Starting phenix.real_space_refine on Sat Feb 7 16:09:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gda_51259/02_2026/9gda_51259.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gda_51259/02_2026/9gda_51259.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 { model { file = "/net/cci-nas-00/data/ceres_data/9gda_51259/02_2026/9gda_51259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gda_51259/02_2026/9gda_51259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gda_51259/02_2026/9gda_51259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gda_51259/02_2026/9gda_51259.map" } 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= 0.016 sd= 1.156 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 5 6.06 5 P 89 5.49 5 Mg 1 5.21 5 S 143 5.16 5 C 20917 2.51 5 N 6004 2.21 5 O 6698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33857 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 223} Chain: "B" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 54, 'TRANS': 1284} Chain: "D" Number of atoms: 10433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1342, 10433 Classifications: {'peptide': 1342} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1286} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 6700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6700 Classifications: {'peptide': 846} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 801} Chain breaks: 1 Chain: "N" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 804 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 791 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "D" 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: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14644 SG CYS D 70 109.408 99.331 91.695 1.00 90.31 S ATOM 14658 SG CYS D 72 109.800 103.172 91.863 1.00 91.97 S ATOM 14766 SG CYS D 85 111.904 100.813 93.980 1.00 92.90 S ATOM 14790 SG CYS D 88 108.085 101.060 94.528 1.00 88.59 S ATOM 20478 SG CYS D 814 84.387 37.847 89.973 1.00 68.01 S ATOM 21043 SG CYS D 888 83.284 41.383 90.121 1.00 69.50 S ATOM 21094 SG CYS D 895 83.908 39.616 86.779 1.00 67.65 S ATOM 21115 SG CYS D 898 80.853 38.748 88.685 1.00 70.07 S ATOM 29933 SG CYS F 599 66.633 91.296 151.283 1.00106.70 S ATOM 29953 SG CYS F 602 66.574 88.208 153.526 1.00 88.44 S ATOM 30073 SG CYS F 619 69.351 90.549 153.903 1.00112.14 S ATOM 30157 SG CYS F 630 69.204 88.475 150.705 1.00107.47 S ATOM 30407 SG CYS F 662 74.410 111.065 163.618 1.00 75.36 S ATOM 30429 SG CYS F 665 77.791 112.323 164.607 1.00 51.41 S ATOM 30570 SG CYS F 683 77.291 110.657 161.287 1.00 55.15 S ATOM 30610 SG CYS F 689 77.203 108.588 164.456 1.00 64.71 S ATOM 30786 SG CYS F 711 69.157 121.515 121.421 1.00102.13 S ATOM 30810 SG CYS F 714 66.154 122.523 123.490 1.00 94.91 S ATOM 30942 SG CYS F 731 67.338 119.043 123.785 1.00128.51 S ATOM 30981 SG CYS F 736 65.848 120.166 120.467 1.00110.55 S Time building chain proxies: 6.80, per 1000 atoms: 0.20 Number of scatterers: 33857 At special positions: 0 Unit cell: (152.698, 176.19, 183.741, 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 5 29.99 S 143 16.00 P 89 15.00 Mg 1 11.99 O 6698 8.00 N 6004 7.00 C 20917 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: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 602 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 619 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 599 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 630 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 665 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 683 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 662 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 689 " pdb=" ZN F1003 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 714 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 736 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 711 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 731 " Number of angles added : 30 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7556 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 57 sheets defined 41.0% alpha, 18.8% beta 38 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.652A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.728A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.199A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.868A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.847A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.761A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 165 through 169 removed outlier: 3.914A pdb=" N LYS C 169 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.583A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.595A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.978A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.557A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.521A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 565 through 569 removed outlier: 4.136A pdb=" N ASN C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 3.969A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.931A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 738 through 741 removed outlier: 3.828A pdb=" N MET C 741 " --> pdb=" O GLU C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 982 Processing helix chain 'C' and resid 985 through 992 Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.886A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.127A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.619A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.521A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.596A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.540A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.745A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.602A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.647A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.611A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.911A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.592A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1068 through 1072 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.262A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.630A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.264A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 91 Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.907A pdb=" N TYR F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY F 22 " --> pdb=" O ASN F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 Processing helix chain 'F' and resid 89 through 103 Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 143 through 153 removed outlier: 3.744A pdb=" N LYS F 153 " --> pdb=" O GLN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 187 removed outlier: 3.554A pdb=" N VAL F 162 " --> pdb=" O ASN F 158 " (cutoff:3.500A) Proline residue: F 181 - end of helix Processing helix chain 'F' and resid 194 through 214 removed outlier: 3.929A pdb=" N VAL F 199 " --> pdb=" O ARG F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 285 through 296 Processing helix chain 'F' and resid 300 through 314 Processing helix chain 'F' and resid 328 through 343 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 376 through 380 Processing helix chain 'F' and resid 384 through 401 Processing helix chain 'F' and resid 478 through 490 Processing helix chain 'F' and resid 496 through 507 removed outlier: 3.759A pdb=" N GLN F 505 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 534 Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 539 through 555 Processing helix chain 'F' and resid 559 through 580 removed outlier: 4.151A pdb=" N LYS F 580 " --> pdb=" O ASP F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 624 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.545A pdb=" N ARG F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 644 through 648 Processing helix chain 'F' and resid 649 through 659 removed outlier: 4.237A pdb=" N THR F 653 " --> pdb=" O GLU F 649 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 659 " --> pdb=" O ALA F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 785 through 790 Processing helix chain 'F' and resid 796 through 803 Processing helix chain 'F' and resid 811 through 817 removed outlier: 3.959A pdb=" N ALA F 815 " --> pdb=" O LEU F 811 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.085A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.145A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 18 removed outlier: 6.325A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 