Starting phenix.real_space_refine on Mon Sep 14 21:10:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymw_73124/09_2026/9ymw_73124.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymw_73124/09_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_73124/09_2026/9ymw_73124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymw_73124/09_2026/9ymw_73124.map" model { file = "/net/cci-nas-00/data/ceres_data/9ymw_73124/09_2026/9ymw_73124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymw_73124/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.21, per 1000 atoms: 0.19 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: 2.80 Conformation dependent library (CDL) restraints added in 1.2 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: 4.04 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: 12.17 Time building geometry restraints manager: 3.72 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=" C3' DC P 68 " pdb=" C2' DC P 68 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DC Q 46 " pdb=" C2' DC Q 46 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DT P 28 " pdb=" C2' DT P 28 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C1' DC Q 35 " pdb=" N1 DC Q 35 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" C3' DT Q 42 " pdb=" C2' DT Q 42 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 32451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 44374 3.70 - 7.40: 24 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=" O4' DG Q 37 " pdb=" C4' DG Q 37 " pdb=" C3' DG Q 37 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.64e+01 angle pdb=" O4' DT Q 38 " pdb=" C4' DT Q 38 " pdb=" C3' DT Q 38 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.60e+01 angle pdb=" N3 DT Q 28 " pdb=" C4 DT Q 28 " pdb=" O4 DT Q 28 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" O4' DG Q 30 " pdb=" C4' DG Q 30 " pdb=" C3' DG Q 30 " ideal model delta sigma weight residual 106.00 103.27 2.73 6.00e-01 2.78e+00 2.07e+01 ... (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 - 0.031: 3141 0.031 - 0.062: 1251 0.062 - 0.093: 402 0.093 - 0.125: 244 0.125 - 0.156: 28 Chirality restraints: 5066 Sorted by residual: chirality pdb=" C3' DA Q 55 " pdb=" C4' DA Q 55 " pdb=" O3' DA Q 55 " pdb=" C2' DA Q 55 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" P DA Q 43 " pdb=" OP1 DA Q 43 " pdb=" OP2 DA Q 43 " pdb=" O5' DA Q 43 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" C2' C R 5 " pdb=" C3' C R 5 " pdb=" O2' C R 5 " pdb=" C1' C R 5 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.74e-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: 5.390 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: 0.660 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 40.760 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 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:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 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= 0.251 Angle : 0.541 18.491 44413 Z= 0.383 Chirality : 0.042 0.156 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 0.00319 / 0.25 (32456) covalent geometry : angle 0.54063 / 0.38 (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 : 1.299 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: 0.9071 (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: 0.9066 time to fit residues: 452.0472 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 : 1.319 ------------------------------------------------------------------------------- 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... I 628 HIS K 15 ASN G 117 HIS J 157 GLN J 229 GLN J 954 ASN J1326 GLN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.109495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.060918 restraints weight = 63453.875| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.54 r_work: 0.2587 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 32464 Z= 0.231 Angle : 0.601 12.772 44413 Z= 0.328 Chirality : 0.044 0.244 5066 Planarity : 0.004 0.065 5316 Dihedral : 17.136 176.184 5606 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.72 % Allowed : 11.03 % Favored : 87.25 % 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: 0.85 (0.14), residues: 3651 helix: 1.79 (0.14), residues: 1450 sheet: 0.50 (0.24), residues: 479 loop : -0.46 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 247 TYR 0.015 0.001 TYR J 631 PHE 0.015 0.001 PHE L 256 TRP 0.007 0.001 TRP J1193 HIS 0.011 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (32456) covalent geometry : angle 0.59942 / 0.33 (44401) hydrogen bonds : bond 0.05253 / 3.43 ( 1441) hydrogen bonds : angle 4.39615 / 3.09 ( 3927) metal coordination : bond 0.00772 / 0.34 ( 8) metal coordination : angle 3.03299 / 1.61 ( 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 320 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 266 time to evaluate : 1.579 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: 0.9293 (ptp-110) cc_final: 0.8952 (ptt-90) REVERT: I 341 LEU cc_start: 0.8618 (pt) cc_final: 0.8400 (mm) REVERT: I 473 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8257 (mtp180) REVERT: K 8 ASP cc_start: 0.8728 (m-30) cc_final: 0.8454 (m-30) REVERT: K 35 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7789 (mptt) REVERT: K 71 GLU cc_start: 0.8887 (tt0) cc_final: 0.8321 (tm-30) REVERT: K 76 GLU cc_start: 0.9274 (tt0) cc_final: 0.8931 (tp30) REVERT: H 145 