15:50:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pss_20462/03_2026/6pss_20462.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pss_20462/03_2026/6pss_20462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pss_20462/03_2026/6pss_20462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pss_20462/03_2026/6pss_20462.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pss_20462/03_2026/6pss_20462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pss_20462/03_2026/6pss_20462.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Zn 3 6.06 5 P 86 5.49 5 Mg 1 5.21 5 S 140 5.16 5 C 20018 2.51 5 N 5722 2.21 5 O 6391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 187 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32361 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1769 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 10502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10502 Classifications: {'peptide': 1337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "J" Number of atoms: 10449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10449 Classifications: {'peptide': 1343} Link IDs: {'CIS': 2, 'PTRANS': 55, 'TRANS': 1285} Chain breaks: 2 Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 577 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 4489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4489 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 5, 'PTRANS': 16, 'TRANS': 536} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "N" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 566 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 883 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "P" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 881 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14403 SG CYS J 72 52.032 63.342 117.405 1.00 49.80 S ATOM 14511 SG CYS J 85 49.490 64.794 119.548 1.00 56.66 S ATOM 14535 SG CYS J 88 51.826 67.255 118.243 1.00 62.07 S ATOM 20223 SG CYS J 814 22.847 115.222 82.104 1.00 37.86 S ATOM 20788 SG CYS J 888 26.266 114.307 82.777 1.00 25.54 S ATOM 20839 SG CYS J 895 24.770 112.696 79.240 1.00 26.49 S ATOM 20860 SG CYS J 898 25.820 116.471 79.796 1.00 23.63 S ATOM 30303 SG CYS N 37 73.399 155.719 76.959 1.00 55.81 S ATOM 30460 SG CYS N 58 77.917 154.245 75.816 1.00 53.67 S Time building chain proxies: 6.40, per 1000 atoms: 0.20 Number of scatterers: 32361 At special positions: 0 Unit cell: (146.9, 191.1, 191.1, 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) Zn 3 29.99 S 140 16.00 P 86 15.00 Mg 1 11.99 O 6391 8.00 N 5722 7.00 C 20018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 58 " Number of angles added : 6 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7260 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 51 sheets defined 41.8% alpha, 12.5% beta 39 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'G' and resid 35 through 50 Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.930A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 removed outlier: 3.547A pdb=" N ILE G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 232 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.853A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 87 Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.692A pdb=" N LYS I 37 " --> pdb=" O ASP I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 207 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 272 through 280 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.559A pdb=" N LEU I 325 " --> pdb=" O LEU I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 352 Processing helix chain 'I' and resid 358 through 371 removed outlier: 3.612A pdb=" N VAL I 364 " --> pdb=" O LEU I 360 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU I 365 " --> pdb=" O SER I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 379 through 390 removed outlier: 3.534A pdb=" N LEU I 384 " --> pdb=" O ALA I 380 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN I 387 " --> pdb=" O SER I 383 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE I 390 " --> pdb=" O GLU I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 removed outlier: 3.592A pdb=" N ILE I 426 " --> pdb=" O LYS I 422 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL I 428 " --> pdb=" O ASP I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 466 removed outlier: 3.789A pdb=" N GLU I 461 " --> pdb=" O GLY I 457 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN I 462 " --> pdb=" O GLU I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 471 Processing helix chain 'I' and resid 471 through 479 removed outlier: 3.530A pdb=" N VAL I 475 " --> pdb=" O VAL I 471 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU I 477 " --> pdb=" O ARG I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 506 removed outlier: 3.550A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU I 504 " --> pdb=" O ALA I 500 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.673A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.670A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 4.247A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 656 through 661 removed outlier: 4.228A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL I 661 " --> pdb=" O GLN I 658 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.856A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 removed outlier: 3.605A pdb=" N ASN I 684 " --> pdb=" O LEU I 680 " (cutoff:3.500A) Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 737 through 741 removed outlier: 3.551A pdb=" N GLU I 740 " --> pdb=" O ASN I 737 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 737 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 860 through 865 removed outlier: 3.543A pdb=" N SER I 863 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 901 through 906 Processing helix chain 'I' and resid 942 through 975 removed outlier: 3.526A pdb=" N GLU I 949 " --> pdb=" O ALA I 945 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU I 960 " --> pdb=" O ALA I 956 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER I 973 " --> pdb=" O ALA I 969 " (cutoff:3.500A) Processing helix chain 'I' and resid 977 through 981 removed outlier: 4.018A pdb=" N VAL I 980 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 998 Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.284A pdb=" N GLU I1016 " --> pdb=" O GLU I1012 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU I1030 " --> pdb=" O GLU I1026 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE I1036 " --> pdb=" O LYS I1032 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR I1037 " --> pdb=" O ARG I1033 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.774A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.323A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.685A pdb=" N LYS I1127 " --> pdb=" O GLY I1123 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA I1130 " --> pdb=" O ASP I1126 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1149 removed outlier: 3.647A pdb=" N GLU I1143 " --> pdb=" O ALA I1139 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN I1146 " --> pdb=" O ARG I1142 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG I1147 " --> pdb=" O GLU I1143 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.575A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1175 removed outlier: 3.519A pdb=" N MET I1170 " --> pdb=" O ASP I1166 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.508A pdb=" N ILE I1195 " --> pdb=" O LYS I1191 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS I1196 " --> pdb=" O GLU I1192 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1280 Processing helix chain 'I' and resid 1283 through 1289 Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.660A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR I1305 " --> pdb=" O ARG I1301 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN I1307 " --> pdb=" O LYS I1303 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1331 removed outlier: 3.582A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL I1325 " --> pdb=" O GLU I1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 122 through 129 removed outlier: 3.599A pdb=" N ASP J 129 " --> pdb=" O GLY J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.575A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 170 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 206 Processing helix chain 'J' and resid 211 through 231 removed outlier: 4.008A pdb=" N LEU J 223 " --> pdb=" O LYS J 219 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY J 231 " --> pdb=" O PHE J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 263 through 285 removed outlier: 4.090A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.533A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.516A pdb=" N PHE J 377 " --> pdb=" O ALA J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.780A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.924A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.775A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 613 through 634 removed outlier: 3.918A pdb=" N THR J 617 " --> pdb=" O GLY J 613 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.708A pdb=" N ASP J 643 " --> pdb=" O GLY J 640 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 640 through 644' Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 removed outlier: 3.638A pdb=" N SER J 728 " --> pdb=" O MET J 724 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.550A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 790 removed outlier: 3.738A pdb=" N THR J 776 " --> pdb=" O TYR J 772 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 791 through 793 No H-bonds generated for 'chain 'J' and resid 791 through 793' Processing helix chain 'J' and resid 794 through 804 removed outlier: 3.724A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.834A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.721A pdb=" N SER J 887 " --> pdb=" O SER J 884 