Starting phenix.real_space_refine on Sun Jun 7 01:38:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymw_73124/06_2026/9ymw_73124.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymw_73124/06_2026/9ymw_73124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ymw_73124/06_2026/9ymw_73124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymw_73124/06_2026/9ymw_73124.map" model { file = "/net/cci-nas-00/data/ceres_data/9ymw_73124/06_2026/9ymw_73124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymw_73124/06_2026/9ymw_73124.cif" } resolution = 2.7 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= 0.020 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 2 6.06 5 P 139 5.49 5 Mg 1 5.21 5 S 129 5.16 5 C 19446 2.51 5 N 5612 2.21 5 O 7105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32434 Number of models: 1 Model: "" Number of chains: 20 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 4} Chain: "P" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1325 Classifications: {'DNA': 64} Link IDs: {'rna3p': 63} Chain breaks: 1 Chain: "G" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1748 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 216} Chain breaks: 1 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1710 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "J" Number of atoms: 10394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10394 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1281} Chain breaks: 2 Chain: "L" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3837 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 15, 'TRANS': 455} Chain breaks: 2 Chain: "Q" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1382 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain breaks: 1 Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} 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: "I" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 314 Classifications: {'water': 314} Link IDs: {None: 313} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "J" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 277 Classifications: {'water': 277} Link IDs: {None: 276} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "Q" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16528 SG CYS J 70 53.631 62.678 118.260 1.00 67.85 S ATOM 16542 SG CYS J 72 55.815 61.725 121.102 1.00 74.67 S ATOM 16650 SG CYS J 85 52.182 61.870 121.628 1.00 72.77 S ATOM 16674 SG CYS J 88 54.146 65.021 121.176 1.00 65.44 S ATOM 22362 SG CYS J 814 26.554 118.411 88.171 1.00 52.05 S ATOM 22927 SG CYS J 888 29.869 116.975 89.223 1.00 37.25 S ATOM 22978 SG CYS J 895 28.246 115.879 86.066 1.00 44.13 S ATOM 22999 SG CYS J 898 29.662 119.293 86.267 1.00 49.45 S Time building chain proxies: 7.70, per 1000 atoms: 0.24 Number of scatterers: 32434 At special positions: 0 Unit cell: (159.96, 194.36, 194.36, 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 2 29.99 S 129 16.00 P 139 15.00 Mg 1 11.99 O 7105 8.00 N 5612 7.00 C 19446 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: 3.04 Conformation dependent library (CDL) restraints added in 1.4 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 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6820 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 49 sheets defined 44.3% alpha, 16.3% beta 57 base pairs and 106 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.548A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.631A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.011A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.751A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.067A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 removed outlier: 3.568A pdb=" N GLY I 401 " --> pdb=" O LEU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.846A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL I 471 " --> pdb=" O GLY I 467 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.817A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 488 through 493' Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.713A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 539 through 543 removed outlier: 3.916A pdb=" N ALA I 543 " --> pdb=" O ARG I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 545 through 549 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.605A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.631A 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 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.670A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 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 713 removed outlier: 4.095A pdb=" N GLY I 713 " --> pdb=" O ALA I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 942 through 961 Processing helix chain 'I' and resid 964 through 979 removed outlier: 3.765A pdb=" N LEU I 979 " --> pdb=" O ILE I 975 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 989 Processing helix chain 'I' and resid 993 through 1000 removed outlier: 4.290A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU I1000 " --> pdb=" O TRP I 997 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1035 removed outlier: 4.144A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU I1026 " --> pdb=" O LYS I1022 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA I1031 " --> pdb=" O LYS I1027 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS I1032 " --> pdb=" O LYS I1028 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS I1035 " --> pdb=" O ALA I1031 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.723A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.787A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.843A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 33 removed outlier: 3.519A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 Processing helix chain 'G' and resid 34 through 51 removed outlier: 3.791A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.738A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 228 through 233 removed outlier: 3.576A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.535A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.693A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 158 Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.643A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.845A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.569A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 264 through 286 removed outlier: 3.773A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.547A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (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 405 through 416 removed outlier: 4.044A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) 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 483 Processing helix chain 'J' and resid 485 through 489 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 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.545A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.898A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.644A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 removed outlier: 3.763A pdb=" N TYR J 679 " --> pdb=" O ALA J 675 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 729 removed outlier: 3.555A pdb=" N GLY J 729 " --> pdb=" O MET J 725 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 774 Processing helix chain 'J' and resid 775 through 805 removed outlier: 3.683A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.556A pdb=" N CYS J 888 " --> pdb=" O VAL J 885 