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8474 (ttpp) REVERT: H 212 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8055 (t0) REVERT: J 66 LYS cc_start: 0.8780 (mttt) cc_final: 0.8540 (mtpm) REVERT: J 151 MET cc_start: 0.8881 (mmm) cc_final: 0.8462 (mpm) REVERT: J 197 GLU cc_start: 0.8913 (tt0) cc_final: 0.8562 (mm-30) REVERT: J 200 GLN cc_start: 0.8709 (tt0) cc_final: 0.8265 (tm-30) REVERT: J 219 LYS cc_start: 0.9317 (mmtm) cc_final: 0.9039 (mmtt) REVERT: J 227 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.9180 (m-80) REVERT: J 982 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8957 (tm) REVERT: J 1025 MET cc_start: 0.8463 (ttp) cc_final: 0.7972 (mpt) REVERT: J 1177 ILE cc_start: 0.9340 (mt) cc_final: 0.9042 (tp) REVERT: J 1186 TYR cc_start: 0.8252 (t80) cc_final: 0.7863 (t80) REVERT: J 1188 GLU cc_start: 0.6949 (pm20) cc_final: 0.6681 (pm20) REVERT: L 277 MET cc_start: 0.8154 (tpt) cc_final: 0.7929 (tmm) REVERT: L 353 LEU cc_start: 0.8037 (tp) cc_final: 0.7766 (mt) REVERT: L 369 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8237 (tm-30) outliers start: 54 outliers final: 20 residues processed: 300 average time/residue: 0.8592 time to fit residues: 299.5338 Evaluate side-chains 266 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 473 ARG Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 959 ASP 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 1341 ASP Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 212 ASP 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 982 LEU Chi-restraints excluded: chain J residue 1324 SER 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: 3.9990 chunk 75 optimal weight: 0.9990 chunk 284 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 319 optimal weight: 3.9990 chunk 303 optimal weight: 7.9990 chunk 116 optimal weight: 0.1980 chunk 222 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 894 GLN I 952 GLN K 43 ASN G 117 HIS L 309 ASN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.109191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.061004 restraints weight = 63214.464| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.53 r_work: 0.2591 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1587 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= 0.176 Angle : 0.550 10.788 44413 Z= 0.300 Chirality : 0.043 0.263 5066 Planarity : 0.004 0.052 5316 Dihedral : 17.238 175.974 5593 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.97 % Allowed : 11.25 % Favored : 86.78 % 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: 1.01 (0.14), residues: 3651 helix: 1.96 (0.14), residues: 1445 sheet: 0.59 (0.24), residues: 474 loop : -0.40 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 77 TYR 0.014 0.001 TYR J 631 PHE 0.013 0.001 PHE I 253 TRP 0.012 0.001 TRP J1193 HIS 0.016 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (32456) covalent geometry : angle 0.54756 / 0.30 (44401) hydrogen bonds : bond 0.04671 / 3.04 ( 1441) hydrogen bonds : angle 4.20758 / 2.95 ( 3927) metal coordination : bond 0.00723 / 0.37 ( 8) metal coordination : angle 2.98005 / 1.58 ( 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 326 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 264 time to evaluate : 1.275 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: 0.9052 (mppt) cc_final: 0.8808 (mppt) REVERT: I 473 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8289 (mtp180) REVERT: I 600 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8704 (t) REVERT: I 971 LEU cc_start: 0.8522 (mm) cc_final: 0.8216 (mt) REVERT: K 8 ASP cc_start: 0.8718 (m-30) cc_final: 0.8422 (m-30) REVERT: K 35 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7786 (mptt) REVERT: K 70 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8335 (tm-30) REVERT: K 71 GLU cc_start: 0.8919 (tt0) cc_final: 0.8355 (tm-30) REVERT: K 75 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8069 (pp30) REVERT: G 127 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: G 206 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: H 212 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8025 (t0) REVERT: J 66 LYS cc_start: 0.8805 (mttt) cc_final: 0.8559 (mtpm) REVERT: J 77 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7998 (tpp-160) REVERT: J 197 GLU cc_start: 0.8941 (tt0) cc_final: 0.8540 (mm-30) REVERT: J 200 GLN cc_start: 0.8774 (tt0) cc_final: 0.8312 (tm-30) REVERT: J 213 LYS cc_start: 0.9388 (mmpt) cc_final: 0.9187 (mptt) REVERT: J 219 LYS cc_start: 0.9299 (mmtm) cc_final: 0.9026 (mmtt) REVERT: J 227 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.9152 (m-80) REVERT: J 1025 MET cc_start: 0.8508 (ttp) cc_final: 0.7996 (mpt) REVERT: J 1040 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.5272 (ttp) REVERT: J 1095 MET cc_start: 0.5240 (pp-130) cc_final: 0.4830 (pp-130) REVERT: J 1177 ILE cc_start: 0.9394 (mt) cc_final: 0.8995 (tp) REVERT: J 1186 TYR cc_start: 0.8189 (t80) cc_final: 0.7778 (t80) REVERT: J 1188 GLU cc_start: 0.7132 (pm20) cc_final: 0.6820 (pm20) REVERT: L 277 MET cc_start: 0.8207 (tpt) cc_final: 0.7980 (tmm) REVERT: L 369 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8244 (tm-30) outliers start: 62 outliers final: 25 residues processed: 306 average time/residue: 0.8373 time to fit residues: 298.6326 Evaluate side-chains 271 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 959 ASP 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 1252 