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 900 removed outlier: 3.539A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 896 through 900' Processing helix chain 'J' and resid 914 through 928 Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1137 through 1146 removed outlier: 3.822A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE J1145 " --> pdb=" O VAL J1141 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 removed outlier: 3.604A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1237 removed outlier: 3.725A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1237 through 1245 removed outlier: 3.697A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1251 through 1261 removed outlier: 3.902A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1292 removed outlier: 3.856A pdb=" N ILE J1287 " --> pdb=" O SER J1283 " (cutoff:3.500A) Processing helix chain 'J' and resid 1321 through 1326 removed outlier: 3.868A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.790A pdb=" N ALA J1338 " --> pdb=" O GLU J1334 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1362 through 1372 removed outlier: 3.847A pdb=" N ARG J1372 " --> pdb=" O ASP J1368 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.819A pdb=" N LEU K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 74 removed outlier: 3.934A pdb=" N GLU K 74 " --> pdb=" O GLN K 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 20 Processing helix chain 'L' and resid 23 through 31 removed outlier: 3.667A pdb=" N VAL L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 50 removed outlier: 3.962A pdb=" N ILE L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU L 42 " --> pdb=" O SER L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 66 removed outlier: 4.142A pdb=" N LEU L 65 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 85 Processing helix chain 'L' and resid 96 through 107 removed outlier: 3.732A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 136 Processing helix chain 'L' and resid 137 through 151 removed outlier: 4.277A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 162 Processing helix chain 'L' and resid 213 through 233 removed outlier: 3.596A pdb=" N PHE L 221 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA L 226 " --> pdb=" O ALA L 222 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR L 231 " --> pdb=" O GLN L 227 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP L 233 " --> pdb=" O VAL L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 255 removed outlier: 3.512A pdb=" N VAL L 255 " --> pdb=" O LYS L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 289 removed outlier: 4.830A pdb=" N LEU L 269 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL L 270 " --> pdb=" O PHE L 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG L 279 " --> pdb=" O VAL L 275 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL L 280 " --> pdb=" O MET L 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 305 Processing helix chain 'L' and resid 324 through 329 removed outlier: 3.576A pdb=" N GLU L 328 " --> pdb=" O LYS L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 333 Processing helix chain 'L' and resid 336 through 349 removed outlier: 3.621A pdb=" N ALA L 340 " --> pdb=" O GLU L 336 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN L 345 " --> pdb=" O LEU L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 383 removed outlier: 3.686A pdb=" N ARG L 363 " --> pdb=" O LYS L 359 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG L 374 " --> pdb=" O ALA L 370 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 392 removed outlier: 3.593A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER L 389 " --> pdb=" O ARG L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 removed outlier: 3.567A pdb=" N ILE L 410 " --> pdb=" O GLN L 406 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP L 417 " --> pdb=" O MET L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 446 removed outlier: 3.870A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR L 432 " --> pdb=" O SER L 428 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR L 440 " --> pdb=" O ARG L 436 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 468 removed outlier: 3.652A pdb=" N ARG L 468 " --> pdb=" O ASN L 464 " (cutoff:3.500A) Processing helix chain 'L' and resid 469 through 472 removed outlier: 3.623A pdb=" N GLN L 472 " --> pdb=" O GLN L 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 469 through 472' Processing helix chain 'L' and resid 479 through 487 removed outlier: 3.573A pdb=" N ALA L 484 " --> pdb=" O PRO L 480 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 500 removed outlier: 3.724A pdb=" N LEU L 498 " --> pdb=" O ILE L 494 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE L 500 " --> pdb=" O LYS L 496 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 522 removed outlier: 3.590A pdb=" N PHE L 522 " --> pdb=" O LEU L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 548 Processing helix chain 'L' and resid 549 through 551 No H-bonds generated for 'chain 'L' and resid 549 through 551' Processing helix chain 'L' and resid 552 through 562 removed outlier: 3.523A pdb=" N ALA L 556 " --> pdb=" O THR L 552 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS L 557 " --> pdb=" O ALA L 553 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 580 removed outlier: 3.604A pdb=" N PHE L 580 " --> pdb=" O VAL L 576 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 598 Processing helix chain 'L' and resid 606 through 611 Processing helix chain 'M' and resid 256 through 260 removed outlier: 3.917A pdb=" N LEU M 260 " --> pdb=" O VAL M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 273 Processing helix chain 'M' and resid 277 through 282 removed outlier: 3.672A pdb=" N LEU M 281 " --> pdb=" O TYR M 277 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL M 282 " --> pdb=" O ILE M 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 277 through 282' Processing helix chain 'M' and resid 285 through 291 Processing helix chain 'M' and resid 296 through 308 Processing helix chain 'N' and resid 6 through 25 Processing helix chain 'N' and resid 26 through 28 No H-bonds generated for 'chain 'N' and resid 26 through 28' Processing helix chain 'N' and resid 45 through 52 Processing helix chain 'N' and resid 58 through 70 Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 18 removed outlier: 6.396A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA G 184 " --> pdb=" O GLU G 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.620A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU G 102 " --> pdb=" O MET G 142 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 110 Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 20 removed outlier: 3.532A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 53 through 60 removed outlier: 7.119A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'H' and resid 187 through 188 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.768A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.854A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU I 106 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL I 114 " --> pdb=" O GLU I 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.701A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 284 through 286 removed outlier: 4.677A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL I 228 " --> pdb=" O THR I 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.442A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 580 through 581 removed outlier: 6.571A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AC3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.772A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 748 through 752 removed outlier: 5.746A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.655A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 835 through 841 removed outlier: 5.619A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD1, first strand: chain 'I' and resid 888 through 889 Processing sheet with id=AD2, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.588A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.514A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS J 345 " --> pdb=" O PHE I1270 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1338 through 1339 Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 4.327A pdb=" N SER J 34 " --> pdb=" O MET J 102 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS J 104 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY J 36 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU J 106 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 161 Processing sheet with id=AD7, first strand: chain 'J' and resid 252 through 254 Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 removed outlier: 7.372A pdb=" N LEU J 527 " --> pdb=" O ARG J 551 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N THR J 553 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 703 through 706 Processing sheet with id=AE1, first strand: chain 'J' and resid 745 through 748 removed outlier: 7.944A pdb=" N GLY J 745 " --> pdb=" O THR J 757 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR J 757 " --> pdb=" O GLY J 745 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET J 747 " --> pdb=" O ILE J 755 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'J' and resid 821 through 822 removed outlier: 3.640A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL J 843 " --> pdb=" O ARG J 883 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.935A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 935 through 936 Processing sheet with id=AE6, first strand: chain 'J' and resid 957 through 960 removed outlier: 6.531A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 965 through 967 removed outlier: 4.214A pdb=" N VAL J 966 " --> pdb=" O VAL J 974 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL J 974 " --> pdb=" O VAL J 966 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'J' and