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.517A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.742A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1260 removed outlier: 4.355A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1318 through 1324 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.844A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1375 Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 112 through 136 Processing helix chain 'L' and resid 137 through 153 Processing helix chain 'L' and resid 157 through 162 Processing helix chain 'L' and resid 215 through 236 removed outlier: 3.700A pdb=" N LYS L 236 " --> pdb=" O ARG L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 259 Processing helix chain 'L' and resid 262 through 296 removed outlier: 4.377A pdb=" N GLN L 294 " --> pdb=" O LEU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 313 through 319 Processing helix chain 'L' and resid 324 through 329 Processing helix chain 'L' and resid 330 through 332 No H-bonds generated for 'chain 'L' and resid 330 through 332' Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 382 removed outlier: 3.517A pdb=" N ASP L 360 " --> pdb=" O GLU L 356 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG L 363 " --> pdb=" O LYS L 359 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 392 removed outlier: 3.525A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 395 No H-bonds generated for 'chain 'L' and resid 393 through 395' Processing helix chain 'L' and resid 400 through 419 removed outlier: 3.673A pdb=" N ILE L 410 " --> pdb=" O GLN L 406 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY L 411 " --> pdb=" O GLU L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.915A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.633A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 488 removed outlier: 3.780A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG L 486 " --> pdb=" O GLU L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 490 through 501 removed outlier: 3.537A pdb=" N ALA L 501 " --> pdb=" O VAL L 497 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.720A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 removed outlier: 3.724A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 564 removed outlier: 3.582A pdb=" N LYS L 557 " --> pdb=" O ALA L 553 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL L 558 " --> pdb=" O ARG L 554 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 581 removed outlier: 3.802A pdb=" N VAL L 576 " --> pdb=" O THR L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 600 removed outlier: 3.954A pdb=" N HIS L 600 " --> pdb=" O ARG L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 606 through 611 Processing sheet with id=AA1, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.572A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.732A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.611A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.521A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AA7, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AA8, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.753A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AB1, first strand: chain 'I' and resid 580 through 581 removed outlier: 7.213A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.418A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.173A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AB6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AB7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.048A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 830 through 841 removed outlier: 6.453A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.693A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AC2, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC3, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.846A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AC5, first strand: chain 'G' and resid 12 through 20 removed outlier: 6.541A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.370A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC8, first strand: chain 'G' and resid 108 through 111 Processing sheet with id=AC9, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AD1, first strand: chain 'H' and resid 13 through 20 removed outlier: 6.343A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP H 197 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA H 190 " --> pdb=" O ASP H 197 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP H 199 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU H 188 " --> pdb=" O ASP H 199 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU H 201 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN H 186 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE H 203 " --> pdb=" O ALA H 184 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA H 184 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET H 205 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG H 182 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR H 207 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL H 180 " --> pdb=" O THR H 207 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 97 through 105 removed outlier: 3.779A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AD4, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.638A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.600A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.404A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.671A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 252 through 254 removed outlier: 6.756A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'J' and resid 703 through 707 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 820 through 822 Processing sheet with id=AE4, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.744A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.883A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 949 through 951 removed outlier: 6.257A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 991 through 997 removed outlier: 3.973A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 965 through 967 removed outlier: 4.480A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1025 through 1028 removed outlier: 5.559A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AF2, first strand: chain 'J' and resid 1046 through 1050 Processing sheet with id=AF3, first strand: chain 'J' and resid 1186 through 1191 Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.888A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1305 hydrogen bonds defined for protein. 