SER Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain G residue 127 GLN 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 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 844 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 862 THR 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 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: 9.9990 chunk 225 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 193 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN G 117 HIS ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3749 r_free = 0.3749 target = 0.109224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.061076 restraints weight = 63075.963| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.53 r_work: 0.2595 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1762 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= 0.156 Angle : 0.537 12.841 44413 Z= 0.291 Chirality : 0.042 0.265 5066 Planarity : 0.004 0.059 5316 Dihedral : 17.281 176.220 5593 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.81 % Allowed : 12.05 % Favored : 86.14 % 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: 1.10 (0.14), residues: 3651 helix: 2.08 (0.14), residues: 1447 sheet: 0.59 (0.24), residues: 474 loop : -0.37 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 69 TYR 0.014 0.001 TYR J 631 PHE 0.019 0.001 PHE L 256 TRP 0.016 0.001 TRP J1193 HIS 0.012 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (32456) covalent geometry : angle 0.53507 / 0.29 (44401) hydrogen bonds : bond 0.04366 / 2.84 ( 1441) hydrogen bonds : angle 4.09457 / 2.87 ( 3927) metal coordination : bond 0.00580 / 0.30 ( 8) metal coordination : angle 2.95162 / 1.56 ( 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 310 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 1.213 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: 0.8120 (pt0) cc_final: 0.7605 (pp20) REVERT: I 191 LYS cc_start: 0.9109 (mppt) cc_final: 0.8862 (mppt) REVERT: I 315 MET cc_start: 0.8991 (ttp) cc_final: 0.8207 (mtm) REVERT: I 341 LEU cc_start: 0.8768 (pt) cc_final: 0.8547 (pp) REVERT: I 473 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8295 (mtp180) REVERT: I 600 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8711 (t) REVERT: I 971 LEU cc_start: 0.8478 (mm) cc_final: 0.8166 (mt) REVERT: K 8 ASP cc_start: 0.8696 (m-30) cc_final: 0.8373 (m-30) REVERT: K 35 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7828 (mptt) REVERT: K 42 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8537 (mt-10) REVERT: K 71 GLU cc_start: 0.8934 (tt0) cc_final: 0.8287 (tm-30) REVERT: K 79 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7302 (pt0) REVERT: G 33 ARG cc_start: 0.8690 (tpp80) cc_final: 0.8330 (tpp-160) REVERT: G 127 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8509 (pm20) REVERT: G 206 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: H 212 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8023 (t0) REVERT: J 66 LYS cc_start: 0.8781 (mttt) cc_final: 0.8525 (mtpm) REVERT: J 151 MET cc_start: 0.8849 (mmm) cc_final: 0.8453 (mpm) REVERT: J 196 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8176 (tm-30) REVERT: J 197 GLU cc_start: 0.8948 (tt0) cc_final: 0.8562 (mm-30) REVERT: J 200 GLN cc_start: 0.8765 (tt0) cc_final: 0.8332 (tm-30) REVERT: J 219 LYS cc_start: 0.9297 (mmtm) cc_final: 0.9018 (mmtt) REVERT: J 227 PHE cc_start: 0.9327 (OUTLIER) cc_final: 0.9107 (m-80) REVERT: J 312 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7869 (tmt-80) REVERT: J 827 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8269 (mt-10) REVERT: J 1025 MET cc_start: 0.8522 (ttp) cc_final: 0.8043 (mpt) REVERT: J 1040 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.5240 (ttp) REVERT: J 1177 ILE cc_start: 0.9394 (mt) cc_final: 0.8939 (tp) REVERT: J 1186 TYR cc_start: 0.8188 (t80) cc_final: 0.7708 (t80) REVERT: J 1188 GLU cc_start: 0.7225 (pm20) cc_final: 0.6908 (pm20) REVERT: L 277 MET cc_start: 0.8212 (tpt) cc_final: 0.7978 (tmm) REVERT: L 369 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8251 (tm-30) REVERT: L 474 MET cc_start: 0.8914 (mmm) cc_final: 0.8658 (mtp) outliers start: 57 outliers final: 24 residues processed: 291 average time/residue: 0.8314 time to fit residues: 284.4971 Evaluate side-chains 266 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 693 LEU 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 I residue 1341 ASP Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 127 GLN 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 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 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 931 THR Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1107 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: 0.8980 chunk 39 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 332 optimal weight: 9.9990 chunk 295 optimal weight: 40.0000 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 952 GLN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.109044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.060903 restraints weight = 63440.714| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.53 r_work: 0.2593 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: 0.9074 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32464 Z= 0.160 Angle : 0.541 14.477 44413 Z= 0.292 Chirality : 0.042 0.268 5066 Planarity : 0.004 0.063 5316 Dihedral : 17.319 176.990 