resid 1002 through 1003 Processing sheet with id=AE9, first strand: chain 'J' and resid 1079 through 1081 removed outlier: 3.752A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE J1115 " --> pdb=" O GLY J1033 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1050 through 1051 removed outlier: 4.194A pdb=" N ASP J1051 " --> pdb=" O LEU J1056 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU J1056 " --> pdb=" O ASP J1051 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'J' and resid 1106 through 1107 Processing sheet with id=AF3, first strand: chain 'J' and resid 1156 through 1157 removed outlier: 4.037A pdb=" N ASP J1208 " --> pdb=" O ALA J1157 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF5, first strand: chain 'J' and resid 1172 through 1173 Processing sheet with id=AF6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.974A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL J1267 " --> pdb=" O THR J1301 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 10.07 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7999 1.33 - 1.45: 6319 1.45 - 1.57: 18277 1.57 - 1.69: 172 1.69 - 1.82: 244 Bond restraints: 33011 Sorted by residual: bond pdb=" CA ARG I 687 " pdb=" C ARG I 687 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.41e-02 5.03e+03 1.56e+01 bond pdb=" C GLU J 418 " pdb=" N HIS J 419 " ideal model delta sigma weight residual 1.332 1.300 0.032 8.60e-03 1.35e+04 1.38e+01 bond pdb=" CA PHE I1270 " pdb=" CB PHE I1270 " ideal model delta sigma weight residual 1.526 1.464 0.062 1.76e-02 3.23e+03 1.25e+01 bond pdb=" C VAL I 550 " pdb=" N HIS I 551 " ideal model delta sigma weight residual 1.331 1.270 0.061 2.07e-02 2.33e+03 8.56e+00 bond pdb=" C LEU M 254 " pdb=" N ARG M 255 " ideal model delta sigma weight residual 1.331 1.392 -0.061 2.07e-02 2.33e+03 8.55e+00 ... (remaining 33006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 44451 3.65 - 7.30: 443 7.30 - 10.95: 47 10.95 - 14.60: 6 14.60 - 18.25: 2 Bond angle restraints: 44949 Sorted by residual: angle pdb=" C THR L 569 " pdb=" N ASP L 570 " pdb=" CA ASP L 570 " ideal model delta sigma weight residual 121.70 136.83 -15.13 1.80e+00 3.09e-01 7.07e+01 angle pdb=" C GLY I 544 " pdb=" N PHE I 545 " pdb=" CA PHE I 545 " ideal model delta sigma weight residual 121.70 135.39 -13.69 1.80e+00 3.09e-01 5.78e+01 angle pdb=" C ILE J 707 " pdb=" N ASN J 708 " pdb=" CA ASN J 708 " ideal model delta sigma weight residual 121.70 134.85 -13.15 1.80e+00 3.09e-01 5.34e+01 angle pdb=" C MET L 51 " pdb=" N GLY L 52 " pdb=" CA GLY L 52 " ideal model delta sigma weight residual 121.70 133.07 -11.37 1.80e+00 3.09e-01 3.99e+01 angle pdb=" C ILE L 511 " pdb=" N GLY L 512 " pdb=" CA GLY L 512 " ideal model delta sigma weight residual 121.70 132.37 -10.67 1.80e+00 3.09e-01 3.51e+01 ... (remaining 44944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 18828 35.59 - 71.18: 1262 71.18 - 106.77: 55 106.77 - 142.36: 1 142.36 - 177.95: 4 Dihedral angle restraints: 20150 sinusoidal: 8898 harmonic: 11252 Sorted by residual: dihedral pdb=" CA GLU L 503 " pdb=" C GLU L 503 " pdb=" N PRO L 504 " pdb=" CA PRO L 504 " ideal model delta harmonic sigma weight residual -180.00 -130.87 -49.13 0 5.00e+00 4.00e-02 9.65e+01 dihedral pdb=" CA VAL I 857 " pdb=" C VAL I 857 " pdb=" N GLY I 858 " pdb=" CA GLY I 858 " ideal model delta harmonic sigma weight residual -180.00 -143.38 -36.62 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA PRO N 33 " pdb=" C PRO N 33 " pdb=" N VAL N 34 " pdb=" CA VAL N 34 " ideal model delta harmonic sigma weight residual 180.00 -145.64 -34.36 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 20147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4476 0.084 - 0.168: 620 0.168 - 0.253: 50 0.253 - 0.337: 0 0.337 - 0.421: 1 Chirality restraints: 5147 Sorted by residual: chirality pdb=" CB VAL H 202 " pdb=" CA VAL H 202 " pdb=" CG1 VAL H 202 " pdb=" CG2 VAL H 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CB ILE I 524 " pdb=" CA ILE I 524 " pdb=" CG1 ILE I 524 " pdb=" CG2 ILE I 524 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ASN M 320 " pdb=" N ASN M 320 " pdb=" C ASN M 320 " pdb=" CB ASN M 320 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 5144 not shown) Planarity restraints: 5573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 854 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO I 855 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO I 855 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO I 855 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO I 190 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 120 " 0.051 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO J 121 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO J 121 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 121 " 0.043 5.00e-02 4.00e+02 ... (remaining 5570 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 27 2.31 - 2.96: 14140 2.96 - 3.61: 47691 3.61 - 4.25: 78474 4.25 - 4.90: 128085 Nonbonded interactions: 268417 Sorted by model distance: nonbonded pdb=" OD1 ASP L 149 " pdb=" NH2 ARG L 225 " model vdw 1.663 3.120 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.073 2.170 nonbonded pdb=" CG ASP L 149 " pdb=" NH2 ARG L 225 " model vdw 2.146 3.350 nonbonded pdb=" OH TYR J 360 " pdb=" OE1 GLN J 448 " model vdw 2.220 3.040 nonbonded pdb=" O ASN J 962 " pdb=" OG1 THR J 980 " model vdw 2.253 3.040 ... (remaining 268412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 158 or resid 171 through 233)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 228 or (resid 229 through 230 an \ d (name N or name CA or name C or name O or name CB )) or resid 231 through 233) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.630 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 : 0.009 0.202 33020 Z= 0.385 Angle : 1.082 18.255 44955 Z= 0.613 Chirality : 0.057 0.421 5147 Planarity : 0.007 0.098 5573 Dihedral : 20.992 177.949 12890 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.66 % Favored : 92.13 % Rotamer: Outliers : 11.08 % Allowed : 22.55 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.70 (0.10), residues: 3875 helix: -3.48 (0.08), residues: 1501 sheet: -2.60 (0.23), residues: 437 loop : -2.90 (0.12), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 45 TYR 0.039 0.003 TYR G 177 PHE 0.026 0.003 PHE J1325 TRP 0.022 0.003 TRP J1020 HIS 0.012 0.002 HIS M 276 Details of bonding type rmsd covalent geometry : bond 0.00843 (33011) covalent geometry : angle 1.07623 (44949) hydrogen bonds : bond 0.22785 ( 1269) hydrogen bonds : angle 9.20319 ( 3502) metal coordination : bond 0.14589 ( 9) metal coordination : angle 9.79180 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 368 poor density : 600 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 177 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: G 208 ASN cc_start: 0.7648 (p0) cc_final: 0.7219 (p0) REVERT: H 68 TYR cc_start: 0.3552 (OUTLIER) cc_final: 0.2760 (m-10) REVERT: H 233 ASP cc_start: 0.5699 (OUTLIER) cc_final: 0.5229 (p0) REVERT: I 29 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7476 (p) REVERT: I 90 VAL cc_start: 0.7719 (t) cc_final: 0.7453 (p) REVERT: I 202 ARG cc_start: 0.7009 (ptt90) cc_final: 0.6236 (ptp-110) REVERT: I 232 ILE cc_start: 0.5684 (OUTLIER) cc_final: 0.5039 (pt) REVERT: I 272 ARG cc_start: 0.6126 (mmp80) cc_final: 0.5854 (mmp80) REVERT: I 274 ILE cc_start: 0.5626 (OUTLIER) cc_final: 0.5304 (pt) REVERT: I 286 GLU cc_start: 0.5601 (OUTLIER) cc_final: 0.5198 (tm-30) REVERT: I 330 HIS cc_start: 0.0302 (OUTLIER) cc_final: -0.0326 (m-70) REVERT: I 386 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6634 (tp30) REVERT: I 496 LYS cc_start: 0.7225 (tptm) cc_final: 0.6753 (ttpp) REVERT: I 498 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7309 (mt) REVERT: I 620 ASN cc_start: 0.8170 (p0) cc_final: 0.7937 (p0) REVERT: I 641 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6222 (pp20) REVERT: I 706 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7699 (tpp-160) REVERT: I 894 GLN cc_start: 0.6205 (mt0) cc_final: 0.5731 (mt0) REVERT: I 941 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7010 (mptt) REVERT: I 974 ARG cc_start: 0.6364 (mtp180) cc_final: 0.5993 (ttp-170) REVERT: I 989 LEU cc_start: 0.5681 (tp) cc_final: 0.4567 (tp) REVERT: I 1085 MET cc_start: 0.8487 (mmm) cc_final: 0.7349 (mmm) REVERT: I 1117 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8660 (tp) REVERT: I 1129 ASN cc_start: 0.8155 (t0) cc_final: 0.7868 (t0) REVERT: I 1136 GLN cc_start: 0.7094 (mm-40) cc_final: 0.6748 (mm-40) REVERT: I 1239 VAL cc_start: 0.8825 (p) cc_final: 0.8541 (p) REVERT: J 137 ARG cc_start: 0.6726 (mtm180) cc_final: 0.6214 (mtp85) REVERT: J 201 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5437 (tt) REVERT: J 203 GLU cc_start: 0.6039 (mt-10) cc_final: 0.5792 (mt-10) REVERT: J 235 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: J 479 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7867 (mt-10) REVERT: J 489 ASN cc_start: 0.7675 (m-40) cc_final: 0.7054 (p0) REVERT: J 560 ASN cc_start: 0.6200 (OUTLIER) cc_final: 0.5678 (m-40) REVERT: J 598 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6982 (tptm) REVERT: J 649 LYS cc_start: 0.7236 (mmtt) cc_final: 0.7020 (mmtp) REVERT: J 737 ILE cc_start: 0.8742 (mm) cc_final: 0.8462 (mm) REVERT: J 838 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6867 (ptp90) REVERT: J 871 LEU cc_start: 0.7237 (tp) cc_final: 0.6934 (tp) REVERT: J 1261 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8427 (pp) REVERT: K 52 ARG cc_start: 0.7558 (mtp180) cc_final: 0.7189 (mtm110) REVERT: L 53 ILE cc_start: 0.4290 (OUTLIER) cc_final: 0.4067 (mp) REVERT: L 90 GLU cc_start: 0.1656 (OUTLIER) cc_final: 0.0892 (mm-30) REVERT: L 98 VAL cc_start: 0.5515 (OUTLIER) cc_final: 0.5188 (p) REVERT: L 99 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6310 (tpt170) REVERT: L 121 LYS cc_start: 0.7213 (ptpp) cc_final: 0.6508 (tppt) REVERT: L 129 GLN cc_start: 0.4558 (tt0) cc_final: 