3651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 276 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 106 stacking parallelities Total time for adding SS restraints: 11.50 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9806 1.34 - 1.45: 4717 1.45 - 1.57: 17435 1.57 - 1.69: 271 1.69 - 1.81: 227 Bond restraints: 32456 Sorted by residual: bond pdb=" O POP I1601 " pdb=" P2 POP I1601 " ideal model delta sigma weight residual 1.661 1.610 0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" O POP I1601 " pdb=" P1 POP I1601 " ideal model delta sigma weight residual 1.660 1.609 0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" C VAL I1103 " pdb=" N PRO I1104 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.64e+00 bond pdb=" C3' DA Q 55 " pdb=" O3' DA Q 55 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" O1 POP I1601 " pdb=" P1 POP I1601 " ideal model delta sigma weight residual 1.531 1.509 0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 32451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 44375 3.70 - 7.40: 23 7.40 - 11.09: 2 11.09 - 14.79: 0 14.79 - 18.49: 1 Bond angle restraints: 44401 Sorted by residual: angle pdb=" P1 POP I1601 " pdb=" O POP I1601 " pdb=" P2 POP I1601 " ideal model delta sigma weight residual 139.66 121.17 18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" C ARG I 233 " pdb=" N ASP I 234 " pdb=" CA ASP I 234 " ideal model delta sigma weight residual 121.54 126.85 -5.31 1.91e+00 2.74e-01 7.73e+00 angle pdb=" N ASP L 513 " pdb=" CA ASP L 513 " pdb=" C ASP L 513 " ideal model delta sigma weight residual 107.73 111.23 -3.50 1.34e+00 5.57e-01 6.82e+00 angle pdb=" N GLU H 29 " pdb=" CA GLU H 29 " pdb=" C GLU H 29 " ideal model delta sigma weight residual 108.22 110.57 -2.35 9.00e-01 1.23e+00 6.81e+00 angle pdb=" O POP I1601 " pdb=" P1 POP I1601 " pdb=" O2 POP I1601 " ideal model delta sigma weight residual 102.11 109.84 -7.73 3.00e+00 1.11e-01 6.64e+00 ... (remaining 44396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 18923 34.96 - 69.92: 724 69.92 - 104.89: 19 104.89 - 139.85: 1 139.85 - 174.81: 2 Dihedral angle restraints: 19669 sinusoidal: 9090 harmonic: 10579 Sorted by residual: dihedral pdb=" CA GLN J 736 " pdb=" C GLN J 736 " pdb=" N ILE J 737 " pdb=" CA ILE J 737 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA VAL H 192 " pdb=" C VAL H 192 " pdb=" N GLU H 193 " pdb=" CA GLU H 193 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" C4' DA Q 55 " pdb=" C3' DA Q 55 " pdb=" O3' DA Q 55 " pdb=" P DG Q 56 " ideal model delta sinusoidal sigma weight residual 220.00 45.19 174.81 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 19666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3082 0.027 - 0.055: 1254 0.055 - 0.082: 411 0.082 - 0.110: 232 0.110 - 0.137: 87 Chirality restraints: 5066 Sorted by residual: chirality pdb=" CA ILE G 123 " pdb=" N ILE G 123 " pdb=" C ILE G 123 " pdb=" CB ILE G 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE J 105 " pdb=" N ILE J 105 " pdb=" C ILE J 105 " pdb=" CB ILE J 105 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE J 826 " pdb=" N ILE J 826 " pdb=" C ILE J 826 " pdb=" CB ILE J 826 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 5063 not shown) Planarity restraints: 5316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO I 590 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 289 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C LYS L 289 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS L 289 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU L 290 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU J 245 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO J 246 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO J 246 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 246 " 0.020 5.00e-02 4.00e+02 ... (remaining 5313 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1110 2.71 - 3.26: 29726 3.26 - 3.81: 51173 3.81 - 4.35: 69076 4.35 - 4.90: 112390 Nonbonded interactions: 263475 Sorted by model distance: nonbonded pdb="MG MG J1501 " pdb=" O HOH J1606 " model vdw 2.163 2.170 nonbonded pdb=" OG1 THR I 843 " pdb=" O GLY I 846 " model vdw 2.172 3.040 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.198 2.170 nonbonded pdb=" O3' C R 5 " pdb="MG MG J1501 " model vdw 2.226 2.170 nonbonded pdb=" OG1 THR L 354 " pdb=" OE1 GLN L 357 " model vdw 2.239 3.040 ... (remaining 263470 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 4 through 158 or resid 167 through 233)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 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: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 43.120 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 : 0.003 0.109 32464 Z= 0.126 Angle : 0.497 18.491 44413 Z= 0.281 Chirality : 0.039 0.137 5066 Planarity : 0.004 0.045 5316 Dihedral : 15.340 174.810 12849 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.72 % Allowed : 5.15 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.72 (0.14), residues: 3651 helix: 1.64 (0.14), residues: 1440 sheet: 0.59 (0.24), residues: 484 loop : -0.54 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I1059 TYR 0.012 0.001 TYR J 631 PHE 0.011 0.001 PHE I 514 TRP 0.005 0.001 TRP J 686 HIS 0.004 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (32456) covalent geometry : angle 0.49727 / 0.28 (44401) hydrogen bonds : bond 0.13039 / 8.78 ( 1441) hydrogen bonds : angle 5.07771 / 3.53 ( 3927) metal coordination : bond 0.05754 / 2.59 ( 8) metal coordination : angle 0.03151 / 0.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 389 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 239 MET cc_start: 0.8522 (tmm) cc_final: 0.7530 (tmm) REVERT: I 315 MET cc_start: 0.8803 (ttm) cc_final: 0.8392 (mtp) REVERT: I 330 HIS cc_start: 0.7730 (m-70) cc_final: 0.7142 (m-70) REVERT: J 200 GLN cc_start: 0.8480 (tt0) cc_final: 0.8277 (tp-100) REVERT: J 227 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: J 1025 MET cc_start: 0.8239 (ttp) cc_final: 0.7953 (mpp) REVERT: J 1040 MET cc_start: 0.5550 (mmm) cc_final: 0.5237 (ttt) REVERT: J 1177 ILE cc_start: 0.9272 (mt) cc_final: 0.9072 (tp) REVERT: J 1186 TYR cc_start: 0.8211 (t80) cc_final: 0.6772 (t80) REVERT: L 143 TYR cc_start: 0.8744 (t80) cc_final: 0.8511 (t80) REVERT: L 277 MET cc_start: 0.8244 (tpt) cc_final: 0.7538 (tmm) REVERT: L 353 LEU cc_start: 0.7913 (tp) cc_final: 0.7696 (mt) outliers start: 54 outliers final: 19 residues processed: 434 average time/residue: 0.9621 time to fit residues: 476.7463 Evaluate side-chains 262 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1119 ASP Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 500 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0010 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 357 ASN I 628 HIS K 15 ASN G 117 HIS G 147 GLN J 229 GLN J 954 ASN J1326 GLN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.108297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.059893 restraints weight = 63375.138| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.53 r_work: 0.2570 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 32464 Z= 0.229 Angle : 0.579 11.980 44413 Z= 0.310 Chirality : 0.043 0.154 5066 Planarity : 0.004 0.055 5316 Dihedral : 17.117 176.017 5606 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.84 % Allowed : 10.84 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.91 (0.14), residues: 3651 helix: 1.89 (0.14), residues: 1440 sheet: 0.51 (0.24), residues: 482 loop : -0.45 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 990 TYR 0.015 0.001 TYR J 631 PHE 0.013 0.001 PHE J1325 TRP 0.005 0.001 TRP J1193 HIS 0.009 0.001 HIS L 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 (32456) covalent geometry : angle 0.57641 / 0.31 (44401) hydrogen bonds : bond 0.05129 / 3.34 ( 1441) hydrogen bonds : angle 4.24605 / 2.98 ( 3927) metal coordination : bond 0.00893 / 0.46 ( 8) metal coordination : angle 3.59731 / 1.