5593 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.94 % Allowed : 12.02 % Favored : 86.05 % 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: 1451 sheet: 0.60 (0.24), residues: 474 loop : -0.35 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 77 TYR 0.014 0.001 TYR J 631 PHE 0.013 0.001 PHE J1325 TRP 0.020 0.001 TRP J1193 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (32456) covalent geometry : angle 0.53936 / 0.29 (44401) hydrogen bonds : bond 0.04314 / 2.81 ( 1441) hydrogen bonds : angle 4.04626 / 2.83 ( 3927) metal coordination : bond 0.00580 / 0.30 ( 8) metal coordination : angle 2.97049 / 1.58 ( 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 311 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 250 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 191 LYS cc_start: 0.9121 (mppt) cc_final: 0.8830 (mppt) REVERT: I 315 MET cc_start: 0.8978 (ttp) cc_final: 0.8212 (mtm) REVERT: I 473 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8028 (mtp180) REVERT: I 600 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8499 (p) REVERT: I 971 LEU cc_start: 0.8459 (mm) cc_final: 0.8136 (mt) REVERT: K 8 ASP cc_start: 0.8694 (m-30) cc_final: 0.8441 (m-30) REVERT: K 71 GLU cc_start: 0.8915 (tt0) cc_final: 0.8422 (tm-30) REVERT: G 125 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8942 (tttp) REVERT: G 127 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8385 (pm20) REVERT: G 206 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: H 12 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7898 (ptp-170) REVERT: J 66 LYS cc_start: 0.8773 (mttt) cc_final: 0.8519 (mtpm) REVERT: J 77 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7925 (tpp-160) REVERT: J 151 MET cc_start: 0.8864 (mmm) cc_final: 0.8447 (mpm) REVERT: J 192 MET cc_start: 0.9036 (ptm) cc_final: 0.8811 (ptm) REVERT: J 197 GLU cc_start: 0.8973 (tt0) cc_final: 0.8508 (mm-30) REVERT: J 200 GLN cc_start: 0.8762 (tt0) cc_final: 0.8303 (tm-30) REVERT: J 213 LYS cc_start: 0.9378 (mmpt) cc_final: 0.8876 (mptt) REVERT: J 219 LYS cc_start: 0.9298 (mmtm) cc_final: 0.9022 (mmtt) REVERT: J 227 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.9086 (m-80) REVERT: J 312 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7872 (tmt-80) REVERT: J 322 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8432 (mtm110) REVERT: J 1025 MET cc_start: 0.8540 (ttp) cc_final: 0.8057 (mpt) REVERT: J 1040 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.5313 (ttp) REVERT: J 1177 ILE cc_start: 0.9423 (mt) cc_final: 0.8933 (tp) REVERT: J 1186 TYR cc_start: 0.8156 (t80) cc_final: 0.7618 (t80) REVERT: J 1188 GLU cc_start: 0.7334 (pm20) cc_final: 0.6922 (pm20) REVERT: L 277 MET cc_start: 0.8195 (tpt) cc_final: 0.7954 (tmm) REVERT: L 297 MET cc_start: 0.3175 (ppp) cc_final: 0.2298 (pmm) REVERT: L 369 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8246 (tm-30) outliers start: 61 outliers final: 30 residues processed: 292 average time/residue: 0.8234 time to fit residues: 281.7193 Evaluate side-chains 278 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 924 VAL 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 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 127 GLN Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 12 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 322 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 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 928 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 291 optimal weight: 30.0000 chunk 294 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 296 optimal weight: 20.0000 chunk 262 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 954 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.108151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.059965 restraints weight = 63041.809| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.52 r_work: 0.2574 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 32464 Z= 0.209 Angle : 0.566 13.469 44413 Z= 0.305 Chirality : 0.043 0.268 5066 Planarity : 0.004 0.060 5316 Dihedral : 17.398 179.095 5591 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.88 % Allowed : 12.65 % Favored : 85.47 % 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: 1.08 (0.14), residues: 3651 helix: 2.07 (0.14), residues: 1445 sheet: 0.54 (0.24), residues: 479 loop : -0.37 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 247 TYR 0.016 0.001 TYR J 631 PHE 0.018 0.001 PHE J1325 TRP 0.025 0.001 TRP J1193 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (32456) covalent geometry : angle 0.56373 / 0.30 (44401) hydrogen bonds : bond 0.04708 / 3.07 ( 1441) hydrogen bonds : angle 4.08217 / 2.86 ( 3927) metal coordination : bond 0.00781 / 0.40 ( 8) metal coordination : angle 3.30284 / 1.78 ( 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 307 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 1.283 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: 0.8152 (pt0) cc_final: 0.7503 (pp20) REVERT: I 191 LYS cc_start: 0.9143 (mppt) cc_final: 0.8825 (mppt) REVERT: I 315 MET cc_start: 0.8977 (ttp) cc_final: 0.8205 (mtm) REVERT: I 473 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8038 (mtp180) REVERT: I 600 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8531 (p) REVERT: I 971 LEU cc_start: 0.8501 (mm) cc_final: 0.8186 (mt) REVERT: K 8 ASP cc_start: 0.8677 (m-30) cc_final: 0.8399 (m-30) REVERT: K 35 