0.4310 (tt0) REVERT: L 476 ARG cc_start: 0.5429 (OUTLIER) cc_final: 0.3149 (mtm180) REVERT: L 477 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6872 (mt-10) REVERT: L 488 LEU cc_start: 0.5502 (OUTLIER) cc_final: 0.5263 (mt) REVERT: L 489 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.5319 (mmt) REVERT: L 610 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.6153 (t80) outliers start: 368 outliers final: 208 residues processed: 915 average time/residue: 0.2119 time to fit residues: 300.8382 Evaluate side-chains 662 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 429 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 286 GLU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 788 SER Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 807 TRP Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 916 SER Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1111 GLN Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 21 LYS Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 85 CYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 337 ARG Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 598 LYS Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 838 ARG Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 861 ASN Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1050 THR Chi-restraints excluded: chain J residue 1058 SER Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1234 VAL Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 418 LYS Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 516 ASP Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 539 SER Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 599 ARG Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS I 343 HIS I 437 ASN ** I 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 649 GLN I 658 GLN I 799 ASN I 811 ASN I1080 ASN I1111 GLN I1116 HIS I1134 GLN J 153 ASN J 206 ASN J 266 ASN J 365 GLN ** J 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN J 504 GLN J 545 HIS J 680 ASN J 702 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 979 ASN J1010 GLN J1023 HIS ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1126 GLN J1227 HIS J1244 GLN J1326 GLN L 28 ASN L 30 HIS L 362 ASN ** L 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 GLN N 62 GLN N 68 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.166651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139372 restraints weight = 55820.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138045 restraints weight = 81428.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138886 restraints weight = 80009.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139079 restraints weight = 49625.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139991 restraints weight = 42173.627| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33020 Z= 0.147 Angle : 0.658 11.236 44955 Z= 0.351 Chirality : 0.043 0.245 5147 Planarity : 0.005 0.087 5573 Dihedral : 17.744 176.046 5629 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 7.04 % Allowed : 25.02 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.12), residues: 3875 helix: -1.78 (0.11), residues: 1554 sheet: -2.05 (0.26), residues: 381 loop : -2.45 (0.12), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I1223 TYR 0.020 0.001 TYR I1229 PHE 0.018 0.001 PHE L 256 TRP 0.015 0.002 TRP I 997 HIS 0.010 0.001 HIS L 600 Details of bonding type rmsd covalent geometry : bond 0.00304 (33011) covalent geometry : angle 0.65727 (44949) hydrogen bonds : bond 0.04394 ( 1269) hydrogen bonds : angle 5.52257 ( 3502) metal coordination : bond 0.00735 ( 9) metal coordination : angle 1.72446 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 519 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 162 GLU cc_start: 0.2350 (OUTLIER) cc_final: 0.2114 (mm-30) REVERT: G 208 ASN cc_start: 0.7572 (p0) cc_final: 0.7291 (p0) REVERT: I 90 VAL cc_start: 0.7679 (t) cc_final: 0.7373 (p) REVERT: I 149 LEU cc_start: 0.8018 (tp) cc_final: 0.7682 (tp) REVERT: I 253 PHE cc_start: 0.4808 (t80) cc_final: 0.4513 (m-80) REVERT: I 274 ILE cc_start: 0.5302 (OUTLIER) cc_final: 0.4968 (pt) REVERT: I 330 HIS cc_start: 0.0772 (OUTLIER) cc_final: -0.0378 (m170) REVERT: I 496 LYS cc_start: 0.7345 (tptm) cc_final: 0.6936 (ttpp) REVERT: I 498 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7266 (pt) REVERT: I 791 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8270 (tt) REVERT: I 814 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: I 894 GLN cc_start: 0.6205 (mt0) cc_final: 0.5821 (mt0) REVERT: I 941 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7019 (mptt) REVERT: I 984 VAL cc_start: 0.3796 (OUTLIER) cc_final: 0.3444 (m) REVERT: I 989 LEU cc_start: 0.5576 (tp) cc_final: 0.4617 (tp) REVERT: I 1085 MET cc_start: 0.8506 (mmm) cc_final: 0.6649 (mmm) REVERT: I 1129 ASN cc_start: 0.8029 (t0) cc_final: 0.7713 (t0) REVERT: I 1239 VAL cc_start: 0.8779 (p) cc_final: 0.8576 (p) REVERT: J 137 ARG cc_start: 0.6773 (mtm180) cc_final: 0.6348 (mtp85) REVERT: J 192 MET cc_start: 0.4890 (OUTLIER) cc_final: 0.4622 (ttm) REVERT: J 201 LEU cc_start: 0.6156 (mm) cc_final: 0.5739 (tp) REVERT: J 204 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5362 (mt-10) REVERT: J 402 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.4803 (tm-30) REVERT: J 489 ASN cc_start: 0.7381 (m-40) cc_final: 0.6497 (p0) REVERT: J 568 SER cc_start: 0.8314 (t) cc_final: 0.8002 (m) REVERT: J 644 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7765 (mtm) REVERT: J 664 ILE cc_start: 0.7922 (mp) cc_final: 0.7708 (mp) REVERT: J 709 ARG cc_start: 0.5728 (OUTLIER) cc_final: 0.4590 (tpm-80) REVERT: J 785 ASP cc_start: 0.7554 (t0) cc_final: 0.7271 (t0) REVERT: J 932 MET cc_start: 0.6575 (ptm) cc_final: 0.6244 (ptm) REVERT: J 1028 ILE cc_start: 0.1147 (OUTLIER) cc_final: 0.0942 (pp) REVERT: J 1061 VAL cc_start: 0.0946 (OUTLIER) cc_final: 0.0265 (m) REVERT: J 1165 PHE cc_start: 0.3490 (p90) cc_final: 0.2392 (p90) REVERT: J 1261 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8351 (pp) REVERT: K 36 ASP cc_start: 0.5827 (p0) cc_final: 0.5572 (p0) REVERT: K 53 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6381 (mt-10) REVERT: L 90 GLU cc_start: 0.2416 (OUTLIER) cc_final: 0.1236 (mm-30) REVERT: L 99 ARG cc_start: 0.6981 (mtt180) cc_final: 0.6496 (tpt170) REVERT: L 121 LYS cc_start: 0.6936 (ptpp) cc_final: 0.6499 (tppt) REVERT: L 277 MET cc_start: 0.4517 (tpt) cc_final: 0.3964 (mtt) REVERT: L 307 THR cc_start: 0.6745 (m) cc_final: 0.6517 (m) REVERT: L 418 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6162 (ttpt) REVERT: L 460 ILE cc_start: 0.8433 (mt) cc_final: 0.8043 (tp) REVERT: L 476 ARG cc_start: 0.4822 (OUTLIER) cc_final: 0.3361 (mtt180) REVERT: L 514 ASP cc_start: 0.1560 (OUTLIER) cc_final: 0.0900 (m-30) REVERT: N 67 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7214 (mtm180) outliers start: 234 outliers final: 125 residues processed: 710 average time/residue: 0.2083 time to fit residues: 231.0325 Evaluate side-chains 568 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 423 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 374 GLU Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1202 GLU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 418 LYS Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 246 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 391 optimal weight: 20.0000 chunk 158 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 chunk 349 optimal weight: 9.9990 chunk 387 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 447 HIS ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 649 GLN J 430 HIS ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 437 GLN N 71 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.163801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136791 restraints weight = 55793.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134833 restraints weight = 85947.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135913 restraints weight = 77738.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136062 restraints weight = 54475.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137972 restraints weight = 43106.302| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 33020 Z= 0.200 Angle : 0.676 11.552 44955 Z= 0.357 Chirality : 0.044 0.183 5147 Planarity : 0.005 0.084 5573 Dihedral : 17.228 176.717 5398 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.02 % Favored : 92.90 % Rotamer: Outliers : 7.22 % Allowed : 26.07 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.12), residues: 3875 helix: -1.03 (0.12), residues: 1553 sheet: -1.87 (0.26), residues: 372 loop : -2.28 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 281 TYR 0.019 0.002 TYR I1229 PHE 0.017 0.002 PHE J1325 TRP 0.025 0.002 TRP I 997 HIS 0.005 0.001 HIS L 600 Details of bonding type rmsd covalent geometry : bond 0.00460 (33011) covalent geometry : angle 0.67508 (44949) hydrogen bonds : bond 0.04279 ( 1269) hydrogen bonds : angle 5.24675 ( 3502) metal coordination : bond 0.00488 ( 9) metal coordination : angle 2.24202 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 428 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 208 ASN cc_start: 0.7639 (p0) cc_final: 0.7412 (p0) REVERT: I 202 ARG cc_start: 0.6945 (ptt90) cc_final: 0.6397 (ptp-110) REVERT: I 239 MET cc_start: 0.5122 (ppp) cc_final: 0.4204 (ttp) REVERT: I 330 HIS cc_start: 0.0616 (OUTLIER) cc_final: 0.0258 (m170) REVERT: I 496 LYS cc_start: 0.7306 (tptm) cc_final: 0.6926 (ttpp) REVERT: I 498 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7348 (pt) REVERT: I 592 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7620 (ptm160) REVERT: I 646 SER cc_start: 0.7786 (OUTLIER) cc_final: 0.7505 (t) REVERT: I 844 LYS cc_start: 0.4919 (mtpp) cc_final: 0.4412 (mtpt) REVERT: I 894 GLN cc_start: 0.6179 (mt0) cc_final: 0.5771 (mt0) REVERT: I 941 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7054 (mptt) REVERT: I 989 LEU cc_start: 0.5423 (tp) cc_final: 0.5177 (tp) REVERT: I 1085 