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 286 time to evaluate : 1.257 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: I 275 ARG cc_start: 0.9318 (ptp-110) cc_final: 0.9081 (ptt-90) REVERT: I 315 MET cc_start: 0.9038 (ttm) cc_final: 0.8235 (mtp) REVERT: I 473 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8042 (mtp180) REVERT: I 600 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8502 (p) REVERT: I 971 LEU cc_start: 0.8496 (mm) cc_final: 0.8209 (mt) REVERT: K 8 ASP cc_start: 0.8777 (m-30) cc_final: 0.8515 (m-30) REVERT: K 35 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7861 (mptt) REVERT: K 71 GLU cc_start: 0.8862 (tt0) cc_final: 0.8288 (tm-30) REVERT: K 76 GLU cc_start: 0.9279 (tt0) cc_final: 0.9008 (tp30) REVERT: G 206 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: H 212 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8119 (t0) REVERT: J 66 LYS cc_start: 0.8816 (mttt) cc_final: 0.8535 (mtpm) REVERT: J 196 GLN cc_start: 0.8440 (tm-30) cc_final: 0.7515 (tm-30) REVERT: J 197 GLU cc_start: 0.8936 (tt0) cc_final: 0.8600 (mm-30) REVERT: J 219 LYS cc_start: 0.9296 (mmtm) cc_final: 0.9031 (mmtt) REVERT: J 227 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.9177 (m-80) REVERT: J 982 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8975 (tm) REVERT: J 1025 MET cc_start: 0.8531 (ttp) cc_final: 0.8004 (mpt) REVERT: J 1172 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7151 (mtpp) REVERT: J 1177 ILE cc_start: 0.9327 (mt) cc_final: 0.8959 (tp) REVERT: J 1186 TYR cc_start: 0.8259 (t80) cc_final: 0.7808 (t80) REVERT: J 1188 GLU cc_start: 0.6925 (pm20) cc_final: 0.6582 (pm20) REVERT: L 277 MET cc_start: 0.8235 (tpt) cc_final: 0.7997 (tmm) REVERT: L 353 LEU cc_start: 0.7905 (tp) cc_final: 0.7637 (mt) REVERT: L 369 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8221 (tm-30) REVERT: L 413 MET cc_start: 0.8841 (mtp) cc_final: 0.8586 (mtm) outliers start: 58 outliers final: 21 residues processed: 324 average time/residue: 0.9188 time to fit residues: 342.1432 Evaluate side-chains 272 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 473 ARG Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1172 LYS Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 500 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 319 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 222 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 357 ASN I 952 GLN K 15 ASN K 43 ASN G 117 HIS G 147 GLN H 186 ASN J 157 GLN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.108909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.060772 restraints weight = 63139.723| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.53 r_work: 0.2594 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32464 Z= 0.154 Angle : 0.524 10.066 44413 Z= 0.281 Chirality : 0.041 0.158 5066 Planarity : 0.004 0.052 5316 Dihedral : 17.060 174.605 5591 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.78 % Allowed : 11.98 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.13 (0.14), residues: 3651 helix: 2.09 (0.14), residues: 1447 sheet: 0.64 (0.24), residues: 471 loop : -0.36 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 247 TYR 0.014 0.001 TYR J 631 PHE 0.013 0.001 PHE J1325 TRP 0.010 0.001 TRP J1193 HIS 0.012 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (32456) covalent geometry : angle 0.52206 / 0.28 (44401) hydrogen bonds : bond 0.04165 / 2.72 ( 1441) hydrogen bonds : angle 4.03417 / 2.83 ( 3927) metal coordination : bond 0.00597 / 0.32 ( 8) metal coordination : angle 3.01170 / 1.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 1.327 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: I 7 GLU cc_start: 0.8111 (pt0) cc_final: 0.7547 (pp20) REVERT: I 191 LYS cc_start: 0.9166 (mppt) cc_final: 0.8939 (mppt) REVERT: I 315 MET cc_start: 0.9050 (ttm) cc_final: 0.8288 (mtp) REVERT: I 600 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8550 (p) REVERT: I 971 LEU cc_start: 0.8505 (mm) cc_final: 0.8210 (mt) REVERT: K 8 ASP cc_start: 0.8743 (m-30) cc_final: 0.8442 (m-30) REVERT: K 35 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7813 (mptt) REVERT: K 71 GLU cc_start: 0.8901 (tt0) cc_final: 0.8401 (tm-30) REVERT: K 75 GLN cc_start: 0.8607 (pp30) cc_final: 0.8199 (pp30) REVERT: H 145 LYS cc_start: 0.8935 (ttpp) cc_final: 0.8707 (ttpt) REVERT: J 66 LYS cc_start: 0.8763 (mttt) cc_final: 0.8506 (mtpm) REVERT: J 77 ARG cc_start: 0.8302 (mmm160) cc_final: 0.7997 (tpp-160) REVERT: J 151 MET cc_start: 0.8909 (mmm) cc_final: 0.8495 (mpm) REVERT: J 196 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7674 (tm-30) REVERT: J 197 GLU cc_start: 0.8931 (tt0) cc_final: 0.8603 (mm-30) REVERT: J 200 GLN cc_start: 0.8216 (mm110) cc_final: 0.7867 (mm110) REVERT: J 213 LYS cc_start: 0.9427 (mmpt) cc_final: 0.9016 (mmpt) REVERT: J 219 LYS cc_start: 0.9289 (mmtm) cc_final: 0.9042 (mmtm) REVERT: J 227 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.9096 (m-80) REVERT: J 873 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: J 983 LYS cc_start: 0.9216 (mttt) cc_final: 0.8938 (mtmm) REVERT: J 1025 MET cc_start: 0.8577 (ttp) cc_final: 0.8057 (mpt) REVERT: J 1040 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.5903 (ttm) REVERT: J 1095 MET cc_start: 0.5242 (pp-130) cc_final: 0.4384 (pp-130) REVERT: J 1172 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7146 (mtpp) REVERT: J 1177 ILE cc_start: 0.9373 (mt) cc_final: 0.8937 (tp) REVERT: J 1186 TYR cc_start: 0.8285 (t80) cc_final: 0.7739 (t80) REVERT: J 1188 GLU cc_start: 0.7170 (pm20) cc_final: 0.6840 (pm20) REVERT: L 277 MET cc_start: 0.8249 (tpt) cc_final: 0.8015 (tmm) REVERT: L 297 MET cc_start: 0.3283 (ppp) cc_final: 0.2592 (ppp) REVERT: L 353 LEU cc_start: 0.7812 (tp) cc_final: 0.7538 (mt) REVERT: L 369 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8198 (tm-30) REVERT: L 413 MET cc_start: 0.8832 (mtp) cc_final: 0.8588 (mtm) REVERT: L 474 MET cc_start: 0.8840 (mmp) cc_final: 0.8524 (mtp) outliers start: 56 outliers final: 21 residues processed: 302 average time/residue: 0.8482 time to fit residues: 297.8461 Evaluate side-chains 261 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1172 LYS Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 500 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 165 optimal weight: 0.0470 chunk 225 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN J 954 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.108344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.060231 restraints weight = 63116.720| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.52 r_work: 0.2582 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32464 Z= 0.174 Angle : 0.530 10.086 44413 Z= 0.283 Chirality : 0.041 0.161 5066 Planarity : 0.004 0.056 5316 Dihedral : 17.085 175.895 5588 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.00 % Allowed : 12.27 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.18 (0.14), residues: 3651 helix: 2.14 (0.14), residues: 1448 sheet: 0.56 (0.23), residues: 491 loop : -0.32 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 247 TYR 0.015 0.001 TYR J 631 PHE 0.022 0.001 PHE L 256 TRP 0.014 0.001 TRP J1193 HIS 0.010 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (32456) covalent geometry : angle 0.52769 / 0.28 (44401) hydrogen bonds : bond 0.04296 / 2.81 ( 1441) hydrogen bonds : angle 4.00041 / 2.80 ( 3927) metal coordination : bond 0.00662 / 0.34 ( 8) metal coordination : angle 3.14514 / 1.