7.660A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.444A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.227A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.550A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 159 removed outlier: 4.842A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.571A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL C 296 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.758A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.380A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.600A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.491A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.675A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.764A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.265A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 3.863A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.455A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 removed outlier: 5.313A pdb=" N VAL D 146 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS D 179 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 148 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AE2, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.389A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.540A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 991 through 997 removed outlier: 3.963A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 984 " --> pdb=" O GLU D 993 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE8, first strand: chain 'D' and resid 1098 through 1100 removed outlier: 3.626A pdb=" N VAL D1113 " --> pdb=" O VAL D1035 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.884A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1155 through 1156 removed outlier: 6.416A pdb=" N ILE D1155 " --> pdb=" O ILE D1210 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1186 through 1191 Processing sheet with id=AF3, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 4.477A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 25 through 29 removed outlier: 6.476A pdb=" N LEU F 5 " --> pdb=" O TYR F 107 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 244 through 245 removed outlier: 4.845A pdb=" N VAL F 222 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N HIS F 240 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 12.670A pdb=" N TRP F 220 " --> pdb=" O HIS F 240 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 457 through 458 removed outlier: 5.737A pdb=" N VAL F 268 " --> pdb=" O GLY F 416 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY F 416 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS F 407 " --> pdb=" O ARG F 430 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG F 421 " --> pdb=" O THR F 239 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG F 425 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ALA F 235 " --> pdb=" O ARG F 425 " (cutoff:3.500A) removed outlier: 12.316A pdb=" N ARG F 427 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 14.800A pdb=" N ALA F 233 " --> pdb=" O ARG F 427 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL F 222 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N HIS F 240 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 12.670A pdb=" N TRP F 220 " --> pdb=" O HIS F 240 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 510 through 513 Processing sheet with id=AF8, first strand: chain 'F' and resid 593 through 595 removed outlier: 3.823A pdb=" N VAL F 593 " --> pdb=" O ILE F 608 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 637 through 638 removed outlier: 3.508A pdb=" N VAL F 637 " --> pdb=" O LEU F 673 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 709 through 710 Processing sheet with id=AG2, first strand: chain 'F' and resid 756 through 762 removed outlier: 3.937A pdb=" N PHE F 770 " --> pdb=" O LEU F 758 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 827 through 832 removed outlier: 7.783A pdb=" N GLN F 838 " --> pdb=" O ALA F 853 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA F 853 " --> pdb=" O GLN F 838 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL F 840 " --> pdb=" O TRP F 851 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TRP F 851 " --> pdb=" O VAL F 840 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N SER F 842 " --> pdb=" O THR F 849 " (cutoff:3.500A) 1510 hydrogen bonds defined for protein. 4227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 8.75 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5718 1.30 - 1.42: 8501 1.42 - 1.55: 19934 1.55 - 1.68: 175 1.68 - 1.81: 244 Bond restraints: 34572 Sorted by residual: bond pdb=" N PRO D 502 " pdb=" CA PRO D 502 " ideal model delta sigma weight residual 1.466 1.672 -0.206 1.17e-02 7.31e+03 3.10e+02 bond pdb=" C VAL D 501 " pdb=" N PRO D 502 " ideal model delta sigma weight residual 1.331 1.437 -0.106 1.27e-02 6.20e+03 6.92e+01 bond pdb=" C PRO D 502 " pdb=" O PRO D 502 " ideal model delta sigma weight residual 1.233 1.169 0.063 1.24e-02 6.50e+03 2.62e+01 bond pdb=" O5' DC N 13 " pdb=" C5' DC N 13 " ideal model delta sigma weight residual 1.423 1.529 -0.106 3.00e-02 1.11e+03 1.24e+01 bond pdb=" C HIS C 628 " pdb=" O HIS C 628 " ideal model delta sigma weight residual 1.234 1.199 0.035 1.22e-02 6.72e+03 8.23e+00 ... (remaining 34567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 46825 3.47 - 6.93: 230 6.93 - 10.40: 15 10.40 - 13.86: 2 13.86 - 17.33: 2 Bond angle restraints: 47074 Sorted by residual: angle pdb=" C VAL D 501 " pdb=" N PRO D 502 " pdb=" CA PRO D 502 " ideal model delta sigma weight residual 119.90 137.23 -17.33 1.02e+00 9.61e-01 2.89e+02 angle pdb=" O5' DC N 24 " pdb=" C5' DC N 24 " pdb=" C4' DC N 24 " ideal model delta sigma weight residual 110.80 99.79 11.01 1.50e+00 4.44e-01 5.38e+01 angle pdb=" N ASN B 208 " pdb=" CA ASN B 208 " pdb=" C ASN B 208 " ideal model delta sigma weight residual 110.41 101.63 8.78 1.23e+00 6.61e-01 5.10e+01 angle pdb=" CA PRO D 502 " pdb=" N PRO D 502 " pdb=" CD PRO D 502 " ideal model delta sigma weight residual 112.00 102.45 9.55 1.40e+00 5.10e-01 4.65e+01 angle pdb=" N PRO D 502 " pdb=" CA PRO D 502 " pdb=" C PRO D 502 " ideal model delta sigma weight residual 111.15 100.84 10.31 1.58e+00 4.01e-01 4.26e+01 ... (remaining 47069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 20466 31.41 - 62.82: 591 62.82 - 94.23: 27 94.23 - 125.63: 1 125.63 - 157.04: 2 Dihedral angle restraints: 21087 sinusoidal: 9342 harmonic: 11745 Sorted by residual: dihedral pdb=" CA ASP F 130 " pdb=" C ASP F 130 " pdb=" N ASP F 131 " pdb=" CA ASP F 131 " ideal model delta harmonic sigma weight residual -180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA PHE F 284 " pdb=" C PHE F 284 " pdb=" N ILE F 285 " pdb=" CA ILE F 285 " ideal model delta harmonic sigma weight residual 180.00 155.51 24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA LYS C1234 " pdb=" C LYS C1234 " pdb=" N LEU C1235 " pdb=" CA LEU C1235 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 21084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4665 0.085 - 0.170: 618 0.170 - 0.255: 27 0.255 - 0.340: 6 0.340 - 0.426: 2 Chirality restraints: 5318 Sorted by residual: chirality pdb=" CA PRO D 502 " pdb=" N PRO D 502 " pdb=" C PRO D 502 " pdb=" CB PRO D 502 " both_signs ideal model delta sigma weight residual False 2.72 3.14 -0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" C1' DC N 13 " pdb=" O4' DC N 13 " pdb=" C2' DC N 13 " pdb=" N1 DC N 13 " both_signs ideal model delta sigma weight residual False 2.47 2.86 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C1' C R 5 " pdb=" O4' C R 5 " pdb=" C2' C R 5 " pdb=" N1 C R 5 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 5315 not shown) Planarity restraints: 5867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG T 28 " -0.063 2.00e-02 2.50e+03 5.44e-02 8.89e+01 pdb=" N9 DG T 28 " 0.152 2.00e-02 2.50e+03 pdb=" C8 DG T 28 " -0.089 2.00e-02 2.50e+03 pdb=" N7 DG T 28 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DG T 28 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DG T 28 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG T 28 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG T 28 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG T 28 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG T 28 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DG T 28 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG T 28 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N 22 " 0.029 2.00e-02 2.50e+03 3.75e-02 3.52e+01 pdb=" N1 DT