MET cc_start: 0.8608 (mmm) cc_final: 0.7437 (mmm) REVERT: I 1129 ASN cc_start: 0.7986 (t0) cc_final: 0.7763 (t0) REVERT: I 1238 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8609 (mt) REVERT: I 1239 VAL cc_start: 0.8917 (p) cc_final: 0.8697 (p) REVERT: J 137 ARG cc_start: 0.6723 (mtm180) cc_final: 0.6261 (mtp85) REVERT: J 201 LEU cc_start: 0.6074 (mm) cc_final: 0.5618 (tp) REVERT: J 204 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5266 (mt-10) REVERT: J 402 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.4895 (tm-30) REVERT: J 489 ASN cc_start: 0.7437 (m-40) cc_final: 0.6534 (p0) REVERT: J 568 SER cc_start: 0.8377 (t) cc_final: 0.8109 (m) REVERT: J 709 ARG cc_start: 0.5618 (OUTLIER) cc_final: 0.4579 (tpm-80) REVERT: J 785 ASP cc_start: 0.7554 (t0) cc_final: 0.7317 (t0) REVERT: J 806 ASP cc_start: 0.6427 (t70) cc_final: 0.6210 (t0) REVERT: J 932 MET cc_start: 0.6575 (ptm) cc_final: 0.6236 (ptm) REVERT: J 1061 VAL cc_start: 0.0729 (OUTLIER) cc_final: 0.0040 (m) REVERT: J 1188 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.5588 (tp30) REVERT: J 1261 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8386 (pp) REVERT: K 36 ASP cc_start: 0.5964 (p0) cc_final: 0.5755 (p0) REVERT: L 90 GLU cc_start: 0.2343 (OUTLIER) cc_final: 0.1223 (mm-30) REVERT: L 99 ARG cc_start: 0.7174 (mtt180) cc_final: 0.6666 (tpt170) REVERT: L 121 LYS cc_start: 0.7015 (ptpp) cc_final: 0.6452 (tppt) REVERT: L 476 ARG cc_start: 0.4561 (OUTLIER) cc_final: 0.3105 (mtm180) REVERT: L 487 MET cc_start: 0.4381 (mtm) cc_final: 0.4160 (mtm) REVERT: L 610 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.5934 (t80) REVERT: N 3 ASP cc_start: 0.8221 (t0) cc_final: 0.7906 (t0) REVERT: N 67 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7231 (mtm180) outliers start: 240 outliers final: 156 residues processed: 636 average time/residue: 0.2098 time to fit residues: 209.0108 Evaluate side-chains 562 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 391 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 585 LYS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 528 LEU Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 39 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 393 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 231 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 76 optimal weight: 30.0000 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 128 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS ** L 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.164772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.139257 restraints weight = 55421.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137168 restraints weight = 79840.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.137945 restraints weight = 81737.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138451 restraints weight = 52134.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139384 restraints weight = 41841.086| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33020 Z= 0.159 Angle : 0.628 11.011 44955 Z= 0.332 Chirality : 0.043 0.170 5147 Planarity : 0.005 0.080 5573 Dihedral : 16.887 177.426 5376 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.65 % Rotamer: Outliers : 7.10 % Allowed : 26.37 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.13), residues: 3875 helix: -0.48 (0.13), residues: 1552 sheet: -1.70 (0.27), residues: 369 loop : -2.17 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 218 TYR 0.022 0.002 TYR I1229 PHE 0.017 0.001 PHE L 610 TRP 0.046 0.002 TRP I 997 HIS 0.003 0.001 HIS G 160 Details of bonding type rmsd covalent geometry : bond 0.00364 (33011) covalent geometry : angle 0.62779 (44949) hydrogen bonds : bond 0.03773 ( 1269) hydrogen bonds : angle 4.96289 ( 3502) metal coordination : bond 0.00346 ( 9) metal coordination : angle 1.43003 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 439 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.8302 (m-80) cc_final: 0.7996 (m-80) REVERT: I 193 ASN cc_start: 0.6743 (m-40) cc_final: 0.6377 (m-40) REVERT: I 202 ARG cc_start: 0.6877 (ptt90) cc_final: 0.6402 (ptp-110) REVERT: I 330 HIS cc_start: 0.0597 (OUTLIER) cc_final: 0.0238 (m170) REVERT: I 496 LYS cc_start: 0.7267 (tptm) cc_final: 0.6913 (ttpp) REVERT: I 498 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7399 (pt) REVERT: I 646 SER cc_start: 0.7519 (OUTLIER) cc_final: 0.7181 (t) REVERT: I 791 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8113 (tt) REVERT: I 894 GLN cc_start: 0.6174 (mt0) cc_final: 0.5745 (mt0) REVERT: I 941 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7023 (mptt) REVERT: I 989 LEU cc_start: 0.5638 (tp) cc_final: 0.5422 (tp) REVERT: I 1085 MET cc_start: 0.8597 (mmm) cc_final: 0.6805 (mmm) REVERT: I 1129 ASN cc_start: 0.7984 (t0) cc_final: 0.7784 (t0) REVERT: I 1238 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8599 (mt) REVERT: I 1239 VAL cc_start: 0.8903 (p) cc_final: 0.8695 (p) REVERT: I 1274 GLU cc_start: 0.7047 (mp0) cc_final: 0.5839 (mp0) REVERT: J 16 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6015 (tt0) REVERT: J 137 ARG cc_start: 0.6765 (mtm180) cc_final: 0.6353 (mtp85) REVERT: J 163 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6882 (pt0) REVERT: J 201 LEU cc_start: 0.5868 (mm) cc_final: 0.5526 (tp) REVERT: J 204 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5290 (mt-10) REVERT: J 402 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.4903 (tm-30) REVERT: J 489 ASN cc_start: 0.7152 (m110) cc_final: 0.6339 (p0) REVERT: J 568 SER cc_start: 0.8384 (t) cc_final: 0.8121 (m) REVERT: J 709 ARG cc_start: 0.5625 (OUTLIER) cc_final: 0.4303 (tpm-80) REVERT: J 866 GLU cc_start: 0.6624 (mp0) cc_final: 0.6364 (mp0) REVERT: J 932 MET cc_start: 0.6435 (ptm) cc_final: 0.6073 (ptm) REVERT: L 90 GLU cc_start: 0.2370 (OUTLIER) cc_final: 0.1260 (mm-30) REVERT: L 99 ARG cc_start: 0.7049 (mtt180) cc_final: 0.6673 (tpt170) REVERT: L 121 LYS cc_start: 0.6891 (ptpp) cc_final: 0.6468 (tppt) REVERT: L 364 ARG cc_start: 0.5713 (mtm180) cc_final: 0.4702 (mtm-85) REVERT: L 460 ILE cc_start: 0.8390 (mt) cc_final: 0.8068 (tp) REVERT: L 476 ARG cc_start: 0.4488 (OUTLIER) cc_final: 0.3132 (mtm180) REVERT: L 514 ASP cc_start: 0.1695 (OUTLIER) cc_final: 0.1071 (m-30) REVERT: L 593 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.6490 (ttpp) REVERT: L 610 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5711 (t80) REVERT: N 3 ASP cc_start: 0.8189 (t0) cc_final: 0.7834 (t0) REVERT: N 67 ARG cc_start: 0.7723 (mtp85) cc_final: 0.7233 (mtm180) outliers start: 236 outliers final: 164 residues processed: 643 average time/residue: 0.2070 time to fit residues: 208.5010 Evaluate side-chains 582 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 402 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 585 LYS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 516 ASP Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 593 LYS Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 chunk 290 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 387 ASN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 554 HIS ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.162549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135661 restraints weight = 55618.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.134749 restraints weight = 83484.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135488 restraints weight = 84771.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.135984 restraints weight = 46526.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137097 restraints weight = 38351.141| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 33020 Z= 0.243 Angle : 0.698 11.258 44955 Z= 0.366 Chirality : 0.046 0.198 5147 Planarity : 0.005 0.081 5573 Dihedral : 16.899 176.952 5364 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.85 % Favored : 92.10 % Rotamer: Outliers : 8.37 % Allowed : 25.68 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.13), residues: 3875 helix: -0.46 (0.13), residues: 1562 sheet: -1.60 (0.27), residues: 354 loop : -2.19 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 211 TYR 0.027 0.002 TYR I1229 PHE 0.049 0.002 PHE I 972 TRP 0.046 0.002 TRP I 997 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00565 (33011) covalent geometry : angle 0.69767 (44949) hydrogen bonds : bond 0.04131 ( 1269) hydrogen bonds : angle 5.11500 ( 3502) metal coordination : bond 0.00669 ( 9) metal coordination : angle 2.20214 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 417 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 330 HIS cc_start: 0.0578 (OUTLIER) cc_final: 0.0274 (m170) REVERT: I 496 LYS cc_start: 0.7145 (tptm) cc_final: 0.6764 (ttpp) REVERT: I 498 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7441 (pt) REVERT: I 592 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7254 (ptm160) REVERT: I 646 SER cc_start: 0.7619 (OUTLIER) cc_final: 0.7341 (t) REVERT: I 789 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7970 (m) REVERT: I 791 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8157 (tt) REVERT: I 814 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: I 894 GLN cc_start: 0.6250 (mt0) cc_final: 0.5925 (mt0) REVERT: I 899 GLU cc_start: 0.7458 (tp30) cc_final: 0.7251 (tp30) REVERT: I 941 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7036 (mptt) REVERT: I 1085 MET cc_start: 0.8614 (mmm) cc_final: 0.6853 (mmm) REVERT: I 1274 GLU cc_start: 0.7122 (mp0) cc_final: 0.5889 (mp0) REVERT: J 137 ARG cc_start: 0.6718 (mtm180) cc_final: 0.6356 (mtp85) REVERT: J 163 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6920 (pt0) REVERT: J 201 LEU cc_start: 0.5904 (mm) cc_final: 0.5463 (tp) REVERT: J 227 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: J 235 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: J 402 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.4975 (tm-30) REVERT: J 489 ASN cc_start: 0.7300 (m110) cc_final: 0.6468 (p0) REVERT: J 932 MET cc_start: 0.6468 (ptm) cc_final: 0.6103 (ptm) REVERT: J 