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 1.320 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: I 7 GLU cc_start: 0.8132 (pt0) cc_final: 0.7602 (pp20) REVERT: I 315 MET cc_start: 0.9042 (ttm) cc_final: 0.8273 (mtp) REVERT: I 473 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8289 (mtp180) REVERT: I 600 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8578 (p) REVERT: I 971 LEU cc_start: 0.8444 (mm) cc_final: 0.8143 (mt) REVERT: I 1138 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8535 (p) REVERT: K 8 ASP cc_start: 0.8702 (m-30) cc_final: 0.8422 (m-30) REVERT: K 35 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7866 (mptt) REVERT: K 71 GLU cc_start: 0.8987 (tt0) cc_final: 0.8333 (tm-30) REVERT: G 125 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9009 (tttp) REVERT: J 66 LYS cc_start: 0.8777 (mttt) cc_final: 0.8520 (mtpm) REVERT: J 77 ARG cc_start: 0.8384 (mmm160) cc_final: 0.8056 (tpp-160) REVERT: J 196 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7790 (tm-30) REVERT: J 197 GLU cc_start: 0.8959 (tt0) cc_final: 0.8511 (mm-30) REVERT: J 200 GLN cc_start: 0.8248 (mm110) cc_final: 0.7934 (mm110) REVERT: J 215 LYS cc_start: 0.9082 (mmpt) cc_final: 0.8813 (mppt) REVERT: J 219 LYS cc_start: 0.9261 (mmtm) cc_final: 0.8986 (mmtm) REVERT: J 227 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.9053 (m-80) REVERT: J 312 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7771 (tmt-80) REVERT: J 500 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9331 (pp) REVERT: J 652 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8441 (tm-30) REVERT: J 873 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: J 983 LYS cc_start: 0.9201 (mttt) cc_final: 0.8838 (mttp) REVERT: J 1025 MET cc_start: 0.8572 (ttp) cc_final: 0.8057 (mpt) REVERT: J 1040 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.5887 (ttm) REVERT: J 1095 MET cc_start: 0.5216 (pp-130) cc_final: 0.4920 (pp-130) REVERT: J 1149 ARG cc_start: 0.8763 (mmt90) cc_final: 0.8563 (mtp-110) REVERT: J 1177 ILE cc_start: 0.9433 (mt) cc_final: 0.8962 (tp) REVERT: J 1186 TYR cc_start: 0.8229 (t80) cc_final: 0.7614 (t80) REVERT: J 1188 GLU cc_start: 0.7276 (pm20) cc_final: 0.6992 (pm20) REVERT: L 277 MET cc_start: 0.8264 (tpt) cc_final: 0.8039 (tmm) REVERT: L 353 LEU cc_start: 0.7872 (tp) cc_final: 0.7452 (mp) REVERT: L 369 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8293 (tm-30) REVERT: L 413 MET cc_start: 0.8834 (mtp) cc_final: 0.8587 (mtm) outliers start: 63 outliers final: 28 residues processed: 301 average time/residue: 0.8033 time to fit residues: 279.9248 Evaluate side-chains 281 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 473 ARG Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 500 ILE Chi-restraints excluded: chain L residue 505 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 192 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 237 optimal weight: 0.6980 chunk 332 optimal weight: 5.9990 chunk 295 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 894 GLN G 147 GLN H 186 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.107453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.059321 restraints weight = 63522.272| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.53 r_work: 0.2561 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32464 Z= 0.222 Angle : 0.563 10.917 44413 Z= 0.299 Chirality : 0.042 0.169 5066 Planarity : 0.004 0.060 5316 Dihedral : 17.181 178.934 5588 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.97 % Allowed : 12.43 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.14 (0.14), residues: 3651 helix: 2.12 (0.14), residues: 1445 sheet: 0.61 (0.23), residues: 481 loop : -0.37 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 247 TYR 0.016 0.001 TYR J 631 PHE 0.016 0.001 PHE J1325 TRP 0.016 0.001 TRP J1193 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.22 (32456) covalent geometry : angle 0.56004 / 0.30 (44401) hydrogen bonds : bond 0.04755 / 3.10 ( 1441) hydrogen bonds : angle 4.04992 / 2.83 ( 3927) metal coordination : bond 0.00799 / 0.41 ( 8) metal coordination : angle 3.52282 / 1.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 256 time to evaluate : 1.216 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 191 LYS cc_start: 0.9108 (mppt) cc_final: 0.8881 (mppt) REVERT: I 315 MET cc_start: 0.9057 (ttm) cc_final: 0.8315 (mtp) REVERT: I 473 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8281 (mtp180) REVERT: I 546 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: I 600 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8637 (p) REVERT: I 909 LYS cc_start: 0.8820 (pmtt) cc_final: 0.8419 (pmtt) REVERT: I 971 LEU cc_start: 0.8439 (mm) cc_final: 0.8131 (mt) REVERT: I 1023 HIS cc_start: 0.8576 (p90) cc_final: 0.8357 (p90) REVERT: K 8 ASP cc_start: 0.8730 (m-30) cc_final: 0.8488 (m-30) REVERT: K 71 GLU cc_start: 0.8941 (tt0) cc_final: 0.8396 (tm-30) REVERT: K 75 GLN cc_start: 0.8565 (pp30) cc_final: 0.7880 (pp30) REVERT: K 79 GLU cc_start: 0.7433 (pt0) cc_final: 0.7183 (pt0) REVERT: G 125 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9002 (tttp) REVERT: G 206 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: H 12 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7902 (ptp-170) REVERT: H 25 LYS cc_start: 0.9047 (ttpp) cc_final: 0.8687 (mtpp) REVERT: H 95 LYS cc_start: 0.9350 (mtmp) cc_final: 0.9125 (mtmm) REVERT: J 66 LYS cc_start: 0.8820 (mttt) cc_final: 0.8541 (mtpm) REVERT: J 151 MET cc_start: 0.8869 (mmm) cc_final: 0.8482 (mpm) REVERT: J 196 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7822 (tm-30) REVERT: J 197 GLU cc_start: 0.8936 (tt0) cc_final: 0.8566 (mm-30) REVERT: J 200 GLN cc_start: 0.8300 (mm110) cc_final: 0.7977 (mm110) REVERT: J 219 LYS cc_start: 0.9267 (mmtm) cc_final: 0.9018 (mmtt) REVERT: J 227 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.9041 (m-80) REVERT: J 312 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7809 (tmt-80) REVERT: J 500 ILE cc_start: 0.9645 (OUTLIER) cc_final: 0.9354 (pp) REVERT: J 652 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8487 (tm-30) REVERT: J 873 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: J 983 LYS cc_start: 0.9235 (mttt) cc_final: 0.8863 (mttp) REVERT: J 1025 MET cc_start: 0.8590 (ttp) cc_final: 0.8077 (mpt) REVERT: J 1040 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6274 (ttm) REVERT: J 1177 ILE cc_start: 0.9447 (mt) cc_final: 0.8982 (tp) REVERT: J 1186 TYR cc_start: 0.8194 (t80) cc_final: 0.7469 (t80) REVERT: J 1188 GLU cc_start: 0.7344 (pm20) cc_final: 0.6911 (pm20) REVERT: J 1189 MET cc_start: 0.8182 (mmm) cc_final: 0.7894 (mmm) REVERT: L 277 MET cc_start: 0.8293 (tpt) cc_final: 0.8034 (tmm) REVERT: L 297 MET cc_start: 0.3481 (OUTLIER) cc_final: 0.2184 (pmm) REVERT: L 322 MET cc_start: 0.6891 (ppp) cc_final: 0.6405 (ppp) REVERT: L 353 LEU cc_start: 0.7894 (tp) cc_final: 0.7458 (mp) REVERT: L 369 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8297 (tm-30) REVERT: L 474 MET cc_start: 0.8931 (mmm) cc_final: 0.8632 (mtp) REVERT: L 588 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8128 (tpt-90) outliers start: 62 outliers final: 30 residues processed: 302 average time/residue: 0.8620 time to fit residues: 300.8731 Evaluate side-chains 285 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 276 GLN Chi-restraints excluded: chain I residue 473 ARG Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 546 GLU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 297 MET Chi-restraints excluded: chain L residue 500 ILE Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 576 VAL Chi-restraints excluded: chain L residue 588 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 291 optimal weight: 9.9990 chunk 294 optimal weight: 0.0060 chunk 55 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 296 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 922 ASN G 147 GLN H 186 ASN J 954 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.109372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.061620 restraints weight = 62786.228| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.51 r_work: 0.2615 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32464 Z= 0.118 Angle : 0.512 11.963 44413 Z= 0.271 Chirality : 0.040 0.156 5066 Planarity : 0.003 0.055 5316 Dihedral : 17.002 173.301 5587 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.40 % Allowed : 13.16 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.40 (0.14), residues: 3651 helix: 2.33 (0.14), residues: 1449 sheet: 0.72 (0.24), residues: 466 loop : -0.20 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 77 TYR 0.012 0.001 TYR J 631 PHE 0.011 0.001 PHE I 405 TRP 0.024 0.001 TRP J1193 HIS 0.005 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (32456) covalent geometry : angle 0.51006 / 0.27 (44401) hydrogen bonds : bond 0.03462 / 2.27 ( 1441) hydrogen bonds : angle 3.82866 / 2.67 ( 3927) metal coordination : bond 0.00384 / 0.22 ( 8) metal coordination : angle 2.79541 / 1.