N 22 " 0.054 2.00e-02 2.50e+03 pdb=" C2 DT N 22 " -0.089 2.00e-02 2.50e+03 pdb=" O2 DT N 22 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT N 22 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DT N 22 " 0.011 2.00e-02 2.50e+03 pdb=" O4 DT N 22 " 0.031 2.00e-02 2.50e+03 pdb=" C5 DT N 22 " -0.011 2.00e-02 2.50e+03 pdb=" C7 DT N 22 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DT N 22 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 12 " -0.071 2.00e-02 2.50e+03 3.87e-02 3.37e+01 pdb=" N1 DC N 12 " 0.088 2.00e-02 2.50e+03 pdb=" C2 DC N 12 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC N 12 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC N 12 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC N 12 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC N 12 " -0.023 2.00e-02 2.50e+03 pdb=" C5 DC N 12 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DC N 12 " 0.004 2.00e-02 2.50e+03 ... (remaining 5864 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 200 2.54 - 3.13: 25549 3.13 - 3.72: 52204 3.72 - 4.31: 73711 4.31 - 4.90: 123768 Nonbonded interactions: 275432 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1500 " model vdw 1.945 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1500 " model vdw 2.053 2.170 nonbonded pdb=" OG SER D 210 " pdb=" OP1 DG T 5 " model vdw 2.080 3.040 nonbonded pdb=" OG SER F 842 " pdb=" OG1 THR F 849 " model vdw 2.129 3.040 nonbonded pdb=" OG1 THR F 227 " pdb=" OG1 THR F 460 " model vdw 2.164 3.040 ... (remaining 275427 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 'A' and resid 4 through 235) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 36.380 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.010 0.206 34592 Z= 0.432 Angle : 0.671 17.328 47104 Z= 0.387 Chirality : 0.056 0.426 5318 Planarity : 0.004 0.054 5867 Dihedral : 12.551 157.043 13531 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.13), residues: 4066 helix: 1.79 (0.14), residues: 1459 sheet: 0.87 (0.20), residues: 647 loop : 0.40 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 451 TYR 0.025 0.002 TYR F 518 PHE 0.017 0.002 PHE C 514 TRP 0.015 0.002 TRP F 560 HIS 0.009 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00988 (34572) covalent geometry : angle 0.66694 (47074) hydrogen bonds : bond 0.12738 ( 1604) hydrogen bonds : angle 5.65531 ( 4429) metal coordination : bond 0.01719 ( 20) metal coordination : angle 3.12814 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1097 time to evaluate : 1.013 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: A 9 LEU cc_start: 0.8756 (mt) cc_final: 0.8521 (mt) REVERT: A 20 SER cc_start: 0.8531 (t) cc_final: 0.8327 (p) REVERT: A 60 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 76 GLU cc_start: 0.8102 (mp0) cc_final: 0.7521 (mp0) REVERT: A 170 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7581 (ttm170) REVERT: A 174 ASP cc_start: 0.8460 (m-30) cc_final: 0.8156 (m-30) REVERT: A 198 LEU cc_start: 0.8426 (mt) cc_final: 0.8201 (mm) REVERT: A 215 GLU cc_start: 0.7597 (tt0) cc_final: 0.7111 (tt0) REVERT: B 7 GLU cc_start: 0.7555 (tt0) cc_final: 0.7266 (tt0) REVERT: B 28 LEU cc_start: 0.8625 (mt) cc_final: 0.8392 (mt) REVERT: B 51 MET cc_start: 0.8849 (mmm) cc_final: 0.8638 (mmp) REVERT: B 58 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7461 (mt-10) REVERT: B 60 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7140 (mt-10) REVERT: B 76 GLU cc_start: 0.7504 (mp0) cc_final: 0.7220 (mp0) REVERT: B 97 GLU cc_start: 0.7593 (tt0) cc_final: 0.7291 (tt0) REVERT: B 110 VAL cc_start: 0.8402 (t) cc_final: 0.8082 (p) REVERT: B 145 LYS cc_start: 0.8299 (tttt) cc_final: 0.7888 (tttt) REVERT: B 148 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.8232 (ttp-170) REVERT: B 171 LEU cc_start: 0.8653 (mt) cc_final: 0.8250 (mm) REVERT: B 174 ASP cc_start: 0.7651 (m-30) cc_final: 0.7297 (m-30) REVERT: B 188 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 200 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8470 (ttpp) REVERT: B 205 MET cc_start: 0.8416 (tpp) cc_final: 0.8041 (ttp) REVERT: B 212 ASP cc_start: 0.7189 (p0) cc_final: 0.6879 (p0) REVERT: B 215 GLU cc_start: 0.7777 (tp30) cc_final: 0.7459 (tp30) REVERT: C 101 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7989 (ttm110) REVERT: C 115 LYS cc_start: 0.8806 (pttt) cc_final: 0.8261 (ptmt) REVERT: C 122 VAL cc_start: 0.8911 (t) cc_final: 0.8626 (p) REVERT: C 227 LYS cc_start: 0.7834 (mttt) cc_final: 0.7529 (mttp) REVERT: C 315 MET cc_start: 0.6937 (mtp) cc_final: 0.6695 (mtp) REVERT: C 321 LEU cc_start: 0.9040 (mt) cc_final: 0.8786 (mt) REVERT: C 336 LEU cc_start: 0.8584 (pp) cc_final: 0.8376 (pp) REVERT: C 365 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7184 (mm-30) REVERT: C 407 ARG cc_start: 0.7946 (mmt180) cc_final: 0.7556 (mmt180) REVERT: C 413 GLU cc_start: 0.7644 (mp0) cc_final: 0.7334 (mp0) REVERT: C 476 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8709 (mttp) REVERT: C 490 GLN cc_start: 0.8479 (tp40) cc_final: 0.8276 (tp40) REVERT: C 546 GLU cc_start: 0.7723 (mp0) cc_final: 0.7391 (mp0) REVERT: C 547 VAL cc_start: 0.8987 (t) cc_final: 0.8707 (p) REVERT: C 628 HIS cc_start: 0.8447 (m-70) cc_final: 0.8154 (m90) REVERT: C 805 MET cc_start: 0.8945 (ptm) cc_final: 0.8719 (ptp) REVERT: C 854 ILE cc_start: 0.8791 (mt) cc_final: 0.8557 (mm) REVERT: C 859 GLU cc_start: 0.7357 (tp30) cc_final: 0.6937 (tp30) REVERT: C 862 LEU cc_start: 0.8326 (mp) cc_final: 0.8092 (mm) REVERT: C 914 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7692 (ttpp) REVERT: C 916 SER cc_start: 0.8513 (m) cc_final: 0.8090 (p) REVERT: C 949 GLU cc_start: 0.7844 (tt0) cc_final: 0.7494 (tt0) REVERT: C 954 LYS cc_start: 0.8393 (mttm) cc_final: 0.8173 (ttmm) REVERT: C 958 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7866 (ttmm) REVERT: C 1032 LYS cc_start: 0.8408 (tttp) cc_final: 0.8054 (tppp) REVERT: C 1140 LYS cc_start: 0.8242 (mttp) cc_final: 0.7858 (mtmm) REVERT: C 1155 VAL cc_start: 0.8535 (t) cc_final: 0.8324 (m) REVERT: C 1170 MET cc_start: 0.8688 (mmm) cc_final: 0.8400 (mmm) REVERT: C 1174 GLU cc_start: 0.7872 (tp30) cc_final: 0.7606 (tp30) REVERT: C 1217 THR cc_start: 0.8932 (p) cc_final: 0.8707 (m) REVERT: D 69 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6952 (mt-10) REVERT: D 79 LYS cc_start: 0.8589 (pttt) cc_final: 0.8291 (ptmt) REVERT: D 83 VAL cc_start: 0.8822 (t) cc_final: 0.8519 (p) REVERT: D 130 MET cc_start: 0.8170 (ttt) cc_final: 0.7952 (ttp) REVERT: D 142 GLU cc_start: 0.7764 (pt0) cc_final: 0.7542 (pt0) REVERT: D 153 ASN cc_start: 0.7929 (t0) cc_final: 0.7071 (t0) REVERT: D 154 LEU cc_start: 0.8762 (mt) cc_final: 0.8501 (mm) REVERT: D 177 ASP cc_start: 0.7867 (t0) cc_final: 0.7519 (t70) REVERT: D 180 MET cc_start: 0.8293 (mtt) cc_final: 0.8048 (mtm) REVERT: D 197 GLU cc_start: 0.8290 (tp30) cc_final: 0.8061 (mm-30) REVERT: D 213 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7733 (mmmt) REVERT: D 215 LYS cc_start: 0.8165 (tttp) cc_final: 0.7847 (tttp) REVERT: D 372 MET cc_start: 0.8666 (mtp) cc_final: 0.8438 (mtp) REVERT: D 398 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7935 (mtmt) REVERT: D 399 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7745 (ttmm) REVERT: D 564 VAL cc_start: 0.8932 (t) cc_final: 0.8712 (p) REVERT: D 649 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7674 (mmmm) REVERT: D 652 GLU cc_start: 0.7691 (pt0) cc_final: 0.7330 (pt0) REVERT: D 656 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7474 (mt-10) REVERT: D 667 GLN cc_start: 0.7830 (tt0) cc_final: 0.7566 (tt0) REVERT: D 695 LYS cc_start: 0.8195 (tptm) cc_final: 0.7949 (tttt) REVERT: D 697 MET cc_start: 0.8705 (ttp) cc_final: 0.8351 (ttp) REVERT: D 698 MET cc_start: 0.8421 (tpt) cc_final: 0.8162 (mmp) REVERT: D 714 GLU cc_start: 0.7842 (tt0) cc_final: 0.7567 (tt0) REVERT: D 811 GLU cc_start: 0.7801 (pt0) cc_final: 0.7575 (pt0) REVERT: D 850 LYS cc_start: 0.8229 (tttt) cc_final: 0.7968 (ttmm) REVERT: D 1025 MET cc_start: 0.6650 (ttp) cc_final: 0.6441 (ttp) REVERT: D 1221 LEU cc_start: 0.8707 (tp) cc_final: 0.8458 (tm) REVERT: D 1266 ILE cc_start: 0.8686 (mm) cc_final: 0.8308 (mt) REVERT: D 1268 ASN cc_start: 0.7990 (t0) cc_final: 0.7683 (t0) REVERT: D 1276 GLU cc_start: 0.7743 (mp0) cc_final: 0.7358 (mm-30) REVERT: D 1278 GLU cc_start: 0.7717 (tt0) cc_final: 0.7503 (tt0) REVERT: D 1305 ASP cc_start: 0.7998 (m-30) cc_final: 0.7777 (m-30) REVERT: D 1311 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8249 (mtpp) REVERT: F 24 ASP cc_start: 0.7664 (t0) cc_final: 0.7343 (t0) REVERT: F 102 LYS cc_start: 0.8289 (mttm) cc_final: 0.8034 (mttm) REVERT: F 171 MET cc_start: 0.8650 (mtp) cc_final: 0.8343 (mtm) REVERT: F 186 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8224 (tppp) REVERT: F 208 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7689 (mm-30) REVERT: F 212 LYS cc_start: 0.8759 (mttt) cc_final: 0.8451 (mttt) REVERT: F 246 PHE cc_start: 0.8220 (t80) cc_final: 0.7802 (t80) REVERT: F 304 THR cc_start: 0.8779 (m) cc_final: 0.8321 (p) REVERT: F 347 TYR cc_start: 0.7814 (m-80) cc_final: 0.7349 (m-80) REVERT: F 382 ASP cc_start: 0.8351 (p0) cc_final: 0.8013 (p0) REVERT: F 395 TRP cc_start: 0.8587 (t60) cc_final: 0.8258 (t60) REVERT: F 422 LEU cc_start: 0.7903 (pp) cc_final: 0.7433 (pp) REVERT: F 432 ASP cc_start: 0.7036 (p0) cc_final: 0.6771 (p0) REVERT: F 541 ASP cc_start: 0.8090 (m-30) cc_final: 0.7889 (m-30) REVERT: F 546 MET cc_start: 0.7651 (tpt) cc_final: 0.7446 (tpp) REVERT: F 547 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7739 (tp30) REVERT: F 568 PHE cc_start: 0.8630 (t80) cc_final: 0.8428 (t80) REVERT: F 580 LYS cc_start: 0.8421 (mttt) cc_final: 0.7547 (mtpp) REVERT: F 711 CYS cc_start: 0.6490 (t) cc_final: 0.6216 (t) outliers start: 3 outliers final: 1 residues processed: 1100 average time/residue: 0.7886 time to fit residues: 1004.8302 Evaluate side-chains 948 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 947 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 736 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0020 chunk 401 optimal weight: 0.0030 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 HIS B 132 HIS C 214 ASN C 330 HIS C 518 ASN C 613 ASN C 618 GLN C 622 ASN C1017 GLN C1070 HIS C1134 GLN C1256 GLN D 157 GLN D 206 ASN D 232 ASN D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN D 739 GLN D 792 ASN D1086 ASN D1235 ASN D1259 GLN F 365 HIS F 468 GLN F 533 ASN F 566 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128218 restraints weight = 48759.050| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.89 r_work: 0.3450 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34592 Z= 0.124 Angle : 0.533 7.982 47104 Z= 0.281 Chirality : 0.041 0.168 5318 Planarity : 0.004 0.046 5867 Dihedral : 14.007 167.108 5508 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.25 % Allowed : 12.73 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 1.53 (0.13), residues: 4066 helix: 2.06 (0.14), residues: 1481 sheet: 0.86 (0.21), residues: 630 loop : 0.35 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 271 TYR 0.021 0.001 TYR F 20 PHE 0.015 0.001 PHE C 405 TRP 0.013 0.001 TRP F 184 HIS 0.007 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00273 (34572) covalent geometry : angle 0.52698 (47074) hydrogen bonds : bond 0.04034 ( 1604) hydrogen bonds : angle 4.53289 ( 4429) metal coordination : bond 0.00589 ( 20) metal coordination : angle 3.16102 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 997 time to evaluate : 1.294 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: A 9 LEU cc_start: 0.8679 (mt) cc_final: 0.8450 (mt) REVERT: A 20 SER cc_start: 0.8503 (t) cc_final: 0.8292 (p) REVERT: A 76 GLU cc_start: 0.8128 (mp0) cc_final: 0.7542 (mp0) REVERT: A 174 ASP cc_start: 0.8535 (m-30) cc_final: 0.8303 (m-30) REVERT: A 215 GLU cc_start: 0.7998 (tt0) cc_final: 0.7764 (tt0) REVERT: B 7 GLU cc_start: 0.8021 (tt0) cc_final: 0.7701 (tt0) REVERT: B 51 MET cc_start: 0.8820 (mmm) cc_final: 0.8612 (mmp) REVERT: B 58 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8078 (mt-10) REVERT: B 60 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 97 GLU cc_start: 0.7998 (tt0) cc_final: 0.7668 (tt0) REVERT: B 110 VAL cc_start: 0.8376 (t) cc_final: 0.8026 (p) REVERT: B 120 ASP cc_start: 0.8051 (m-30) cc_final: 0.7849 (m-30) REVERT: B 144 ILE cc_start: 0.8576 (pt) cc_final: 0.7999 (pp) REVERT: B 145 LYS cc_start: 0.8466 (tttt) cc_final: 0.8110 (tttt) REVERT: B 174 ASP cc_start: 0.7872 (m-30) cc_final: 0.7536 (m-30) REVERT: B 188 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 200 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8427 (ttpp) REVERT: B 205 MET cc_start: 0.8549 (tpp) cc_final: 0.8211 (ttp) REVERT: B 212 ASP cc_start: 0.7297 (p0) cc_final: 0.6859 (p0) REVERT: B 214 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7384 (mp0) REVERT: B 215 GLU cc_start: 0.7936 (tp30) cc_final: 0.7348 (tp30) REVERT: C 101 ARG cc_start: 0.8331 (ttm110) cc_final: 0.7955 (mtm110) REVERT: C 115 LYS cc_start: 0.8763 (pttt) cc_final: 0.8260 (ptmt) REVERT: C 119 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7157 (mt-10) REVERT: C 122 VAL cc_start: 0.8840 (t) cc_final: 0.8621 (p) REVERT: C 192 ASP cc_start: 0.8389 (m-30) cc_final: 0.8140 (m-30) REVERT: C 197 ARG cc_start: 0.8274 (ptp-110) cc_final: 0.7890 (ptp90) REVERT: C 227 LYS cc_start: 0.7949 (mttt) cc_final: 0.7633 (mttp) REVERT: C 299 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8104 (ptpp) REVERT: C 315 MET cc_start: 0.7510 (mtp) cc_final: 0.7241 (mtp) REVERT: C 316 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7232 (mm-30) REVERT: C 321 LEU cc_start: 0.9217 (mt) cc_final: 0.8857 (mt) REVERT: C 324 LYS cc_start: 0.9060 (mttt) cc_final: 0.8775 (mttt) REVERT: C 365 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7397 (mm-30) REVERT: C 407 ARG cc_start: 0.8428 (mmt180) cc_final: 0.7987 (mmt180) REVERT: C 413 GLU cc_start: 0.7954 (mp0) cc_final: 0.7633 (mp0) REVERT: C 476 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8698 (mttp) REVERT: C 490 GLN cc_start: 0.8422 (tp40) cc_final: 0.8215 (tp40) REVERT: C 492 MET cc_start: 0.8233 (mtp) cc_final: 0.7958 (mtp) REVERT: C 546 GLU cc_start: 0.7954 (mp0) cc_final: 0.7708 (mp0) REVERT: C 611 GLU cc_start: 0.7961 (tt0) cc_final: 0.7736 (tt0) REVERT: C 778 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7979 (mm-30) REVERT: C 785 ASP cc_start: 0.8168 (m-30) cc_final: 0.7934 (m-30) REVERT: C 805 MET cc_start: 0.8937 (ptm) cc_final: 0.8699 (ptp) REVERT: C 854 ILE cc_start: 0.8719 (mt) cc_final: 0.8457 (mm) REVERT: C 859 GLU cc_start: 0.7506 (tp30) cc_final: 0.7001 (tp30) REVERT: C 862 LEU cc_start: 0.8266 (mp) cc_final: 0.8038 (mm) REVERT: C 914 LYS cc_start: 0.8086 (ttpt) cc_final: 0.7619 (ttpp) REVERT: C 949 GLU cc_start: 0.8166 (tt0) cc_final: 0.7828 (tt0) REVERT: C 958 LYS cc_start: 0.8143 (ttmm) cc_final: 0.7931 (ttmm) REVERT: C 1032 LYS cc_start: 0.8493 (tttp) cc_final: 0.8175 (tppp) REVERT: C 1037 THR cc_start: 0.8778 (m) cc_final: 0.8550 (p) REVERT: C 1082 ILE cc_start: 0.8692 (mt) cc_final: 0.8481 (tt) REVERT: C 1140 LYS cc_start: 0.8498 (mttp) cc_final: 0.8223 (mtmm) REVERT: C 1170 MET cc_start: 0.8710 (mmm) cc_final: 0.8455 (mmm) REVERT: C 1174 GLU cc_start: 0.8035 (tp30) cc_final: 0.7761 (tp30) REVERT: C 1216 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7824 (mtp180) REVERT: C 1340 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7680 (mt-10) REVERT: D 21 LYS cc_start: 0.8488 (tptm) cc_final: 0.8281 (tttm) REVERT: D 50 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8532 (mtmp) REVERT: D 52 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7888 (mp0) REVERT: D 69 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7206 (mt-10) REVERT: D 79 LYS cc_start: 0.8677 (pttt) cc_final: 0.8371 (ptmt) REVERT: D 83 VAL cc_start: 0.8839 (t) cc_final: 0.8525 (p) REVERT: D 130 MET cc_start: 0.8221 (ttt) cc_final: 0.7936 (ttp) REVERT: D 133 ARG cc_start: 0.8235 (mtt180) cc_final: 0.8034 (mmt180) REVERT: D 153 ASN cc_start: 0.7937 (t0) cc_final: 0.7730 (t0) REVERT: D 157 GLN cc_start: 0.8709 (mt0) cc_final: 0.8357 (tt0) REVERT: D 175 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7845 (tm-30) REVERT: D 177 ASP cc_start: 0.7884 (t0) cc_final: 0.7168 (p0) REVERT: D 197 GLU cc_start: 0.8315 (tp30) cc_final: 0.8055 (mm-30) REVERT: D 202 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8409 (mtt90) REVERT: D 213 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7702 (mmmt) REVERT: D 215 LYS cc_start: 0.8088 (tttp) cc_final: 0.7729 (tttp) REVERT: D 281 ARG cc_start: 0.8657 (ttt90) cc_final: 0.8419 (ttt90) REVERT: D 398 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8002 (mtmt) REVERT: D 399 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7796 (mtpp) REVERT: D 403 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7742 (mtm-85) REVERT: D 547 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7780 (mtt90) REVERT: D 564 VAL cc_start: 0.8909 (t) cc_final: 0.8685 (p) REVERT: D 656 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7714 (mt-10) REVERT: D 667 GLN cc_start: 0.7781 (tt0) cc_final: 0.7510 (tt0) REVERT: D 695 LYS cc_start: 0.8310 (tptm) cc_final: 0.8014 (tttt) REVERT: D 697 MET cc_start: 0.8670 (ttp) cc_final: 0.8364 (ttp) REVERT: D 698 MET cc_start: 0.8486 (tpt) cc_final: 0.8238 (mmp) REVERT: D 818 GLU cc_start: 0.7673 (mp0) cc_final: 0.7296 (mp0) REVERT: D 850 LYS cc_start: 0.8292 (tttt) cc_final: 0.8015 (ttmm) REVERT: D 871 LEU cc_start: 0.8288 (tt) cc_final: 0.7941 (tp) REVERT: D 874 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7281 (mt-10) REVERT: D 876 SER cc_start: 0.8683 (m) cc_final: 0.8168 (p) REVERT: D 1025 MET cc_start: 0.7059 (ttp) cc_final: 0.6728 (ttp) REVERT: D 1189 MET cc_start: 0.7628 (mtp) cc_final: 0.7398 (mtp) REVERT: D 1222 ARG cc_start: 0.8207 (ptt-90) cc_final: 0.7834 (ptt-90) REVERT: D 1231 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7747 (ttm-80) REVERT: D 1266 ILE cc_start: 0.8752 (mm) cc_final: 0.8324 (mt) REVERT: D 1268 ASN cc_start: 0.8113 (t0) cc_final: 0.7808 (t0) REVERT: D 1276 GLU cc_start: 0.7981 (mp0) cc_final: 0.7523 (mm-30) REVERT: D 1361 THR cc_start: 0.8616 (m) cc_final: 0.8372 (p) REVERT: E 55 GLU cc_start: 0.7975 (tt0) cc_final: 0.7694 (tt0) REVERT: F 24 ASP cc_start: 0.7793 (t0) cc_final: 0.7494 (t0) REVERT: F 68 VAL cc_start: 0.8741 (p) cc_final: 0.8496 (t) REVERT: F 171 MET cc_start: 0.8599 (mtp) cc_final: 0.8386 (mtm) REVERT: F 208 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7423 (tp30) REVERT: F 246 PHE cc_start: 0.8528 (t80) cc_final: 0.8102 (t80) REVERT: F 304 THR cc_start: 0.8232 (m) cc_final: 0.7758 (p) REVERT: F 343 PHE cc_start: 0.7484 (m-10) cc_final: 0.7011 (m-10) REVERT: F 382 ASP cc_start: 0.8470 (p0) cc_final: 0.8124 (p0) REVERT: F 395 TRP cc_start: 0.8385 (t60) cc_final: 0.8144 (t60) REVERT: F 432 ASP cc_start: 0.7809 (p0) cc_final: 0.7516 (p0) REVERT: F 457 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7164 (t70) REVERT: F 533 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7332 (m-40) REVERT: F 568 PHE cc_start: 0.8699 (t80) cc_final: 0.8491 (t80) REVERT: F 580 LYS cc_start: 0.8547 (mttt) cc_final: 0.8316 (mtpt) REVERT: F 632 THR cc_start: 0.7574 (m) cc_final: 0.7319 (p) REVERT: F 763 CYS cc_start: 0.7539 (m) cc_final: 0.7182 (m) REVERT: F 774 ASP cc_start: 0.7857 (t0) cc_final: 0.7391 (t0) outliers start: 78 outliers final: 20 residues processed: 1020 average time/residue: 0.8607 time to fit residues: 1020.0063 Evaluate side-chains 960 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 934 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1216 ARG Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 1079 LYS Chi-restraints excluded: chain D residue 1283 SER Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 533 ASN Chi-restraints excluded: chain F residue 645 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 34 optimal weight: 10.0000 chunk 136 optimal weight: 0.4980 chunk 363 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 chunk 328 optimal weight: 1.9990 chunk 388 optimal weight: 0.5980 chunk 269 optimal weight: 3.9990 chunk 294 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN C 214 ASN C 518 ASN C 613 ASN C1134 GLN C1236 ASN C1264 GLN D 80 HIS D 206 ASN D 232 ASN D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 736 GLN D 739 GLN D1235 ASN ** D1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN F 163 ASN F 165 GLN F 353 ASN F 365 HIS F 533 ASN F 545 GLN F 548 ASN F 574 GLN F 591 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122285 restraints weight = 47800.737| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.12 r_work: 0.3386 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 34592 Z= 0.290 Angle : 0.616 10.736 47104 Z= 0.324 Chirality : 0.046 0.185 5318 Planarity : 0.004 0.045 5867 Dihedral : 14.180 169.721 5507 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.91 % Allowed : 15.55 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 1.17 (0.13), residues: 4066 helix: 1.80 (0.13), residues: 1479 sheet: 0.67 (0.20), residues: 650 loop : 0.10 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 271 TYR 0.022 0.002 TYR F 20 PHE 0.021 0.002 PHE F 534 TRP 0.017 0.002 TRP F 184 HIS 0.010 0.002 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00664 (34572) covalent geometry : angle 0.60458 (47074) hydrogen bonds : bond 0.04881 ( 1604) hydrogen bonds : angle 4.65241 ( 4429) metal coordination : bond 0.01539 ( 20) metal coordination : angle 4.61513 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 963 time to evaluate : 1.178 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: A 9 LEU cc_start: 0.8724 (mt) cc_final: 0.8477 (mt) REVERT: A 76 GLU cc_start: 0.8148 (mp0) cc_final: 0.7593 (mp0) REVERT: A 170 ARG cc_start: 0.8567 (ttm170) cc_final: 0.8355 (ttm-80) REVERT: A 174 ASP cc_start: 0.8563 (m-30) cc_final: 0.8272 (m-30) REVERT: B 7 GLU cc_start: 0.8027 (tt0) cc_final: 0.7694 (tt0) REVERT: B 58 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8068 (mt-10) REVERT: B 60 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7769 (mt-10) REVERT: B 76 GLU cc_start: 0.7591 (mp0) cc_final: 0.7245 (mp0) REVERT: B 97 GLU cc_start: 0.8118 (tt0) cc_final: 0.7895 (tt0) REVERT: B 110 VAL cc_start: 0.8416 (t) cc_final: 0.8013 (p) REVERT: B 120 ASP cc_start: 0.8035 (m-30) cc_final: 0.7797 (m-30) REVERT: B 144 ILE cc_start: 0.8569 (pt) cc_final: 0.7993 (pp) REVERT: B 145 LYS cc_start: 0.8497 (tttt) cc_final: 0.8290 (tttt) REVERT: B 174 ASP cc_start: 0.7878 (m-30) cc_final: 0.7508 (m-30) REVERT: B 188 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8001 (mt-10) REVERT: B 200 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8450 (ttpp) REVERT: B 212 ASP cc_start: 0.7438 (p0) cc_final: 0.7026 (p0) REVERT: B 214 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7460 (mp0) REVERT: B 215 GLU cc_start: 0.8044 (tp30) cc_final: 0.7470 (tp30) REVERT: C 101 ARG cc_start: 0.8356 (ttm110) cc_final: 0.8062 (mtm110) REVERT: C 115 LYS cc_start: 0.8763 (pttt) cc_final: 0.8276 (ptmt) REVERT: C 119 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7240 (mt-10) REVERT: C 122 VAL cc_start: 0.8862 (t) cc_final: 0.8623 (p) REVERT: C 197 ARG cc_start: 0.8265 (ptp-110) cc_final: 0.7924 (ptp90) REVERT: C 227 LYS cc_start: 0.8039 (mttt) cc_final: 0.7714 (mttp) REVERT: C 295 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7441 (mmtm) REVERT: C 299 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8179 (ttpp) REVERT: C 315 MET cc_start: 0.7556 (mtp) cc_final: 0.7216 (mtp) REVERT: C 316 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7222 (mm-30) REVERT: C 320 ASP cc_start: 0.8338 (p0) cc_final: 0.8015 (p0) REVERT: C 321 LEU cc_start: 0.9214 (mt) cc_final: 0.8669 (mt) REVERT: C 324 LYS cc_start: 0.9100 (mttt) cc_final: 0.8737 (mppt) REVERT: C 365 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7503 (mm-30) REVERT: C 407 ARG cc_start: 0.8422 (mmt180) cc_final: 0.8000 (mmt180) REVERT: C 413 GLU cc_start: 0.7980 (mp0) cc_final: 0.7639 (mp0) REVERT: C 476 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8820 (mttp) REVERT: C 490 GLN cc_start: 0.8483 (tp40) cc_final: 0.8217 (tp40) REVERT: C 628 HIS cc_start: 0.8342 (m-70) cc_final: 0.8123 (m90) REVERT: C 778 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8022 (mm-30) REVERT: C 805 MET cc_start: 0.8917 (ptm) cc_final: 0.8670 (ptp) REVERT: C 854 ILE cc_start: 0.8739 (mt) cc_final: 0.8473 (mm) REVERT: C 859 GLU cc_start: 0.7674 (tp30) cc_final: 0.7161 (tp30) REVERT: C 862 LEU cc_start: 0.8448 (mp) cc_final: 0.8201 (mm) REVERT: C 914 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7631 (ttpp) REVERT: C 949 GLU cc_start: 0.8139 (tt0) cc_final: 0.7828 (tt0) REVERT: C 1032 LYS cc_start: 0.8434 (tttp) cc_final: 0.8110 (tppp) REVERT: C 1140 LYS cc_start: 0.8624 (mttp) cc_final: 0.8336 (mtmm) REVERT: C 1170 MET cc_start: 0.8746 (mmm) cc_final: 0.8516 (mmm) REVERT: C 1174 GLU cc_start: 0.8081 (tp30) cc_final: 0.7784 (tp30) REVERT: C 1217 THR cc_start: 0.8911 (p) cc_final: 0.8623 (m) REVERT: C 1303 LYS cc_start: 0.8636 (mtmp) cc_final: 0.8367 (mttp) REVERT: C 1340 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7552 (mt-10) REVERT: D 21 LYS cc_start: 0.8539 (tptm) cc_final: 0.8322 (tttm) REVERT: D 52 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7889 (mp0) REVERT: D 69 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7311 (mt-10) REVERT: D 79 LYS cc_start: 0.8709 (pttt) cc_final: 0.8367 (ptmt) REVERT: D 83 VAL cc_start: 0.8818 (t) cc_final: 0.8613 (p) REVERT: D 130 MET cc_start: 0.8350 (ttt) cc_final: 0.8081 (ttp) REVERT: D 157 GLN cc_start: 0.8743 (mt0) cc_final: 0.8395 (tt0) REVERT: D 174 ASP cc_start: 0.8262 (m-30) cc_final: 0.8042 (m-30) REVERT: D 177 ASP cc_start: 0.7899 (t0) cc_final: 0.7613 (t70) REVERT: D 197 GLU cc_start: 0.8301 (tp30) cc_final: 0.8031 (mm-30) REVERT: D 202 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.8370 (mtt90) REVERT: D 213 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7811 (mmmt) REVERT: D 215 LYS cc_start: 0.8160 (tttp) cc_final: 0.7797 (tttp) REVERT: D 225 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: D 281 ARG cc_start: 0.8685 (ttt90) cc_final: 0.8442 (ttt90) REVERT: D 398 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8037 (mtmt) REVERT: D 403 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7650 (mtm-85) REVERT: D 547 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8120 (mtt90) REVERT: D 564 VAL cc_start: 0.8906 (t) cc_final: 0.8667 (p) REVERT: D 567 THR cc_start: 0.8885 (t) cc_final: 0.8607 (m) REVERT: D 667 GLN cc_start: 0.7860 (tt0) cc_final: 0.7600 (tt0) REVERT: D 669 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7727 (mm-40) REVERT: D 697 MET cc_start: 0.8698 (ttp) cc_final: 0.8456 (ttp) REVERT: D 698 MET cc_start: 0.8554 (tpt) cc_final: 0.8269 (mmp) REVERT: D 850 LYS cc_start: 0.8270 (tttt) cc_final: 0.7986 (ttmm) REVERT: D 874 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7354 (mt-10) REVERT: D 1025 MET cc_start: 0.7131 (ttp) cc_final: 0.6802 (ttp) REVERT: D 1222 ARG cc_start: 0.8180 (ptt-90) cc_final: 0.7964 (ptt-90) REVERT: D 1231 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7808 (ttm-80) REVERT: D 1268 ASN cc_start: 0.8240 (t0) cc_final: 0.7872 (t0) REVERT: D 1276 GLU cc_start: 0.7967 (mp0) cc_final: 0.7472 (mp0) REVERT: D 1284 ARG cc_start: 0.8666 (mmt-90) cc_final: 0.8465 (mmt-90) REVERT: D 1311 LYS cc_start: 0.8530 (mtpm) cc_final: 0.8312 (mtpp) REVERT: E 55 GLU cc_start: 0.8038 (tt0) cc_final: 0.7767 (tt0) REVERT: F 68 VAL cc_start: 0.8814 (p) cc_final: 0.8555 (t) REVERT: F 69 ASN cc_start: 0.8002 (t0) cc_final: 0.7720 (t0) REVERT: F 102 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8260 (mmtt) REVERT: F 104 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.6329 (t0) REVERT: F 208 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7510 (tp30) REVERT: F 246 PHE cc_start: 0.8504 (t80) cc_final: 0.8051 (t80) REVERT: F 304 THR cc_start: 0.8370 (m) cc_final: 0.7755 (p) REVERT: F 382 ASP cc_start: 0.8480 (p0) cc_final: 0.8182 (p0) REVERT: F 432 ASP cc_start: 0.7768 (p0) cc_final: 0.7513 (p0) REVERT: F 574 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8003 (mm-40) REVERT: F 763 CYS cc_start: 0.7428 (m) cc_final: 0.7037 (m) outliers start: 101 outliers final: 35 residues processed: 1002 average time/residue: 0.8324 time to fit residues: 966.5225 Evaluate side-chains 968 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 927 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1283 SER Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 345 LYS Chi-restraints excluded: chain F residue 645 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 243 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 380 optimal weight: 4.9990 chunk 237 optimal weight: 0.0470 chunk 66 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN C 214 ASN C 613 ASN C1134 GLN C1264 GLN D 206 ASN D 232 ASN D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN D1235 ASN D1295 ASN F 163 ASN F 240 HIS F 365 HIS F 738 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124833 restraints weight = 47712.711| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.86 r_work: 0.3422 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34592 Z= 0.151 Angle : 0.550 10.281 47104 Z= 0.287 Chirality : 0.042 0.199 5318 Planarity : 0.004 0.050 5867 Dihedral : 14.094 172.075 5507 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.85 % Allowed : 16.99 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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 (0.13), residues: 4066 helix: 2.01 (0.13), residues: 1474 sheet: 0.63 (0.20), residues: 645 loop : 0.15 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 271 TYR 0.024 0.001 TYR F 20 PHE 0.013 0.001 PHE C 405 TRP 0.015 0.001 TRP F 395 HIS 0.005 0.001 HIS C 628 Details of bonding type rmsd covalent geometry : bond 0.00341 (34572) covalent geometry : angle 0.54339 (47074) hydrogen bonds : bond 0.04012 ( 1604) hydrogen bonds : angle 4.42753 ( 4429) metal coordination : bond 0.00762 ( 20) metal coordination : angle 3.48242 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 947 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8735 (mt) cc_final: 0.8498 (mt) REVERT: A 76 GLU cc_start: 0.8112 (mp0) cc_final: 0.7567 (mp0) REVERT: A 174 ASP cc_start: 0.8537 (m-30) cc_final: 0.8314 (m-30) REVERT: A 215 GLU cc_start: 0.8101 (tt0) cc_final: 0.7769 (tt0) REVERT: B 7 GLU cc_start: 0.8010 (tt0) cc_final: 0.7699 (tt0) REVERT: B 58 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7974 (mt-10) REVERT: B 60 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7718 (mt-10) REVERT: B 76 GLU cc_start: 0.7550 (mp0) cc_final: 0.7269 (mp0) REVERT: B 97 GLU cc_start: 0.8068 (tt0) cc_final: 0.7814 (tt0) REVERT: B 110 VAL cc_start: 0.8410 (t) cc_final: 0.8048 (p) REVERT: B 120 ASP cc_start: 0.8025 (m-30) cc_final: 0.7777 (m-30) REVERT: B 141 SER cc_start: 0.8818 (t) cc_final: 0.8544 (t) REVERT: B 144 ILE cc_start: 0.8589 (pt) cc_final: 0.8087 (pp) REVERT: B 145 LYS cc_start: 0.8478 (tttt) cc_final: 0.8245 (tttt) REVERT: B 174 ASP cc_start: 0.7886 (m-30) cc_final: 0.7527 (m-30) REVERT: B 188 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8119 (mt-10) REVERT: B 205 MET cc_start: 0.8585 (tpp) cc_final: 0.8231 (ttp) REVERT: B 212 ASP cc_start: 0.7290 (p0) cc_final: 0.6855 (p0) REVERT: B 214 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7442 (mp0) REVERT: B 215 GLU cc_start: 0.7967 (tp30) cc_final: 0.7396 (tp30) REVERT: C 101 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7959 (mtm110) REVERT: C 115 LYS cc_start: 0.8760 (pttt) cc_final: 0.8272 (ptmt) REVERT: C 119 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7126 (mt-10) REVERT: C 122 VAL cc_start: 0.8843 (t) cc_final: 0.8600 (p) REVERT: C 197 ARG cc_start: 0.8260 (ptp-110) cc_final: 0.7951 (ptp90) REVERT: C 227 LYS cc_start: 0.8044 (mttt) cc_final: 0.7726 (mttp) REVERT: C 295 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7336 (mmtm) REVERT: C 299 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8178 (ttpp) REVERT: C 315 MET cc_start: 0.7506 (mtp) cc_final: 0.7146 (mtp) REVERT: C 316 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7238 (mm-30) REVERT: C 320 ASP cc_start: 0.8245 (p0) cc_final: 0.7691 (p0) REVERT: C 321 LEU cc_start: 0.9198 (mt) cc_final: 0.8560 (mt) REVERT: C 324 LYS cc_start: 0.9096 (mttt) cc_final: 0.8722 (mppt) REVERT: C 407 ARG cc_start: 0.8381 (mmt180) cc_final: 0.7952 (mmt180) REVERT: C 413 GLU cc_start: 0.7941 (mp0) cc_final: 0.7626 (mp0) REVERT: C 490 GLN cc_start: 0.8455 (tp40) cc_final: 0.8242 (tp40) REVERT: C 628 HIS cc_start: 0.8327 (m-70) cc_final: 0.8103 (m90) REVERT: C 778 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7961 (mm-30) REVERT: C 854 ILE cc_start: 0.8753 (mt) cc_final: 0.8479 (mm) REVERT: C 859 GLU cc_start: 0.7626 (tp30) cc_final: 0.7224 (tp30) REVERT: C 862 LEU cc_start: 0.8406 (mp) cc_final: 0.8121 (mm) REVERT: C 878 THR cc_start: 0.8753 (t) cc_final: 0.8498 (p) REVERT: C 914 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7606 (ttpp) REVERT: C 949 GLU cc_start: 0.8144 (tt0) cc_final: 0.7830 (tt0) REVERT: C 1032 LYS cc_start: 0.8440 (tttp) cc_final: 0.8140 (tppp) REVERT: C 1057 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8248 (mtmm) REVERT: C 1140 LYS cc_start: 0.8543 (mttp) cc_final: 0.8237 (mtmm) REVERT: C 1170 MET cc_start: 0.8721 (mmm) cc_final: 0.8492 (mmm) REVERT: C 1174 GLU cc_start: 0.8080 (tp30) cc_final: 0.7774 (tp30) REVERT: C 1216 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7793 (mtp180) REVERT: C 1303 LYS cc_start: 0.8626 (mtmp) cc_final: 0.8416 (mttm) REVERT: C 1340 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7683 (mt-10) REVERT: D 69 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7248 (mt-10) REVERT: D 79 LYS cc_start: 0.8678 (pttt) cc_final: 0.8352 (ptmt) REVERT: D 130 MET cc_start: 0.8291 (ttt) cc_final: 0.8020 (ttp) REVERT: D 157 GLN cc_start: 0.8715 (mt0) cc_final: 0.8330 (tt0) REVERT: D 172 PHE cc_start: 0.8087 (m-10) cc_final: 0.7494 (m-10) REVERT: D 175 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7138 (tm-30) REVERT: D 177 ASP cc_start: 0.7916 (t0) cc_final: 0.7638 (t70) REVERT: D 197 GLU cc_start: 0.8269 (tp30) cc_final: 0.7963 (mm-30) REVERT: D 202 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8355 (mtt90) REVERT: D 213 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7749 (mmmt) REVERT: D 215 LYS cc_start: 0.8106 (tttp) cc_final: 0.7736 (tttp) REVERT: D 278 ARG cc_start: 0.8318 (ttm170) cc_final: 0.8046 (ttm170) REVERT: D 398 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8006 (mtmt) REVERT: D 403 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7665 (mtm-85) REVERT: D 547 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7783 (mtt90) REVERT: D 564 VAL cc_start: 0.8903 (t) cc_final: 0.8670 (p) REVERT: D 567 THR cc_start: 0.8890 (t) cc_final: 0.8595 (m) REVERT: D 649 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7835 (mmmm) REVERT: D 652 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: D 667 GLN cc_start: 0.7815 (tt0) cc_final: 0.7568 (tt0) REVERT: D 697 MET cc_start: 0.8677 (ttp) cc_final: 0.8471 (ttp) REVERT: D 698 MET cc_start: 0.8522 (tpt) cc_final: 0.8263 (mmp) REVERT: D 818 GLU cc_start: 0.7725 (mp0) cc_final: 0.7254 (mp0) REVERT: D 850 LYS cc_start: 0.8233 (tttt) cc_final: 0.7955 (ttmm) REVERT: D 873 GLU cc_start: 0.7983 (tt0) cc_final: 0.7699 (tt0) REVERT: D 1025 MET cc_start: 0.7111 (ttp) cc_final: 0.6770 (ttp) REVERT: D 1222 ARG cc_start: 0.8186 (ptt-90) cc_final: 0.7914 (ptt-90) REVERT: D 1231 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7770 (ttm-80) REVERT: D 1268 ASN cc_start: 0.8259 (t0) cc_final: 0.7902 (t0) REVERT: D 1276 GLU cc_start: 0.7942 (mp0) cc_final: 0.7457 (mm-30) REVERT: D 1311 LYS cc_start: 0.8495 (mtpm) cc_final: 0.8263 (mtpp) REVERT: D 1361 THR cc_start: 0.8719 (m) cc_final: 0.8307 (p) REVERT: E 55 GLU cc_start: 0.7993 (tt0) cc_final: 0.7705 (tt0) REVERT: F 68 VAL cc_start: 0.8810 (p) cc_final: 0.8540 (t) REVERT: F 69 ASN cc_start: 0.7964 (t0) cc_final: 0.7666 (t0) REVERT: F 102 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8247 (mmtt) REVERT: F 104 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.6104 (t0) REVERT: F 208 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: F 246 PHE cc_start: 0.8491 (t80) cc_final: 0.8035 (t80) REVERT: F 304 THR cc_start: 0.8319 (m) cc_final: 0.7764 (p) REVERT: F 382 ASP cc_start: 0.8494 (p0) cc_final: 0.8131 (p0) REVERT: F 427 ARG cc_start: 0.7535 (ptm160) cc_final: 0.7286 (ptm160) REVERT: F 432 ASP cc_start: 0.7600 (p0) cc_final: 0.7396 (p0) REVERT: F 568 PHE cc_start: 0.8688 (t80) cc_final: 0.8470 (t80) REVERT: F 580 LYS cc_start: 0.8541 (mttt) cc_final: 0.8235 (mtpp) REVERT: F 637 VAL cc_start: 0.8697 (t) cc_final: 0.8481 (m) REVERT: F 712 GLU cc_start: 0.7747 (pm20) cc_final: 0.7514 (pm20) REVERT: F 763 CYS cc_start: 0.7437 (m) cc_final: 0.7058 (m) outliers start: 99 outliers final: 42 residues processed: 988 average time/residue: 0.8654 time to fit residues: 992.5166 Evaluate side-chains 978 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 928 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1057 LYS Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1216 ARG Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1079 LYS Chi-restraints excluded: chain D residue 1283 SER Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 632 THR Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 709 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 90 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 171 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 348 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 410 optimal weight: 3.9990 chunk 357 optimal weight: 3.9990 chunk 333 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN C 214 ASN C 518 ASN C 613 ASN C 952 GLN C1134 GLN C1264 GLN D 206 ASN D 232 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN D 817 HIS D1235 ASN D1295 ASN F 77 HIS F 365 HIS F 533 ASN F 738 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.154732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.123691 restraints weight = 48015.656| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.09 r_work: 0.3409 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34592 Z= 0.159 Angle : 0.558 9.451 47104 Z= 0.291 Chirality : 0.042 0.217 5318 Planarity : 0.004 0.058 5867 Dihedral : 14.064 173.562 5507 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.08 % Allowed : 17.86 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 1.33 (0.13), residues: 4066 helix: 2.06 (0.13), residues: 1473 sheet: 0.61 (0.21), residues: 643 loop : 0.14 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 271 TYR 0.023 0.001 TYR F 20 PHE 0.016 0.001 PHE D1037 TRP 0.020 0.001 TRP F 395 HIS 0.007 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00363 (34572) covalent geometry : angle 0.55220 (47074) hydrogen bonds : bond 0.03983 ( 1604) hydrogen bonds : angle 4.39633 ( 4429) metal coordination : bond 0.00752 ( 20) metal coordination : angle 3.27345 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 936 time to evaluate : 1.164 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: A 9 LEU cc_start: 0.8737 (mt) cc_final: 0.8500 (mt) REVERT: A 25 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8336 (mtpp) REVERT: A 76 GLU cc_start: 0.8126 (mp0) cc_final: 0.7578 (mp0) REVERT: A 174 ASP cc_start: 0.8558 (m-30) cc_final: 0.8337 (m-30) REVERT: A 215 GLU cc_start: 0.8164 (tt0) cc_final: 0.7852 (tt0) REVERT: B 7 GLU cc_start: 0.8050 (tt0) cc_final: 0.7732 (tt0) REVERT: B 58 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 60 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 97 GLU cc_start: 0.8073 (tt0) cc_final: 0.7802 (tt0) REVERT: B 110 VAL cc_start: 0.8440 (t) cc_final: 0.8091 (p) REVERT: B 120 ASP cc_start: 0.8026 (m-30) cc_final: 0.7773 (m-30) REVERT: B 144 ILE cc_start: 0.8618 (pt) cc_final: 0.8139 (pp) REVERT: B 145 LYS cc_start: 0.8505 (tttt) cc_final: 0.8231 (tttt) REVERT: B 171 LEU cc_start: 0.8572 (mt) cc_final: 0.8247 (mm) REVERT: B 174 ASP cc_start: 0.7848 (m-30) cc_final: 0.7503 (m-30) REVERT: B 205 MET cc_start: 0.8605 (tpp) cc_final: 0.8180 (ttp) REVERT: B 212 ASP cc_start: 0.7304 (p0) cc_final: 0.6861 (p0) REVERT: B 214 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7518 (mp0) REVERT: B 215 GLU cc_start: 0.8019 (tp30) cc_final: 0.7517 (tp30) REVERT: C 101 ARG cc_start: 0.8339 (ttm110) cc_final: 0.8083 (ttm110) REVERT: C 115 LYS cc_start: 0.8735 (pttt) cc_final: 0.8280 (ptmt) REVERT: C 119 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7200 (mt-10) REVERT: C 122 VAL cc_start: 0.8857 (t) cc_final: 0.8621 (p) REVERT: C 197 ARG cc_start: 0.8289 (ptp-110) cc_final: 0.7904 (ptp90) REVERT: C 227 LYS cc_start: 0.8059 (mttt) cc_final: 0.7738 (mttp) REVERT: C 295 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7334 (mmtm) REVERT: C 299 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8189 (ttpp) REVERT: C 315 MET cc_start: 0.7520 (mtp) cc_final: 0.7149 (mtp) REVERT: C 316 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7261 (mm-30) REVERT: C 321 LEU cc_start: 0.9173 (mt) cc_final: 0.8769 (mt) REVERT: C 324 LYS cc_start: 0.9064 (mttt) cc_final: 0.8815 (mttt) REVERT: C 407 ARG cc_start: 0.8435 (mmt180) cc_final: 0.7994 (mmt180) REVERT: C 413 GLU cc_start: 0.7938 (mp0) cc_final: 0.7624 (mp0) REVERT: C 490 GLN cc_start: 0.8470 (tp40) cc_final: 0.8255 (tp40) REVERT: C 628 HIS cc_start: 0.8325 (m-70) cc_final: 0.8120 (m90) REVERT: C 778 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 854 ILE cc_start: 0.8759 (mt) cc_final: 0.8497 (mm) REVERT: C 859 GLU cc_start: 0.7662 (tp30) cc_final: 0.7323 (tp30) REVERT: C 862 LEU cc_start: 0.8438 (mp) cc_final: 0.8172 (mm) REVERT: C 878 THR cc_start: 0.8730 (t) cc_final: 0.8496 (p) REVERT: C 914 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7701 (ttpp) REVERT: C 949 GLU cc_start: 0.8183 (tt0) cc_final: 0.7876 (tt0) REVERT: C 1032 LYS cc_start: 0.8417 (tttp) cc_final: 0.8144 (tppp) REVERT: C 1057 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8342 (mtmm) REVERT: C 1140 LYS cc_start: 0.8529 (mttp) cc_final: 0.8165 (mtmm) REVERT: C 1170 MET cc_start: 0.8750 (mmm) cc_final: 0.8515 (mmm) REVERT: C 1174 GLU cc_start: 0.8129 (tp30) cc_final: 0.7833 (tp30) REVERT: C 1303 LYS cc_start: 0.8630 (mtmp) cc_final: 0.8424 (mttm) REVERT: C 1340 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7638 (mt-10) REVERT: D 50 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8521 (mtmp) REVERT: D 69 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7286 (mt-10) REVERT: D 79 LYS cc_start: 0.8676 (pttt) cc_final: 0.8362 (ptmt) REVERT: D 130 MET cc_start: 0.8336 (ttt) cc_final: 0.8066 (ttp) REVERT: D 155 GLU