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7938 (mptt) REVERT: K 71 GLU cc_start: 0.8934 (tt0) cc_final: 0.8190 (tm-30) REVERT: G 125 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8894 (tttp) REVERT: G 127 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: G 206 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: H 12 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7872 (ptp-170) REVERT: H 95 LYS cc_start: 0.9408 (mtmp) cc_final: 0.9012 (mtmm) REVERT: J 66 LYS cc_start: 0.8812 (mttt) cc_final: 0.8523 (mtpm) REVERT: J 192 MET cc_start: 0.9052 (ptm) cc_final: 0.8825 (ptm) REVERT: J 196 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8209 (tm-30) REVERT: J 197 GLU cc_start: 0.8973 (tt0) cc_final: 0.8620 (mm-30) REVERT: J 200 GLN cc_start: 0.8769 (tt0) cc_final: 0.8362 (tm-30) REVERT: J 219 LYS cc_start: 0.9276 (mmtm) cc_final: 0.9006 (mmtt) REVERT: J 227 PHE cc_start: 0.9336 (OUTLIER) cc_final: 0.9097 (m-80) REVERT: J 322 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8479 (mtm110) REVERT: J 827 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8243 (mt-10) REVERT: J 1003 LEU cc_start: 0.9215 (pp) cc_final: 0.9006 (pt) REVERT: J 1025 MET cc_start: 0.8563 (ttp) cc_final: 0.8067 (mpt) REVERT: J 1040 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.5420 (ttp) REVERT: J 1149 ARG cc_start: 0.8737 (mmt90) cc_final: 0.8528 (mtp-110) REVERT: J 1177 ILE cc_start: 0.9438 (mt) cc_final: 0.8950 (tp) REVERT: J 1186 TYR cc_start: 0.8116 (t80) cc_final: 0.7530 (t80) REVERT: J 1188 GLU cc_start: 0.7392 (pm20) cc_final: 0.6719 (pm20) REVERT: J 1189 MET cc_start: 0.8453 (mmm) cc_final: 0.8224 (mmm) REVERT: L 277 MET cc_start: 0.8191 (tpt) cc_final: 0.7962 (tmm) REVERT: L 297 MET cc_start: 0.3375 (ppp) cc_final: 0.2429 (pmm) REVERT: L 369 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8245 (tm-30) REVERT: L 474 MET cc_start: 0.8847 (mmp) cc_final: 0.8602 (mtp) outliers start: 59 outliers final: 34 residues processed: 292 average time/residue: 0.8326 time to fit residues: 284.0303 Evaluate side-chains 284 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 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 693 LEU Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 924 VAL 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 I residue 1252 SER Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 107 ILE 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 322 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 507 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 928 THR 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 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 Chi-restraints excluded: chain L residue 576 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 202 optimal weight: 0.3980 chunk 253 optimal weight: 6.9990 chunk 302 optimal weight: 5.9990 chunk 218 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 323 optimal weight: 0.3980 chunk 205 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 357 ASN I 922 ASN I 952 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 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 = 0.3760 r_free = 0.3760 target = 0.109801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.061958 restraints weight = 63255.935| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.52 r_work: 0.2620 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32464 Z= 0.110 Angle : 0.534 14.649 44413 Z= 0.287 Chirality : 0.041 0.276 5066 Planarity : 0.004 0.074 5316 Dihedral : 17.345 176.102 5590 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.30 % Allowed : 13.67 % Favored : 85.03 % 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: 1.31 (0.14), residues: 3651 helix: 2.24 (0.14), residues: 1445 sheet: 0.63 (0.24), residues: 486 loop : -0.23 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 77 TYR 0.020 0.001 TYR L 137 PHE 0.012 0.001 PHE I 405 TRP 0.033 0.001 TRP J1193 HIS 0.007 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (32456) covalent geometry : angle 0.53277 / 0.29 (44401) hydrogen bonds : bond 0.03685 / 2.41 ( 1441) hydrogen bonds : angle 3.91362 / 2.73 ( 3927) metal coordination : bond 0.00340 / 0.20 ( 8) metal coordination : angle 2.60320 / 1.36 ( 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 300 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 259 time to evaluate : 1.344 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: 0.7850 (pt0) cc_final: 0.7476 (pm20) REVERT: I 191 LYS cc_start: 0.9140 (mppt) cc_final: 0.8857 (mppt) REVERT: I 600 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8489 (p) REVERT: I 971 LEU cc_start: 0.8444 (mm) cc_final: 0.8125 (mt) REVERT: K 8 ASP cc_start: 0.8717 (m-30) cc_final: 0.8457 (m-30) REVERT: K 71 GLU cc_start: 0.8921 (tt0) cc_final: 0.8366 (tm-30) REVERT: G 125 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8919 (tttp) REVERT: G 127 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8376 (pm20) REVERT: H 25 LYS cc_start: 0.8860 (ttpp) cc_final: 0.8551 (mtpp) REVERT: H 95 LYS cc_start: 0.9407 (mtmp) cc_final: 0.9031 (mtmm) REVERT: J 66 LYS cc_start: 0.8657 (mttt) cc_final: 0.8408 (mtpm) REVERT: J 196 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8136 (tm-30) REVERT: J 197 GLU cc_start: 0.8902 (tt0) cc_final: 0.8544 (mm-30) REVERT: J 200 GLN cc_start: 0.8715 (tt0) cc_final: 0.8301 (tm-30) REVERT: J 213 LYS cc_start: 0.9210 (mmpt) cc_final: 0.8839 (mptt) REVERT: J 219 LYS cc_start: 0.9251 (mmtm) cc_final: 0.8994 (mmtt) REVERT: J 227 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.9067 (m-80) REVERT: J 322 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8332 (mtm110) REVERT: J 982 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8656 (tm) REVERT: J 1025 MET cc_start: 0.8559 (ttp) cc_final: 0.8084 (mpt) REVERT: J 1177 ILE cc_start: 0.9435 (mt) cc_final: 0.8932 (tp) REVERT: J 1186 TYR cc_start: 0.8188 (t80) cc_final: 0.7637 (t80) REVERT: J 1188 GLU cc_start: 0.7339 (pm20) cc_final: 0.6723 (pm20) REVERT: J 1189 MET cc_start: 0.8357 (mmm) cc_final: 0.8081 (mmm) REVERT: L 297 MET cc_start: 0.3018 (OUTLIER) cc_final: 0.2095 (pmm) REVERT: L 369 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8138 (tm-30) outliers start: 41 outliers final: 22 residues processed: 289 average time/residue: 0.8320 time to fit residues: 281.0260 Evaluate side-chains 269 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 888 THR Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 1082 ILE 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 127 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 322 ARG 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 982 LEU Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1107 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 31 optimal weight: 8.9990 chunk 146 optimal weight: 40.0000 chunk 131 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 250 optimal weight: 4.9990 chunk 341 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 186 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.107812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.059666 restraints weight = 63340.805| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.52 r_work: 0.2568 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2426 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 32464 Z= 0.236 Angle : 0.600 13.630 44413 Z= 0.319 Chirality : 0.044 0.272 5066 Planarity : 0.004 0.075 5316 Dihedral : 17.431 179.575 5589 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.62 % Allowed : 13.86 % Favored : 84.52 % 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: 1.16 (0.14), residues: 3651 helix: 2.13 (0.14), residues: 1440 sheet: 0.57 (0.23), residues: 491 loop : -0.33 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 247 TYR 0.017 0.001 TYR J 631 PHE 0.022 0.001 PHE J1325 TRP 0.038 0.001 TRP J1193 HIS 0.007 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 (32456) covalent geometry : angle 0.59744 / 0.32 (44401) hydrogen bonds : bond 0.04831 / 3.16 ( 1441) hydrogen bonds : angle 4.05723 / 2.84 ( 3927) metal coordination : bond 0.00847 / 0.42 ( 8) metal coordination : angle 3.43058 / 1.86 ( 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: 51 poor density : 249 time to evaluate : 1.260 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: 0.8148 (pt0) cc_final: 0.7549 (pp20) REVERT: I 191 LYS cc_start: 0.9196 (mppt) cc_final: 0.8964 (mppt) REVERT: I 315 MET cc_start: 0.9000 (ttp) cc_final: 0.8234 (mtm) REVERT: I 473 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8290 (mtp180) REVERT: I 600 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8610 (p) REVERT: I 971 LEU cc_start: 0.8483 (mm) cc_final: 0.8163 (mt) REVERT: K 35 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8014 (mptt) REVERT: K 71 GLU cc_start: 0.8933 (tt0) cc_final: 0.8194 (tm-30) REVERT: G 125 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8928 (tttp) REVERT: G 127 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8450 (pm20) REVERT: H 12 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7894 (ptp-170) REVERT: H 25 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8655 (mtpp) REVERT: H 95 LYS cc_start: 0.9382 (mtmp) cc_final: 0.8975 (mtmm) REVERT: J 66 LYS cc_start: 0.8839 (mttt) cc_final: 0.8557 (mtpm) REVERT: J 77 ARG cc_start: 0.8260 (tpp-160) cc_final: 0.7977 (mmm160) REVERT: J 151 MET cc_start: 0.8796 (mmm) cc_final: 0.8381 (mpm) REVERT: J 196 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8216 (tm-30) REVERT: J 197 GLU cc_start: 0.8995 (tt0) cc_final: 0.8575 (mm-30) REVERT: J 200 GLN cc_start: 0.8780 (tt0) cc_final: 0.8394 (tm-30) REVERT: J 215 LYS cc_start: 0.9096 (mmpt) cc_final: 0.8457 (mtmm) REVERT: J 219 LYS cc_start: 0.9270 (mmtm) cc_final: 0.9035 (mmtm) REVERT: J 227 PHE cc_start: 0.9335 (OUTLIER) cc_final: 0.9080 (m-80) REVERT: J 322 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8484 (mtm110) REVERT: J 827 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8297 (mt-10) REVERT: J 1003 LEU cc_start: 0.9257 (pp) cc_final: 0.9002 (pt) REVERT: J 1025 MET cc_start: 0.8590 (ttp) cc_final: 0.8087 (mpt) REVERT: J 1040 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.5426 (ttp) REVERT: J 1177 ILE cc_start: 0.9457 (mt) cc_final: 0.8971 (tp) REVERT: J 1186 TYR cc_start: 0.8119 (t80) cc_final: 0.7566 (t80) REVERT: J 1188 GLU cc_start: 0.7459 (pm20) cc_final: 0.7184 (pm20) REVERT: L 297 MET cc_start: 0.3137 (OUTLIER) cc_final: 0.2139 (pmm) REVERT: L 369 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8285 (tm-30) outliers start: 51 outliers final: 29 residues processed: 285 average time/residue: 0.7786 time to fit residues: 259.4682 Evaluate side-chains 280 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 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 693 LEU Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 