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 1.390 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: I 7 GLU cc_start: 0.8108 (pt0) cc_final: 0.7546 (pp20) REVERT: I 191 LYS cc_start: 0.9122 (mppt) cc_final: 0.8900 (mppt) REVERT: I 315 MET cc_start: 0.9066 (ttm) cc_final: 0.8317 (mtp) REVERT: I 600 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8641 (p) REVERT: I 894 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8820 (mm110) REVERT: I 971 LEU cc_start: 0.8466 (mm) cc_final: 0.8172 (mt) REVERT: I 1023 HIS cc_start: 0.8630 (p90) cc_final: 0.8351 (p90) REVERT: I 1138 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8502 (p) REVERT: K 8 ASP cc_start: 0.8751 (m-30) cc_final: 0.8538 (m-30) REVERT: K 71 GLU cc_start: 0.8935 (tt0) cc_final: 0.8322 (tm-30) REVERT: G 33 ARG cc_start: 0.8718 (tpp80) cc_final: 0.8307 (tpp-160) REVERT: G 125 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9027 (tttp) REVERT: G 181 GLU cc_start: 0.9320 (mt-10) cc_final: 0.8757 (mm-30) REVERT: H 25 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8704 (mtpp) REVERT: J 66 LYS cc_start: 0.8707 (mttt) cc_final: 0.8465 (mtpm) REVERT: J 196 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7774 (tm-30) REVERT: J 197 GLU cc_start: 0.8876 (tt0) cc_final: 0.8472 (mm-30) REVERT: J 200 GLN cc_start: 0.8354 (mm110) cc_final: 0.8014 (mm110) REVERT: J 213 LYS cc_start: 0.9269 (mmpt) cc_final: 0.9068 (mptt) REVERT: J 219 LYS cc_start: 0.9251 (mmtm) cc_final: 0.9020 (mmtt) REVERT: J 312 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7714 (tmt-80) REVERT: J 500 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9304 (pp) REVERT: J 827 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8155 (mt-10) REVERT: J 873 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: J 983 LYS cc_start: 0.9232 (mttt) cc_final: 0.8901 (mttp) REVERT: J 1025 MET cc_start: 0.8634 (ttp) cc_final: 0.8181 (mpt) REVERT: J 1040 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6194 (ttm) REVERT: J 1186 TYR cc_start: 0.8271 (t80) cc_final: 0.7814 (t80) REVERT: J 1188 GLU cc_start: 0.7484 (pm20) cc_final: 0.7001 (pm20) REVERT: J 1189 MET cc_start: 0.8036 (mmm) cc_final: 0.7750 (mmm) REVERT: L 353 LEU cc_start: 0.7865 (tp) cc_final: 0.7401 (mp) REVERT: L 369 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8199 (tm-30) REVERT: L 588 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8114 (tpt-90) outliers start: 44 outliers final: 27 residues processed: 299 average time/residue: 0.8273 time to fit residues: 286.9019 Evaluate side-chains 281 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 276 GLN Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1252 SER Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 500 ILE Chi-restraints excluded: chain L residue 576 VAL Chi-restraints excluded: chain L residue 588 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 202 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 302 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 323 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.108620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.060532 restraints weight = 63173.016| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.53 r_work: 0.2592 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32464 Z= 0.151 Angle : 0.539 12.460 44413 Z= 0.283 Chirality : 0.041 0.169 5066 Planarity : 0.004 0.055 5316 Dihedral : 17.003 175.770 5586 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.43 % Allowed : 14.02 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.40 (0.14), residues: 3651 helix: 2.31 (0.14), residues: 1449 sheet: 0.73 (0.24), residues: 471 loop : -0.19 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 77 TYR 0.014 0.001 TYR J 631 PHE 0.015 0.001 PHE J1325 TRP 0.031 0.001 TRP J1193 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (32456) covalent geometry : angle 0.53666 / 0.28 (44401) hydrogen bonds : bond 0.03911 / 2.55 ( 1441) hydrogen bonds : angle 3.85110 / 2.68 ( 3927) metal coordination : bond 0.00535 / 0.28 ( 8) metal coordination : angle 2.99249 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 1.366 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: I 7 GLU cc_start: 0.8147 (pt0) cc_final: 0.7569 (pp20) REVERT: I 315 MET cc_start: 0.9073 (ttm) cc_final: 0.8307 (mtp) REVERT: I 600 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8645 (p) REVERT: I 894 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8862 (mm-40) REVERT: I 971 LEU cc_start: 0.8467 (mm) cc_final: 0.8157 (mt) REVERT: I 1023 HIS cc_start: 0.8658 (p90) cc_final: 0.8450 (p90) REVERT: K 8 ASP cc_start: 0.8739 (m-30) cc_final: 0.8535 (m-30) REVERT: K 71 GLU cc_start: 0.8942 (tt0) cc_final: 0.8434 (tm-30) REVERT: K 75 GLN cc_start: 0.8366 (pp30) cc_final: 0.7628 (pp30) REVERT: G 125 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8939 (tttp) REVERT: G 127 GLN cc_start: 0.8890 (pm20) cc_final: 0.8550 (pm20) REVERT: G 181 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8795 (mm-30) REVERT: H 25 LYS cc_start: 0.9028 (ttpp) cc_final: 0.8691 (mtpp) REVERT: H 95 LYS cc_start: 0.9327 (mtmp) cc_final: 0.9040 (mtmm) REVERT: J 66 LYS cc_start: 0.8731 (mttt) cc_final: 0.8484 (mtpm) REVERT: J 77 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7897 (tpp-160) REVERT: J 151 MET cc_start: 0.8897 (mmm) cc_final: 0.8582 (mpm) REVERT: J 196 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7768 (tm-30) REVERT: J 197 GLU cc_start: 0.8917 (tt0) cc_final: 0.8472 (mm-30) REVERT: J 200 GLN cc_start: 0.8346 (mm110) cc_final: 0.7980 (mm110) REVERT: J 219 LYS cc_start: 0.9253 (mmtm) cc_final: 0.9035 (mmtt) REVERT: J 312 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7713 (tmt-80) REVERT: J 500 ILE cc_start: 0.9611 (OUTLIER) cc_final: 0.9324 (pp) REVERT: J 873 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: J 983 LYS cc_start: 0.9248 (mttt) cc_final: 0.8874 (mttp) REVERT: J 1003 LEU cc_start: 0.9228 (pp) cc_final: 0.9013 (pt) REVERT: J 1025 MET cc_start: 0.8631 (ttp) cc_final: 0.8176 (mpt) REVERT: J 1040 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6253 (ttm) REVERT: J 1095 MET cc_start: 0.4698 (ppp) cc_final: 0.4455 (tmt) REVERT: J 1186 TYR cc_start: 0.8216 (t80) cc_final: 0.7721 (t80) REVERT: J 1188 GLU cc_start: 0.7497 (pm20) cc_final: 0.7240 (pm20) REVERT: L 277 MET cc_start: 0.8382 (tpp) cc_final: 0.8149 (tpp) REVERT: L 369 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8227 (tm-30) REVERT: L 474 MET cc_start: 0.8925 (mmm) cc_final: 0.8635 (mtp) REVERT: L 588 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8130 (tpt-90) outliers start: 45 outliers final: 28 residues processed: 