1061 VAL cc_start: 0.1185 (OUTLIER) cc_final: 0.0555 (m) REVERT: J 1104 LYS cc_start: 0.2942 (OUTLIER) cc_final: 0.2239 (mmmt) REVERT: L 78 GLU cc_start: 0.3193 (OUTLIER) cc_final: 0.2421 (mm-30) REVERT: L 90 GLU cc_start: 0.2329 (OUTLIER) cc_final: 0.1285 (mm-30) REVERT: L 99 ARG cc_start: 0.7223 (mtt180) cc_final: 0.6837 (tpt170) REVERT: L 121 LYS cc_start: 0.6912 (ptpp) cc_final: 0.6554 (tppt) REVERT: L 235 ILE cc_start: 0.1775 (OUTLIER) cc_final: 0.1532 (mt) REVERT: L 364 ARG cc_start: 0.5928 (mtm180) cc_final: 0.5524 (mtm-85) REVERT: L 476 ARG cc_start: 0.4579 (OUTLIER) cc_final: 0.3076 (mtm180) REVERT: L 487 MET cc_start: 0.4541 (mtm) cc_final: 0.4304 (mtm) REVERT: L 593 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6462 (ttpp) REVERT: L 610 PHE cc_start: 0.6195 (OUTLIER) cc_final: 0.5877 (t80) REVERT: M 265 ARG cc_start: 0.4356 (mmt90) cc_final: 0.4110 (mmm-85) REVERT: N 67 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7603 (mtm180) outliers start: 278 outliers final: 206 residues processed: 656 average time/residue: 0.2000 time to fit residues: 206.9268 Evaluate side-chains 609 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 383 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 180 ARG Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 825 GLU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 585 LYS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 981 GLU Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1104 LYS Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 516 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 593 LYS Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 226 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 261 optimal weight: 0.1980 chunk 87 optimal weight: 7.9990 chunk 296 optimal weight: 7.9990 chunk 221 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 chunk 257 optimal weight: 0.0970 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 31 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 ASN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN J 341 ASN ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.164904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138143 restraints weight = 55442.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.136786 restraints weight = 82107.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137700 restraints weight = 83371.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.138270 restraints weight = 48688.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.139099 restraints weight = 40434.394| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33020 Z= 0.149 Angle : 0.624 11.165 44955 Z= 0.328 Chirality : 0.043 0.181 5147 Planarity : 0.004 0.078 5573 Dihedral : 16.720 177.651 5361 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.40 % Favored : 93.55 % Rotamer: Outliers : 6.89 % Allowed : 27.33 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.13), residues: 3875 helix: -0.09 (0.13), residues: 1550 sheet: -1.67 (0.27), residues: 377 loop : -2.02 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1341 TYR 0.024 0.001 TYR I1229 PHE 0.020 0.001 PHE L 256 TRP 0.047 0.002 TRP I 997 HIS 0.003 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00340 (33011) covalent geometry : angle 0.62432 (44949) hydrogen bonds : bond 0.03620 ( 1269) hydrogen bonds : angle 4.84097 ( 3502) metal coordination : bond 0.00849 ( 9) metal coordination : angle 1.21085 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 425 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6900 (m-30) REVERT: H 35 PHE cc_start: 0.8435 (m-80) cc_final: 0.8141 (m-80) REVERT: I 193 ASN cc_start: 0.6817 (m-40) cc_final: 0.6364 (m-40) REVERT: I 201 ARG cc_start: 0.6608 (ttm110) cc_final: 0.6358 (ttm110) REVERT: I 202 ARG cc_start: 0.6681 (ptt90) cc_final: 0.6253 (ptp-110) REVERT: I 239 MET cc_start: 0.5330 (ppp) cc_final: 0.4025 (ttp) REVERT: I 330 HIS cc_start: 0.0394 (OUTLIER) cc_final: 0.0151 (m170) REVERT: I 494 ASN cc_start: 0.6170 (OUTLIER) cc_final: 0.5199 (p0) REVERT: I 496 LYS cc_start: 0.7247 (tptm) cc_final: 0.6854 (ttpp) REVERT: I 498 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7397 (pt) REVERT: I 646 SER cc_start: 0.7614 (OUTLIER) cc_final: 0.7223 (t) REVERT: I 789 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7989 (m) REVERT: I 791 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8225 (tt) REVERT: I 941 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.6988 (mptt) REVERT: I 971 LEU cc_start: 0.4626 (OUTLIER) cc_final: 0.4186 (tp) REVERT: I 1029 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.6107 (mt) REVERT: I 1085 MET cc_start: 0.8608 (mmm) cc_final: 0.6831 (mmm) REVERT: I 1238 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8528 (mt) REVERT: I 1239 VAL cc_start: 0.8993 (p) cc_final: 0.8728 (p) REVERT: I 1274 GLU cc_start: 0.7140 (mp0) cc_final: 0.5893 (mp0) REVERT: J 42 GLU cc_start: 0.7831 (pt0) cc_final: 0.7522 (pt0) REVERT: J 137 ARG cc_start: 0.6751 (mtm180) cc_final: 0.6337 (mtp85) REVERT: J 163 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6873 (pt0) REVERT: J 200 GLN cc_start: 0.6290 (OUTLIER) cc_final: 0.5904 (tp40) REVERT: J 201 LEU cc_start: 0.6014 (mm) cc_final: 0.5638 (tp) REVERT: J 227 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: J 341 ASN cc_start: 0.6722 (OUTLIER) cc_final: 0.6234 (t0) REVERT: J 402 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.4911 (tm-30) REVERT: J 443 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: J 479 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: J 489 ASN cc_start: 0.7108 (m110) cc_final: 0.6295 (p0) REVERT: J 709 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.4346 (tpm-80) REVERT: J 932 MET cc_start: 0.6421 (ptm) cc_final: 0.6066 (ptm) REVERT: J 1095 MET cc_start: 0.2476 (mtt) cc_final: 0.2004 (mmp) REVERT: J 1104 LYS cc_start: 0.2722 (OUTLIER) cc_final: 0.1828 (mmmt) REVERT: J 1369 ARG cc_start: 0.6132 (ttp80) cc_final: 0.5755 (ttp80) REVERT: L 90 GLU cc_start: 0.2311 (OUTLIER) cc_final: 0.1333 (mm-30) REVERT: L 99 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6820 (tpt170) REVERT: L 121 LYS cc_start: 0.6819 (ptpp) cc_final: 0.6584 (tppt) REVERT: L 163 THR cc_start: 0.5105 (p) cc_final: 0.4590 (p) REVERT: L 364 ARG cc_start: 0.5836 (mtm180) cc_final: 0.5478 (mtm-85) REVERT: L 393 LYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6406 (mmtt) REVERT: L 460 ILE cc_start: 0.8395 (mt) cc_final: 0.8055 (tp) REVERT: L 476 ARG cc_start: 0.4476 (OUTLIER) cc_final: 0.3123 (mtm180) REVERT: L 514 ASP cc_start: 0.1711 (OUTLIER) cc_final: 0.1128 (m-30) REVERT: L 593 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6459 (ttpp) REVERT: N 38 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6972 (mm-30) REVERT: N 67 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7417 (mtm180) outliers start: 229 outliers final: 154 residues processed: 623 average time/residue: 0.2052 time to fit residues: 201.1607 Evaluate side-chains 567 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 388 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 341 ASN Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 585 LYS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1104 LYS Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 393 LYS Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 593 LYS Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 375 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 339 optimal weight: 9.9990 chunk 288 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 270 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.162175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134023 restraints weight = 55394.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132428 restraints weight = 94247.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133552 restraints weight = 86147.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134284 restraints weight = 51499.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134579 restraints weight = 46677.295| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 33020 Z= 0.242 Angle : 0.704 11.263 44955 Z= 0.368 Chirality : 0.046 0.228 5147 Planarity : 0.005 0.084 5573 Dihedral : 16.789 176.947 5356 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.90 % Favored : 92.05 % Rotamer: Outliers : 7.50 % Allowed : 27.15 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.13), residues: 3875 helix: -0.21 (0.13), residues: 1556 sheet: -1.69 (0.27), residues: 373 loop : -2.10 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 69 TYR 0.028 0.002 TYR I1229 PHE 0.024 0.002 PHE I 157 TRP 0.056 0.002 TRP I 997 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00564 (33011) covalent geometry : angle 0.70366 (44949) hydrogen bonds : bond 0.04064 ( 1269) hydrogen bonds : angle 5.01407 ( 3502) metal coordination : bond 0.00775 ( 9) metal coordination : angle 2.02473 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 394 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7047 (m-30) REVERT: I 124 MET cc_start: 0.7014 (ptm) cc_final: 0.6564 (ptm) REVERT: I 201 ARG cc_start: 0.6758 (ttm110) cc_final: 0.6435 (ttm110) REVERT: I 330 HIS cc_start: 0.0394 (OUTLIER) cc_final: 0.0164 (m170) REVERT: I 496 LYS cc_start: 0.7218 (tptm) cc_final: 0.6793 (ttpp) REVERT: I 498 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7428 (pt) REVERT: I 592 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7303 (ptm160) REVERT: I 646 SER cc_start: 0.7625 (OUTLIER) cc_final: 0.7388 (t) REVERT: I 789 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7957 (m) REVERT: I 791 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8202 (tt) REVERT: I 805 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8109 (ptm) REVERT: I 941 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7040 (mptt) REVERT: I 1085 MET cc_start: 0.8602 (mmm) cc_final: 0.6897 (mmm) REVERT: I 1274 GLU cc_start: 0.7217 (mp0) cc_final: 0.5979 (mp0) REVERT: J 96 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7008 (pttp) REVERT: J 137 ARG cc_start: 0.6819 (mtm180) cc_final: 0.6499 (mtp85) REVERT: J 163 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6861 (pt0) REVERT: J 200 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.5890 (tp40) REVERT: J 201 LEU cc_start: 0.5852 (mm) cc_final: 0.5502 (tp) REVERT: J 235 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: J 402 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5012 (tm-30) REVERT: J 443 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: J 479 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: J 489 ASN cc_start: 0.7244 (m110) cc_final: 0.6423 (p0) REVERT: J 932 MET cc_start: 0.6491 (ptm) cc_final: 0.6134 (ptm) REVERT: J 1061 VAL cc_start: 0.1740 (OUTLIER) cc_final: 0.1030 (m) REVERT: J 1095 MET cc_start: 0.2508 (mtt) cc_final: 0.2030 (mmp) REVERT: J 1104 LYS cc_start: 0.2635 (OUTLIER) cc_final: 0.1897 (mmmt) REVERT: J 1261 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8217 (pp) REVERT: J 1369 ARG cc_start: 0.6263 (ttp80) cc_final: 0.5814 (ttp80) REVERT: L 90 GLU cc_start: 0.2122 (OUTLIER) cc_final: 0.1135 (mm-30) REVERT: L 99 ARG cc_start: 0.7474 (mtt180) cc_final: 0.6879 (tpt170) REVERT: L 121 LYS cc_start: 0.6996 (ptpp) cc_final: 0.6643 (tppt) REVERT: L 163 THR cc_start: 0.4565 (p) cc_final: 0.4289 (p) REVERT: L 235 ILE cc_start: 0.1734 (OUTLIER) cc_final: 0.1508 (mt) REVERT: L 364 ARG cc_start: 0.5792 (mtm180) cc_final: 0.5524 (mtm-85) REVERT: L 393 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6487 (mmtt) REVERT: L 476 ARG cc_start: 0.4561 (OUTLIER) cc_final: 0.3031 (mtt180) REVERT: L 593 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6530 (ttpp) REVERT: N 38 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7178 (mm-30) REVERT: N 67 ARG cc_start: 0.7858 (mtp85) cc_final: 0.7568 (mtm180) outliers start: 249 outliers final: 189 residues processed: 610 average time/residue: 0.2014 time to fit residues: 194.5805 Evaluate side-chains 592 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 379 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 585 LYS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1104 LYS Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 393 LYS Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 593 LYS Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 169 optimal weight: 7.9990 chunk 305 optimal weight: 4.9990 chunk 369 optimal weight: 6.9990 chunk 220 optimal weight: 0.9980 chunk 366 optimal weight: 9.9990 chunk 389 optimal weight: 10.0000 chunk 121 optimal weight: 0.0970 chunk 264 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.164337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135903 restraints weight = 55556.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135362 restraints weight = 98658.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136503 restraints weight = 87812.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136610 restraints weight = 56274.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.137491 restraints weight = 48727.427| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33020 Z= 0.164 Angle : 0.648 11.747 44955 Z= 0.337 Chirality : 0.044 0.213 5147 Planarity : 0.005 0.078 5573 Dihedral : 16.706 177.343 5354 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.68 % Favored : 93.26 % Rotamer: Outliers : 7.01 % Allowed : 27.81 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.13), residues: 3875 helix: -0.01 (0.13), residues: 1556 sheet: -1.64 (0.27), residues: 375 loop : -2.04 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1156 TYR 0.025 0.002 TYR I1229 PHE 0.039 0.002 PHE L 221 TRP 0.051 0.002 TRP I 997 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00380 (33011) covalent geometry : angle 0.64750 (44949) hydrogen bonds : bond 0.03668 ( 1269) hydrogen bonds : angle 4.83455 ( 3502) metal coordination : bond 0.00449 ( 9) metal coordination : angle 1.27573 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 408 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.6946 (m-30) REVERT: H 35 PHE cc_start: 0.8462 (m-80) cc_final: 0.8189 (m-80) REVERT: I 193 ASN cc_start: 0.6796 (m-40) cc_final: 0.6311 (m-40) REVERT: I 201 ARG cc_start: 0.6666 (ttm110) cc_final: 0.6439 (ttm110) REVERT: I 239 MET cc_start: 0.5270 (ppp) cc_final: 0.3940 (ttp) REVERT: I 320 ASP cc_start: 0.4167 (p0) cc_final: 0.3935 (p0) REVERT: I 330 HIS cc_start: 0.0522 (OUTLIER) cc_final: 0.0289 (m170) REVERT: I 496 LYS cc_start: 0.7302 (tptm) cc_final: 0.6893 (ttpp) REVERT: I 498 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7357 (pt) REVERT: I 592 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7259 (ptm160) REVERT: I 646 SER cc_start: 0.7647 (OUTLIER) cc_final: 0.7289 (t) REVERT: I 789 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7921 (m) REVERT: I 791 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8254 (tt) REVERT: I 805 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8052 (ptm) REVERT: I 941 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.6996 (mptt) REVERT: I 971 LEU cc_start: 0.4507 (OUTLIER) cc_final: 0.4138 (tp) REVERT: I 1085 MET cc_start: 0.8597 (mmm) cc_final: 0.6848 (mmm) REVERT: I 1238 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8575 (mt) REVERT: I 1239 VAL cc_start: 0.9011 (p) cc_final: 0.8736 (p) REVERT: I 1274 GLU cc_start: 0.7114 (mp0) cc_final: 0.5882 (mp0) REVERT: I 1319 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.5918 (ptt) REVERT: J 96 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.6946 (pttp) REVERT: J 137 ARG cc_start: 0.6667 (mtm180) cc_final: 0.6462 (mtp85) REVERT: J 163 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6729 (pt0) REVERT: J 193 ASP cc_start: 0.5219 (t0) cc_final: 0.4733 (t0) REVERT: J 200 GLN cc_start: 0.6203 (OUTLIER) cc_final: 0.5823 (tp40) REVERT: J 201 LEU cc_start: 0.5905 (mm) cc_final: 0.5337 (tp) REVERT: J 235 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: J 402 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.4930 (tm-30) REVERT: J 443 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: J 479 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: J 489 ASN cc_start: 0.7228 (m110) cc_final: 0.6321 (p0) REVERT: J 709 ARG cc_start: 0.5684 (OUTLIER) cc_final: 0.4557 (tpm-80) REVERT: J 818 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6509 (mm-30) REVERT: J 1095 MET cc_start: 0.2532 (mtt) cc_final: 0.2114 (mmp) REVERT: J 1104 LYS cc_start: 0.2893 (OUTLIER) cc_final: 0.2182 (mmmt) REVERT: J 1261 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8203 (pp) REVERT: J 1283 SER cc_start: 0.8227 (t) cc_final: 0.7901 (p) REVERT: J 1369 ARG cc_start: 0.6134 (ttp80) cc_final: 0.5805 (ttp80) REVERT: K 30 MET cc_start: 0.8167 (mtm) cc_final: 0.7824 (mtm) REVERT: L 99 ARG cc_start: 0.7414 (mtt180) cc_final: 0.6880 (tpt170) REVERT: L 163 THR cc_start: 0.4557 (p) cc_final: 0.4006 (p) REVERT: L 235 ILE cc_start: 0.1607 (OUTLIER) cc_final: 0.1371 (mt) REVERT: L 364 ARG cc_start: 0.5636 (mtm180) cc_final: 0.5409 (mtm-85) REVERT: L 393 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6438 (mmtt) REVERT: L 460 ILE cc_start: 0.8458 (mt) cc_final: 0.8098 (tp) REVERT: L 476 ARG cc_start: 0.4476 (OUTLIER) cc_final: 0.2980 (mtm180) outliers start: 233 outliers final: 175 residues processed: 613 average time/residue: 0.1953 time to fit residues: 190.5383 Evaluate side-chains 584 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 383 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 952 GLN Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 585 LYS Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1104 LYS Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 393 LYS Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 228 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 326 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 316 optimal weight: 0.9990 chunk 374 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 93 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1098 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.164259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.137274 restraints weight = 55389.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135327 restraints weight = 90138.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136208 restraints weight = 74918.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137414 restraints weight = 48204.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137534 restraints weight = 39919.448| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33020 Z= 0.173 Angle : 0.662 13.826 44955 Z= 0.342 Chirality : 0.044 0.226 5147 Planarity : 0.005 0.079 5573 Dihedral : 16.618 177.345 5350 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.30 % Favored : 92.65 % Rotamer: Outliers : 6.56 % Allowed : 28.51 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.13), residues: 3875 helix: -0.00 (0.13), residues: 1561 sheet: -1.60 (0.27), residues: 370 loop : -2.00 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1156 TYR 0.026 0.002 TYR I1229 PHE 0.028 0.002 PHE L 221 TRP 0.045 0.002 TRP I 997 HIS 0.004 0.001 HIS G 160 Details of bonding type rmsd covalent geometry : bond 0.00402 (33011) covalent geometry : angle 0.66153 (44949) hydrogen bonds : bond 0.03636 ( 1269) hydrogen bonds : angle 4.81236 ( 3502) metal coordination : bond 0.00471 ( 9) metal coordination : angle 1.27018 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 392 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: H 35 PHE cc_start: 0.8423 (m-80) cc_final: 0.8153 (m-80) REVERT: I 193 ASN cc_start: 0.6808 (m-40) cc_final: 0.6326 (m-40) REVERT: I 201 ARG cc_start: 0.6828 (ttm110) cc_final: 0.6549 (ttm110) REVERT: I 492 MET cc_start: 0.5652 (ptp) cc_final: 0.5345 (ptp) REVERT: I 494 ASN cc_start: 0.6150 (OUTLIER) cc_final: 0.5104 (p0) REVERT: I 496 LYS cc_start: 0.7244 (tptm) cc_final: 0.6797 (ttpp) REVERT: I 498 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7320 (pt) REVERT: I 592 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7276 (ptm160) REVERT: I 646 SER cc_start: 0.7638 (OUTLIER) cc_final: 0.7286 (t) REVERT: I 789 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7998 (m) REVERT: I 791 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8265 (tt) REVERT: I 805 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8080 (ptm) REVERT: I 941 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7004 (mptt) REVERT: I 971 LEU cc_start: 0.4468 (OUTLIER) cc_final: 0.4156 (tp) REVERT: I 989 LEU cc_start: 0.5421 (tp) cc_final: 0.5101 (tp) REVERT: I 1085 MET cc_start: 0.8606 (mmm) cc_final: 0.6833 (mmm) REVERT: I 1238 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8565 (mt) REVERT: I 1239 VAL cc_start: 0.8998 (p) cc_final: 0.8725 (p) REVERT: I 1274 GLU cc_start: 0.7089 (mp0) cc_final: 0.5865 (mp0) REVERT: I 1319 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.5934 (ptt) REVERT: J 96 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.6980 (pttp) REVERT: J 137 ARG cc_start: 0.6743 (mtm180) cc_final: 0.6440 (mtp85) REVERT: J 163 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6870 (pt0) REVERT: J 193 ASP cc_start: 0.5070 (t0) cc_final: 0.4630 (t0) REVERT: J 200 GLN cc_start: 0.6453 (OUTLIER) cc_final: 0.5901 (tp40) REVERT: J 201 LEU cc_start: 0.5987 (mm) cc_final: 0.5438 (tp) REVERT: J 235 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7447 (pm20) REVERT: J 402 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5005 (tm-30) REVERT: J 443 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: J 479 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7895 (mt-10) REVERT: J 489 ASN cc_start: 0.7142 (m110) cc_final: 0.6283 (p0) REVERT: J 709 ARG cc_start: 0.5645 (OUTLIER) cc_final: 0.4520 (tpm-80) REVERT: J 1095 MET cc_start: 0.2520 (mtt) cc_final: 0.2048 (mmp) REVERT: J 1104 LYS cc_start: 0.2880 (OUTLIER) cc_final: 0.2220 (mmmt) REVERT: J 1261 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8196 (pp) REVERT: J 1283 SER cc_start: 0.8235 (t) cc_final: 0.7931 (p) REVERT: J 1369 ARG cc_start: 0.6032 (ttp80) cc_final: 0.5737 (ttp80) REVERT: L 69 GLU cc_start: 0.2752 (OUTLIER) cc_final: 0.1915 (mp0) REVERT: L 99 ARG cc_start: 0.7444 (mtt180) cc_final: 0.6768 (tpt170) REVERT: L 163 THR cc_start: 0.4770 (p) cc_final: 0.4218 (p) REVERT: L 235 ILE cc_start: 0.1551 (OUTLIER) cc_final: 0.1331 (mt) REVERT: L 277 MET cc_start: 0.3762 (mtt) cc_final: 0.2929 (tpt) REVERT: L 364 ARG cc_start: 0.5923 (mtm180) cc_final: 0.5575 (mtm-85) REVERT: L 393 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6501 (mmtt) REVERT: L 460 ILE cc_start: 0.8418 (mt) cc_final: 0.8086 (tp) REVERT: L 476 ARG cc_start: 0.4515 (OUTLIER) cc_final: 0.2988 (mtm180) REVERT: L 514 ASP cc_start: 0.1346 (OUTLIER) cc_final: 0.0799 (m-30) REVERT: N 67 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7280 (ttm110) outliers start: 218 outliers final: 179 residues processed: 585 average time/residue: 0.2022 time to fit residues: 187.8257 Evaluate side-chains 585 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 380 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 180 ARG Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 952 GLN Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 585 LYS Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1104 LYS Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 393 LYS Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 335 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 334 optimal weight: 20.0000 chunk 375 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 372 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 93 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1019 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.162111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.133657 restraints weight = 55816.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132202 restraints weight = 96790.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133230 restraints weight = 89226.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134330 restraints weight = 52480.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134554 restraints weight = 45257.229| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 33020 Z= 0.260 Angle : 0.738 13.022 44955 Z= 0.382 Chirality : 0.047 0.230 5147 Planarity : 0.006 0.078 5573 Dihedral : 16.708 176.862 5346 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.18 % Favored : 91.77 % Rotamer: Outliers : 6.68 % Allowed : 28.66 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.13), residues: 3875 helix: -0.20 (0.13), residues: 1556 sheet: -1.65 (0.26), residues: 390 loop : -2.09 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 371 TYR 0.027 0.002 TYR I1229 PHE 0.028 0.002 PHE L 221 TRP 0.042 0.002 TRP I 997 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00609 (33011) covalent geometry : angle 0.73796 (44949) hydrogen bonds : bond 0.04097 ( 1269) hydrogen bonds : angle 5.03804 ( 3502) metal coordination : bond 0.00826 ( 9) metal coordination : angle 2.15808 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 387 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7166 (m-30) REVERT: I 201 ARG cc_start: 0.6776 (ttm110) cc_final: 0.6503 (ttm110) REVERT: I 330 HIS cc_start: 0.1287 (OUTLIER) cc_final: 0.0344 (m90) REVERT: I 496 LYS cc_start: 0.7086 (tptm) cc_final: 0.6662 (ttpp) REVERT: I 498 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7335 (pt) REVERT: I 592 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7322 (ptm160) REVERT: I 646 SER cc_start: 0.7594 (OUTLIER) cc_final: 0.7345 (t) REVERT: I 789 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7966 (m) REVERT: I 791 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8246 (tt) REVERT: I 805 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8132 (ptm) REVERT: I 941 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7037 (mptt) REVERT: I 1085 MET cc_start: 0.8557 (mmm) cc_final: 0.6852 (mmm) REVERT: I 1274 GLU cc_start: 0.7197 (mp0) cc_final: 0.5978 (mp0) REVERT: J 96 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.6998 (pttp) REVERT: J 137 ARG cc_start: 0.6811 (mtm180) cc_final: 0.6498 (mtp85) REVERT: J 163 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6834 (pt0) REVERT: J 180 MET cc_start: 0.5407 (tpt) cc_final: 0.4997 (tpt) REVERT: J 193 ASP cc_start: 0.5056 (t0) cc_final: 0.4597 (t0) REVERT: J 201 LEU cc_start: 0.5805 (mm) cc_final: 0.5428 (tp) REVERT: J 252 LEU cc_start: 0.8733 (tp) cc_final: 0.8388 (tt) REVERT: J 402 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5015 (tm-30) REVERT: J 443 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: J 479 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7995 (mt-10) REVERT: J 489 ASN cc_start: 0.7339 (m110) cc_final: 0.6414 (p0) REVERT: J 644 MET cc_start: 0.8221 (mtm) cc_final: 0.8007 (mtm) REVERT: J 818 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6471 (mm-30) REVERT: J 1061 VAL cc_start: 0.1552 (OUTLIER) cc_final: 0.0873 (m) REVERT: J 1104 LYS cc_start: 0.3237 (OUTLIER) cc_final: 0.2683 (mmmt) REVERT: J 1261 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8193 (pp) REVERT: J 1283 SER cc_start: 0.8305 (t) cc_final: 0.7964 (p) REVERT: J 1369 ARG cc_start: 0.6127 (ttp80) cc_final: 0.5810 (ttp80) REVERT: K 74 GLU cc_start: 0.6387 (mp0) cc_final: 0.5948 (mp0) REVERT: L 69 GLU cc_start: 0.2526 (OUTLIER) cc_final: 0.1454 (mp0) REVERT: L 99 ARG cc_start: 0.7464 (mtt180) cc_final: 0.6814 (tpt170) REVERT: L 235 ILE cc_start: 0.1609 (OUTLIER) cc_final: 0.1379 (mt) REVERT: L 277 MET cc_start: 0.3641 (mtt) cc_final: 0.2985 (tpt) REVERT: L 393 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6368 (mmtt) REVERT: L 476 ARG cc_start: 0.4698 (OUTLIER) cc_final: 0.3153 (mtm180) REVERT: N 67 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7404 (ttm110) outliers start: 222 outliers final: 187 residues processed: 581 average time/residue: 0.1984 time to fit residues: 183.2766 Evaluate side-chains 587 residues out of total 3347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 379 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 952 GLN Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 585 LYS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1104 LYS Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 393 LYS Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 6 optimal weight: 8.9990 chunk 74 optimal weight: 40.0000 chunk 24 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 250 optimal weight: 0.6980 chunk 358 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 93 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.165451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136982 restraints weight = 55608.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.136688 restraints weight = 96793.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137814 restraints weight = 85289.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137879 restraints weight = 55521.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139670 restraints weight = 48196.519| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33020 Z= 0.138 Angle : 0.643 12.409 44955 Z= 0.333 Chirality : 0.043 0.188 5147 Planarity : 0.005 0.078 5573 Dihedral : 16.536 177.674 5346 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.32 % Favored : 93.63 % Rotamer: Outliers : 5.48 % Allowed : 29.74 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.13), residues: 3875 helix: 0.13 (0.13), residues: 1556 sheet: -1.62 (0.27), residues: 376 loop : -1.91 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 371 TYR 0.022 0.001 TYR I1229 PHE 0.024 0.001 PHE L 221 TRP 0.045 0.002 TRP I 997 HIS 0.003 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00315 (33011) covalent geometry : angle 0.64304 (44949) hydrogen bonds : bond 0.03434 ( 1269) hydrogen bonds : angle 4.72845 ( 3502) metal coordination : bond 0.00293 ( 9) metal coordination : angle 1.14085 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5428.66 seconds wall clock time: 94 minutes 34.88 seconds (5674.88 seconds total)