959 ASP 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 K residue 80 LEU Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain H residue 12 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 322 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 507 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 862 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 368 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 205 optimal weight: 0.0270 chunk 295 optimal weight: 0.5980 chunk 296 optimal weight: 0.9990 chunk 309 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 192 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 922 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3760 r_free = 0.3760 target = 0.109706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.061882 restraints weight = 63123.352| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.52 r_work: 0.2619 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 32464 Z= 0.111 Angle : 0.557 13.229 44413 Z= 0.297 Chirality : 0.041 0.280 5066 Planarity : 0.004 0.081 5316 Dihedral : 17.369 176.493 5589 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.34 % Allowed : 14.34 % Favored : 84.33 % 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: 1.36 (0.14), residues: 3651 helix: 2.26 (0.14), residues: 1446 sheet: 0.70 (0.24), residues: 485 loop : -0.19 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG I 247 TYR 0.015 0.001 TYR L 137 PHE 0.012 0.001 PHE L 259 TRP 0.045 0.001 TRP J1193 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (32456) covalent geometry : angle 0.55522 / 0.30 (44401) hydrogen bonds : bond 0.03670 / 2.40 ( 1441) hydrogen bonds : angle 3.92282 / 2.74 ( 3927) metal coordination : bond 0.00324 / 0.18 ( 8) metal coordination : angle 2.62496 / 1.38 ( 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 295 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 7 GLU cc_start: 0.7861 (pt0) cc_final: 0.7492 (pm20) REVERT: I 191 LYS cc_start: 0.9183 (mppt) cc_final: 0.8909 (mppt) REVERT: I 315 MET cc_start: 0.8898 (ttp) cc_final: 0.8176 (mtm) REVERT: I 600 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8543 (p) REVERT: I 971 LEU cc_start: 0.8479 (mm) cc_final: 0.8175 (mt) REVERT: K 68 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8709 (pp20) REVERT: K 71 GLU cc_start: 0.8916 (tt0) cc_final: 0.8333 (tm-30) REVERT: G 33 ARG cc_start: 0.8380 (tpp-160) cc_final: 0.8167 (tpp80) REVERT: G 125 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8920 (tttp) REVERT: G 127 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: G 181 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8568 (mm-30) REVERT: H 25 LYS cc_start: 0.8881 (ttpp) cc_final: 0.8575 (mtpp) REVERT: J 66 LYS cc_start: 0.8682 (mttt) cc_final: 0.8431 (mtpm) REVERT: J 77 ARG cc_start: 0.8097 (tpp-160) cc_final: 0.7795 (mmm160) REVERT: J 151 MET cc_start: 0.8670 (mmm) cc_final: 0.8327 (mpm) REVERT: J 196 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8142 (tm-30) REVERT: J 197 GLU cc_start: 0.8853 (tt0) cc_final: 0.8457 (mm-30) REVERT: J 200 GLN cc_start: 0.8709 (tt0) cc_final: 0.8292 (tm-30) REVERT: J 213 LYS cc_start: 0.9228 (mmpt) cc_final: 0.8950 (mptt) REVERT: J 215 LYS cc_start: 0.9080 (mmpt) cc_final: 0.8437 (mtmm) REVERT: J 219 LYS cc_start: 0.9260 (mmtm) cc_final: 0.9023 (mmtm) REVERT: J 312 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7622 (tmt-80) REVERT: J 322 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8363 (mtm110) REVERT: J 827 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8222 (mt-10) REVERT: J 873 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: J 1003 LEU cc_start: 0.9259 (pp) cc_final: 0.9028 (pt) REVERT: J 1025 MET cc_start: 0.8608 (ttp) cc_final: 0.8118 (mpt) REVERT: J 1040 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.5275 (ttp) REVERT: J 1177 ILE cc_start: 0.9441 (mt) cc_final: 0.8954 (tp) REVERT: J 1186 TYR cc_start: 0.8164 (t80) cc_final: 0.7685 (t80) REVERT: J 1188 GLU cc_start: 0.7342 (pm20) cc_final: 0.6765 (pm20) REVERT: J 1189 MET cc_start: 0.8359 (mmm) cc_final: 0.8101 (mmm) REVERT: L 297 MET cc_start: 0.3060 (OUTLIER) cc_final: 0.2198 (pmm) REVERT: L 369 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8108 (tm-30) outliers start: 42 outliers final: 25 residues processed: 282 average time/residue: 0.8363 time to fit residues: 274.7420 Evaluate side-chains 277 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 959 ASP 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 127 GLN Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 322 ARG 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 967 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain L residue 166 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 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: 3.9990 chunk 32 optimal weight: 20.0000 chunk 118 optimal weight: 0.0770 chunk 197 optimal weight: 4.9990 chunk 293 optimal weight: 30.0000 chunk 319 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 288 optimal weight: 40.0000 chunk 370 optimal weight: 2.9990 chunk 359 optimal weight: 2.