290 average time/residue: 0.8902 time to fit residues: 298.1765 Evaluate side-chains 277 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 500 ILE Chi-restraints excluded: chain L residue 576 VAL Chi-restraints excluded: chain L residue 588 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 31 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 293 optimal weight: 30.0000 chunk 250 optimal weight: 3.9990 chunk 341 optimal weight: 30.0000 chunk 102 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN H 186 ASN J 954 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.107000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.058864 restraints weight = 63284.067| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.52 r_work: 0.2552 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2410 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 32464 Z= 0.239 Angle : 0.600 13.326 44413 Z= 0.314 Chirality : 0.043 0.172 5066 Planarity : 0.004 0.058 5316 Dihedral : 17.181 179.502 5586 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.40 % Allowed : 14.21 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.22 (0.14), residues: 3651 helix: 2.17 (0.14), residues: 1443 sheet: 0.62 (0.23), residues: 493 loop : -0.30 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 69 TYR 0.016 0.001 TYR J 631 PHE 0.019 0.001 PHE J1325 TRP 0.035 0.002 TRP J1193 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.24 (32456) covalent geometry : angle 0.59704 / 0.31 (44401) hydrogen bonds : bond 0.04894 / 3.20 ( 1441) hydrogen bonds : angle 4.04957 / 2.83 ( 3927) metal coordination : bond 0.00864 / 0.43 ( 8) metal coordination : angle 3.61598 / 1.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 1.297 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: I 7 GLU cc_start: 0.8195 (pt0) cc_final: 0.7572 (pp20) REVERT: I 315 MET cc_start: 0.9091 (ttm) cc_final: 0.8374 (mtp) REVERT: I 600 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8647 (p) REVERT: I 894 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8779 (mm-40) REVERT: I 971 LEU cc_start: 0.8472 (mm) cc_final: 0.8155 (mt) REVERT: I 1023 HIS cc_start: 0.8627 (p90) cc_final: 0.8410 (p90) REVERT: K 71 GLU cc_start: 0.8938 (tt0) cc_final: 0.8319 (tm-30) REVERT: G 33 ARG cc_start: 0.8769 (tpp80) cc_final: 0.8425 (tpp-160) REVERT: G 125 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9003 (tttp) REVERT: H 12 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7873 (ptp-170) REVERT: H 25 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8706 (mtpp) REVERT: J 66 LYS cc_start: 0.8812 (mttt) cc_final: 0.8546 (mtpm) REVERT: J 77 ARG cc_start: 0.8316 (mmm160) cc_final: 0.7967 (tpp-160) REVERT: J 151 MET cc_start: 0.8886 (mmm) cc_final: 0.8568 (mpm) REVERT: J 196 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7773 (tm-30) REVERT: J 197 GLU cc_start: 0.8957 (tt0) cc_final: 0.8495 (mm-30) REVERT: J 200 GLN cc_start: 0.8345 (mm110) cc_final: 0.8003 (mm110) REVERT: J 213 LYS cc_start: 0.9244 (mmpt) cc_final: 0.9028 (mptt) REVERT: J 215 LYS cc_start: 0.9006 (mmpt) cc_final: 0.8433 (mtmm) REVERT: J 219 LYS cc_start: 0.9252 (mmtm) cc_final: 0.9031 (mmtm) REVERT: J 312 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7993 (tmt-80) REVERT: J 500 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9353 (pp) REVERT: J 652 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8543 (tm-30) REVERT: J 736 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.8624 (mt0) REVERT: J 827 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8272 (mt-10) REVERT: J 873 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: J 983 LYS cc_start: 0.9224 (mttt) cc_final: 0.8893 (mttp) REVERT: J 1003 LEU cc_start: 0.9246 (pp) cc_final: 0.9011 (pt) REVERT: J 1025 MET cc_start: 0.8643 (ttp) cc_final: 0.8225 (mpt) REVERT: J 1040 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6373 (ttm) REVERT: J 1186 TYR cc_start: 0.8181 (t80) cc_final: 0.7539 (t80) REVERT: J 1188 GLU cc_start: 0.7601 (pm20) cc_final: 0.7095 (pm20) REVERT: J 1189 MET cc_start: 0.8412 (mmm) cc_final: 0.8154 (mmm) REVERT: L 369 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8255 (tm-30) REVERT: L 474 MET cc_start: 0.8954 (mmm) cc_final: 0.8659 (mtp) REVERT: L 588 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8203 (tpt-90) outliers start: 44 outliers final: 27 residues processed: 293 average time/residue: 0.8603 time to fit residues: 290.5610 Evaluate side-chains 280 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 243 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 736 GLN Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 500 ILE Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 576 VAL Chi-restraints excluded: chain L residue 588 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 368 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 295 optimal weight: 30.0000 chunk 296 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN H 186 ASN J 157 GLN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.106244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.058312 restraints weight = 63239.507| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.49 r_work: 0.2543 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2404 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 32464 Z= 0.283 Angle : 0.628 12.343 44413 Z= 0.331 Chirality : 0.044 0.157 5066 Planarity : 0.004 0.058 5316 Dihedral : 17.337 177.893 5586 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.53 % Allowed : 14.34 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.05 (0.14), residues: 3651 helix: 2.03 (0.14), residues: 1436 sheet: 0.54 (0.23), residues: 491 loop : -0.38 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 275 TYR 0.015 0.001 TYR J 631 PHE 0.020 0.002 PHE J1325 TRP 0.038 0.002 TRP J1193 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.28 (32456) covalent geometry : angle 0.62477 / 0.33 (44401) hydrogen bonds : bond 0.05223 / 3.41 ( 1441) hydrogen bonds : angle 4.14130 / 2.89 ( 3927) metal coordination : bond 0.01024 / 0.52 ( 8) metal coordination : angle 3.86429 / 2.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 7 GLU cc_start: 0.8195 (pt0) cc_final: 0.7596 (pp20) REVERT: I 315 MET cc_start: 0.9107 (ttm) cc_final: 0.8357 (mtp) REVERT: I 546 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: I 600 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8673 (p) REVERT: I 894 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8760 (mm-40) REVERT: I 971 LEU cc_start: 0.8397 (mm) cc_final: 0.8109 (mt) REVERT: I 1023 HIS cc_start: 0.8668 (p90) cc_final: 0.8404 (p90) REVERT: K 41 GLU cc_start: 0.8998 (tt0) cc_final: 0.8374 (tm-30) REVERT: K 71 GLU cc_start: 0.8937 (tt0) cc_final: 0.8478 (tm-30) REVERT: G 33 ARG cc_start: 0.8782 (tpp80) cc_final: 0.8494 (tpp-160) REVERT: G 125 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8905 (tttp) REVERT: G 127 GLN cc_start: 0.8923 (pm20) cc_final: 0.8500 (pm20) REVERT: G 181 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8752 (mm-30) REVERT: G 206 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8536 (tt0) REVERT: H 12 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7878 (ptp-170) REVERT: H 25 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8724 (mtpp) REVERT: J 66 LYS cc_start: 0.8850 (mttt) cc_final: 0.8552 (mtpm) REVERT: J 77 ARG cc_start: 0.8338 (mmm160) cc_final: 0.7982 (tpp-160) REVERT: J 151 MET cc_start: 0.8931 (mmm) cc_final: 0.8594 (mpm) REVERT: J 196 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7834 (tm-30) REVERT: J 200 GLN cc_start: 0.8374 (mm110) cc_final: 0.8075 (mm110) REVERT: J 215 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8427 (mtmm) REVERT: J 219 LYS cc_start: 0.9244 (mmtm) cc_final: 0.9019 (mmtm) REVERT: J 312 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8012 (tmt-80) REVERT: J 500 ILE cc_start: 0.9648 (OUTLIER) cc_final: 0.9356 (pp) REVERT: J 652 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8508 (tm-30) REVERT: J 736 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.8715 (mt0) REVERT: J 873 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: J 983 LYS cc_start: 0.9269 (mttt) cc_final: 0.8906 (mttp) REVERT: J 1003 LEU cc_start: 0.9279 (pp) cc_final: 0.9072 (pt) REVERT: J 1040 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6479 (ttm) REVERT: J 1095 MET cc_start: 0.4418 (tmt) cc_final: 0.4135 (tmt) REVERT: J 1186 TYR cc_start: 0.8216 (t80) cc_final: 0.7517 (t80) REVERT: J 1188 GLU cc_start: 0.7557 (pm20) cc_final: 0.7075 (pm20) REVERT: J 1189 MET cc_start: 0.8286 (mmm) cc_final: 0.8007 (mmm) REVERT: L 369 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8263 (tm-30) REVERT: L 474 MET cc_start: 0.8969 (mmm) cc_final: 0.8634 (mtp) outliers start: 48 outliers final: 30 residues processed: 287 average time/residue: 0.8746 time to fit residues: 289.6423 Evaluate side-chains 269 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 546 GLU Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1252 SER Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 736 GLN Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 500 ILE Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 24 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 197 optimal weight: 0.0970 chunk 293 optimal weight: 20.0000 chunk 319 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 288 optimal weight: 10.0000 chunk 370 optimal weight: 3.9990 chunk 359 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN J 157 GLN J 954 ASN ** L 283 GLN ** 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 = 0.3750 r_free = 0.3750 target = 0.108752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.061084 restraints weight = 63328.252| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.52 r_work: 0.2608 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32464 Z= 0.125 Angle : 0.552 12.803 44413 Z= 0.290 Chirality : 0.041 0.163 5066 Planarity : 0.004 0.078 5316 Dihedral : 17.091 172.937 5586 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.08 % Allowed : 14.94 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.32 (0.14), residues: 3651 helix: 2.19 (0.14), residues: 1451 sheet: 0.67 (0.24), residues: 473 loop : -0.18 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 69 TYR 0.011 0.001 TYR I1281 PHE 0.011 0.001 PHE I 405 TRP 0.035 0.001 TRP J1193 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (32456) covalent geometry : angle 0.55006 / 0.29 (44401) hydrogen bonds : bond 0.03519 / 2.31 ( 1441) hydrogen bonds : angle 3.88627 / 2.71 ( 3927) metal coordination : bond 0.00417 / 0.24 ( 8) metal coordination : angle 2.71750 / 1.47 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 7 GLU cc_start: 0.8195 (pt0) cc_final: 0.7673 (pm20) REVERT: I 315 MET cc_start: 0.9116 (ttm) cc_final: 0.8361 (mtp) REVERT: I 340 ASP cc_start: 0.8713 (t70) cc_final: 0.8376 (t0) REVERT: I 600 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8630 (p) REVERT: I 894 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8791 (mm-40) REVERT: I 971 LEU cc_start: 0.8419 (mm) cc_final: 0.8137 (mt) REVERT: I 1023 HIS cc_start: 0.8684 (p90) cc_final: 0.8401 (p90) REVERT: K 71 GLU cc_start: 0.8927 (tt0) cc_final: 0.8319 (tm-30) REVERT: G 33 ARG cc_start: 0.8752 (tpp80) cc_final: 0.8392 (tpp80) REVERT: G 125 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8978 (tttp) REVERT: G 127 GLN cc_start: 0.8895 (pm20) cc_final: 0.8562 (pm20) REVERT: G 181 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8804 (mm-30) REVERT: H 25 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8701 (mtpp) REVERT: J 66 LYS cc_start: 0.8773 (mttt) cc_final: 0.8523 (mtpm) REVERT: J 77 ARG cc_start: 0.8295 (mmm160) cc_final: 0.7930 (tpp-160) REVERT: J 151 MET cc_start: 0.8935 (mmm) cc_final: 0.8608 (mpm) REVERT: J 196 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7815 (tm-30) REVERT: J 197 GLU cc_start: 0.8930 (tt0) cc_final: 0.8640 (tp30) REVERT: J 200 GLN cc_start: 0.8370 (mm110) cc_final: 0.8045 (mm110) REVERT: J 213 LYS cc_start: 0.9248 (mmpt) cc_final: 0.8787 (mptt) REVERT: J 215 LYS cc_start: 0.8968 (mmpt) cc_final: 0.8389 (mtmm) REVERT: J 312 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7863 (tmt-80) REVERT: J 388 ARG cc_start: 0.8799 (ttm-80) cc_final: 0.8493 (mmt-90) REVERT: J 500 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9290 (pp) REVERT: J 821 MET cc_start: 0.9088 (tpp) cc_final: 0.8859 (tpp) REVERT: J 827 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8120 (mt-10) REVERT: J 853 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8667 (p) REVERT: J 873 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: J 983 LYS cc_start: 0.9237 (mttt) cc_final: 0.8902 (mtpp) REVERT: J 1040 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6435 (ttt) REVERT: J 1095 MET cc_start: 0.4175 (tmt) cc_final: 0.3898 (tmt) REVERT: J 1186 TYR cc_start: 0.8243 (t80) cc_final: 0.7787 (t80) REVERT: J 1188 GLU cc_start: 0.7562 (pm20) cc_final: 0.7155 (pm20) REVERT: J 1189 MET cc_start: 0.8286 (mmm) cc_final: 0.7993 (mmm) REVERT: L 297 MET cc_start: 0.4019 (ppp) cc_final: 0.3256 (pmm) REVERT: L 369 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8130 (tm-30) REVERT: L 474 MET cc_start: 0.8897 (mmm) cc_final: 0.8576 (mtp) outliers start: 34 outliers final: 23 residues processed: 280 average time/residue: 0.8657 time to fit residues: 279.9463 Evaluate side-chains 271 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 873 GLU Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 500 ILE Chi-restraints excluded: chain L residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 21 optimal weight: 0.7980 chunk 262 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 275 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 chunk 300 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN J1195 GLN ** L 283 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 = 0.3745 r_free = 0.3745 target = 0.108432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.060653 restraints weight = 63277.460| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.52 r_work: 0.2596 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32464 Z= 0.139 Angle : 0.562 12.690 44413 Z= 0.296 Chirality : 0.041 0.170 5066 Planarity : 0.003 0.054 5316 Dihedral : 17.059 174.590 5584 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.02 % Allowed : 15.07 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.35 (0.14), residues: 3651 helix: 2.20 (0.14), residues: 1452 sheet: 0.71 (0.24), residues: 472 loop : -0.16 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 275 TYR 0.012 0.001 TYR J 631 PHE 0.014 0.001 PHE J1325 TRP 0.033 0.001 TRP J1193 HIS 0.016 0.001 HIS I 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (32456) covalent geometry : angle 0.56045 / 0.30 (44401) hydrogen bonds : bond 0.03758 / 2.46 ( 1441) hydrogen bonds : angle 3.89050 / 2.71 ( 3927) metal coordination : bond 0.00478 / 0.26 ( 8) metal coordination : angle 2.93411 / 1.59 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18323.90 seconds wall clock time: 310 minutes 44.55 seconds (18644.55 seconds total)