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3735 r_free = 0.3735 target = 0.107986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.059895 restraints weight = 63574.467| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.53 r_work: 0.2574 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 32464 Z= 0.225 Angle : 0.598 13.961 44413 Z= 0.319 Chirality : 0.044 0.275 5066 Planarity : 0.004 0.084 5316 Dihedral : 17.411 179.032 5586 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.21 % Allowed : 14.88 % 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: 1.22 (0.14), residues: 3651 helix: 2.17 (0.14), residues: 1439 sheet: 0.63 (0.24), residues: 491 loop : -0.30 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 247 TYR 0.017 0.001 TYR J 631 PHE 0.020 0.001 PHE J1325 TRP 0.038 0.002 TRP J1193 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (32456) covalent geometry : angle 0.59528 / 0.32 (44401) hydrogen bonds : bond 0.04614 / 3.02 ( 1441) hydrogen bonds : angle 4.04049 / 2.82 ( 3927) metal coordination : bond 0.00814 / 0.41 ( 8) metal coordination : angle 3.26837 / 1.77 ( 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 287 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 191 LYS cc_start: 0.9193 (mppt) cc_final: 0.8958 (mppt) REVERT: I 315 MET cc_start: 0.9031 (ttp) cc_final: 0.8281 (mtm) REVERT: I 600 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8633 (p) REVERT: I 971 LEU cc_start: 0.8502 (mm) cc_final: 0.8197 (mt) REVERT: K 8 ASP cc_start: 0.8621 (m-30) cc_final: 0.8355 (m-30) REVERT: K 11 GLU cc_start: 0.8224 (pp20) cc_final: 0.7949 (pm20) REVERT: K 71 GLU cc_start: 0.8920 (tt0) cc_final: 0.8300 (tm-30) REVERT: G 33 ARG cc_start: 0.8522 (tpp-160) cc_final: 0.8269 (tpp-160) REVERT: G 125 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8952 (tttp) REVERT: G 127 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8487 (pm20) REVERT: H 25 LYS cc_start: 0.9022 (ttpp) cc_final: 0.8675 (mtpp) REVERT: J 66 LYS cc_start: 0.8840 (mttt) cc_final: 0.8579 (mtpm) REVERT: J 151 MET cc_start: 0.8864 (mmm) cc_final: 0.8469 (mpm) REVERT: J 196 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8207 (tm-30) REVERT: J 197 GLU cc_start: 0.8948 (tt0) cc_final: 0.8487 (mm-30) REVERT: J 200 GLN cc_start: 0.8782 (tt0) cc_final: 0.8418 (tm-30) REVERT: J 213 LYS cc_start: 0.9286 (mmpt) cc_final: 0.9007 (mptt) REVERT: J 215 LYS cc_start: 0.9090 (mmpt) cc_final: 0.8410 (mtmm) REVERT: J 219 LYS cc_start: 0.9275 (mmtm) cc_final: 0.9026 (mmtm) REVERT: J 312 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7739 (tmt-80) REVERT: J 322 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8501 (mtm110) REVERT: J 827 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8245 (mt-10) REVERT: J 873 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7811 (mp0) REVERT: J 1003 LEU cc_start: 0.9234 (pp) cc_final: 0.9006 (pt) REVERT: J 1025 MET cc_start: 0.8629 (ttp) cc_final: 0.8138 (mpt) REVERT: J 1040 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.5550 (ttp) REVERT: J 1149 ARG cc_start: 0.8770 (mmt90) cc_final: 0.8568 (mtp-110) REVERT: J 1177 ILE cc_start: 0.9452 (mt) cc_final: 0.8971 (tp) REVERT: J 1186 TYR cc_start: 0.8102 (t80) cc_final: 0.7597 (t80) REVERT: J 1188 GLU cc_start: 0.7463 (pm20) cc_final: 0.7024 (pm20) REVERT: J 1189 MET cc_start: 0.8438 (mmm) cc_final: 0.8208 (mmm) REVERT: L 369 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8241 (tm-30) outliers start: 38 outliers final: 26 residues processed: 277 average time/residue: 0.8391 time to fit residues: 270.9051 Evaluate side-chains 273 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 959 ASP 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 127 GLN Chi-restraints excluded: chain J residue 312 ARG Chi-restraints excluded: chain J residue 322 ARG 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 928 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 1204 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL 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 21 optimal weight: 0.0060 chunk 262 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 275 optimal weight: 0.2980 chunk 127 optimal weight: 0.6980 chunk 250 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 271 optimal weight: 0.2980 chunk 300 optimal weight: 10.0000 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 894 GLN I 922 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN J 954 ASN L 265 GLN ** 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 = 0.3765 r_free = 0.3765 target = 0.109960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.062221 restraints weight = 63351.004| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.53 r_work: 0.2628 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 32464 Z= 0.111 Angle : 0.560 14.192 44413 Z= 0.301 Chirality : 0.041 0.283 5066 Planarity : 0.004 0.104 5316 Dihedral : 17.344 175.774 5586 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.11 % Allowed : 14.94 % Favored : 83.95 % 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: 1.37 (0.14), residues: 3651 helix: 2.25 (0.14), residues: 1446 sheet: 0.75 (0.24), residues: 470 loop : -0.16 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG K 69 TYR 0.012 0.001 TYR J 679 PHE 0.013 0.001 PHE I 405 TRP 0.047 0.002 TRP L 326 HIS 0.004 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (32456) covalent geometry : angle 0.55870 / 0.30 (44401) hydrogen bonds : bond 0.03548 / 2.33 ( 1441) hydrogen bonds : angle 3.92495 / 2.74 ( 3927) metal coordination : bond 0.00259 / 0.15 ( 8) metal coordination : angle 2.56828 / 1.34 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16781.67 seconds wall clock time: 284 minutes 50.04 seconds (17090.04 seconds total)