cc_start: 0.7128 (pm20) cc_final: 0.6832 (pm20) REVERT: D 157 GLN cc_start: 0.8712 (mt0) cc_final: 0.8333 (tt0) REVERT: D 171 GLU cc_start: 0.7654 (pt0) cc_final: 0.7416 (pp20) REVERT: D 175 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7211 (tm-30) REVERT: D 177 ASP cc_start: 0.7898 (t0) cc_final: 0.7602 (t70) REVERT: D 197 GLU cc_start: 0.8275 (tp30) cc_final: 0.7979 (mm-30) REVERT: D 202 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8359 (mtt90) REVERT: D 213 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7735 (mmmt) REVERT: D 215 LYS cc_start: 0.8107 (tttp) cc_final: 0.7736 (tttp) REVERT: D 281 ARG cc_start: 0.8726 (ttt90) cc_final: 0.8487 (ttt90) REVERT: D 295 GLU cc_start: 0.8309 (tp30) cc_final: 0.8094 (tp30) REVERT: D 330 MET cc_start: 0.8506 (mmm) cc_final: 0.8186 (mmm) REVERT: D 398 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8015 (mtmt) REVERT: D 403 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7697 (mtm-85) REVERT: D 547 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8112 (mtt90) REVERT: D 564 VAL cc_start: 0.8927 (t) cc_final: 0.8699 (p) REVERT: D 567 THR cc_start: 0.8880 (t) cc_final: 0.8591 (m) REVERT: D 649 LYS cc_start: 0.8306 (mmmt) cc_final: 0.7910 (mmmm) REVERT: D 652 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: D 667 GLN cc_start: 0.7828 (tt0) cc_final: 0.7585 (tt0) REVERT: D 698 MET cc_start: 0.8565 (tpt) cc_final: 0.8301 (mmp) REVERT: D 818 GLU cc_start: 0.7796 (mp0) cc_final: 0.7353 (mp0) REVERT: D 850 LYS cc_start: 0.8249 (tttt) cc_final: 0.7979 (ttmm) REVERT: D 873 GLU cc_start: 0.7983 (tt0) cc_final: 0.7719 (tt0) REVERT: D 1025 MET cc_start: 0.7107 (ttp) cc_final: 0.6775 (ttp) REVERT: D 1222 ARG cc_start: 0.8220 (ptt-90) cc_final: 0.7990 (ptt-90) REVERT: D 1231 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7792 (ttm-80) REVERT: D 1268 ASN cc_start: 0.8269 (t0) cc_final: 0.7890 (t0) REVERT: D 1276 GLU cc_start: 0.7957 (mp0) cc_final: 0.7454 (mm-30) REVERT: D 1361 THR cc_start: 0.8768 (m) cc_final: 0.8388 (p) REVERT: E 55 GLU cc_start: 0.8069 (tt0) cc_final: 0.7781 (tt0) REVERT: F 68 VAL cc_start: 0.8850 (p) cc_final: 0.8575 (t) REVERT: F 69 ASN cc_start: 0.7993 (t0) cc_final: 0.7696 (t0) REVERT: F 102 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8235 (mmtt) REVERT: F 104 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.5997 (t0) REVERT: F 208 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: F 304 THR cc_start: 0.8317 (m) cc_final: 0.7766 (p) REVERT: F 382 ASP cc_start: 0.8468 (p0) cc_final: 0.8092 (p0) REVERT: F 427 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7314 (ptm160) REVERT: F 432 ASP cc_start: 0.7569 (p0) cc_final: 0.7363 (p0) REVERT: F 497 TYR cc_start: 0.8049 (m-10) cc_final: 0.7839 (m-10) REVERT: F 580 LYS cc_start: 0.8592 (mttt) cc_final: 0.8316 (mtpp) REVERT: F 637 VAL cc_start: 0.8701 (t) cc_final: 0.8481 (m) REVERT: F 640 ASN cc_start: 0.7950 (p0) cc_final: 0.7645 (p0) REVERT: F 650 ASP cc_start: 0.7626 (m-30) cc_final: 0.6988 (m-30) REVERT: F 763 CYS cc_start: 0.7475 (m) cc_final: 0.7110 (m) outliers start: 107 outliers final: 51 residues processed: 982 average time/residue: 0.7937 time to fit residues: 909.2706 Evaluate side-chains 975 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 916 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1057 LYS Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1283 SER Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 345 LYS Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 427 ARG Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 709 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 354 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 396 optimal weight: 0.4980 chunk 375 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 268 optimal weight: 0.0970 chunk 272 optimal weight: 30.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN C 214 ASN C 613 ASN C 952 GLN C1134 GLN C1264 GLN D 206 ASN D 232 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN D 817 HIS D1227 HIS D1235 ASN D1295 ASN F 77 HIS F 365 HIS F 574 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123749 restraints weight = 47557.458| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.07 r_work: 0.3418 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34592 Z= 0.162 Angle : 0.560 10.126 47104 Z= 0.292 Chirality : 0.042 0.210 5318 Planarity : 0.004 0.057 5867 Dihedral : 14.042 175.265 5507 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.88 % Allowed : 18.92 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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 (0.13), residues: 4066 helix: 2.07 (0.13), residues: 1475 sheet: 0.58 (0.21), residues: 633 loop : 0.12 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 271 TYR 0.023 0.001 TYR F 20 PHE 0.021 0.001 PHE C 337 TRP 0.025 0.001 TRP F 395 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00370 (34572) covalent geometry : angle 0.55347 (47074) hydrogen bonds : bond 0.03957 ( 1604) hydrogen bonds : angle 4.34889 ( 4429) metal coordination : bond 0.00749 ( 20) metal coordination : angle 3.45379 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 947 time to evaluate : 1.448 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: A 9 LEU cc_start: 0.8736 (mt) cc_final: 0.8480 (mt) REVERT: A 25 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8330 (mtpp) REVERT: A 60 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8099 (mt-10) REVERT: A 76 GLU cc_start: 0.8106 (mp0) cc_final: 0.7598 (mp0) REVERT: A 174 ASP cc_start: 0.8536 (m-30) cc_final: 0.8316 (m-30) REVERT: A 215 GLU cc_start: 0.8133 (tt0) cc_final: 0.7832 (tt0) REVERT: A 219 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.8039 (ttp-170) REVERT: A 234 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7433 (pt) REVERT: B 7 GLU cc_start: 0.8041 (tt0) cc_final: 0.7712 (tt0) REVERT: B 58 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7961 (mt-10) REVERT: B 60 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7714 (mt-10) REVERT: B 97 GLU cc_start: 0.8058 (tt0) cc_final: 0.7690 (tt0) REVERT: B 110 VAL cc_start: 0.8416 (t) cc_final: 0.8049 (p) REVERT: B 120 ASP cc_start: 0.8035 (m-30) cc_final: 0.7775 (m-30) REVERT: B 143 ARG cc_start: 0.8010 (mtm110) cc_final: 0.7501 (mtm110) REVERT: B 144 ILE cc_start: 0.8568 (pt) cc_final: 0.8027 (pp) REVERT: B 145 LYS cc_start: 0.8463 (tttt) cc_final: 0.8049 (tttt) REVERT: B 148 ARG cc_start: 0.8517 (ttm110) cc_final: 0.8306 (ttp-110) REVERT: B 171 LEU cc_start: 0.8522 (mt) cc_final: 0.8194 (mm) REVERT: B 174 ASP cc_start: 0.7849 (m-30) cc_final: 0.7481 (m-30) REVERT: B 200 LYS cc_start: 0.8751 (ttpp) cc_final: 0.8363 (ttpp) REVERT: B 205 MET cc_start: 0.8609 (tpp) cc_final: 0.8156 (ttp) REVERT: B 212 ASP cc_start: 0.7263 (p0) cc_final: 0.6804 (p0) REVERT: B 214 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7535 (mp0) REVERT: B 215 GLU cc_start: 0.8002 (tp30) cc_final: 0.7506 (tp30) REVERT: C 101 ARG cc_start: 0.8282 (ttm110) cc_final: 0.7815 (mtm110) REVERT: C 115 LYS cc_start: 0.8739 (pttt) cc_final: 0.8269 (ptmt) REVERT: C 119 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7074 (mt-10) REVERT: C 122 VAL cc_start: 0.8839 (t) cc_final: 0.8599 (p) REVERT: C 197 ARG cc_start: 0.8301 (ptp-110) cc_final: 0.7934 (ptp90) REVERT: C 227 LYS cc_start: 0.8003 (mttt) cc_final: 0.7681 (mttp) REVERT: C 295 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7280 (mmtm) REVERT: C 299 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8158 (ttpp) REVERT: C 315 MET cc_start: 0.7451 (mtp) cc_final: 0.7073 (mtp) REVERT: C 316 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: C 321 LEU cc_start: 0.9144 (mt) cc_final: 0.8768 (mt) REVERT: C 324 LYS cc_start: 0.9098 (mttt) cc_final: 0.8835 (mttt) REVERT: C 407 ARG cc_start: 0.8426 (mmt180) cc_final: 0.7972 (mmt180) REVERT: C 413 GLU cc_start: 0.7908 (mp0) cc_final: 0.7599 (mp0) REVERT: C 490 GLN cc_start: 0.8468 (tp40) cc_final: 0.8219 (tp40) REVERT: C 595 THR cc_start: 0.8484 (m) cc_final: 0.8169 (p) REVERT: C 778 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7981 (mm-30) REVERT: C 854 ILE cc_start: 0.8770 (mt) cc_final: 0.8492 (mm) REVERT: C 859 GLU cc_start: 0.7605 (tp30) cc_final: 0.7246 (tp30) REVERT: C 862 LEU cc_start: 0.8436 (mp) cc_final: 0.8151 (mm) REVERT: C 878 THR cc_start: 0.8722 (t) cc_final: 0.8479 (p) REVERT: C 914 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7633 (ttpp) REVERT: C 949 GLU cc_start: 0.8180 (tt0) cc_final: 0.7878 (tt0) REVERT: C 1032 LYS cc_start: 0.8431 (tttp) cc_final: 0.8112 (tppp) REVERT: C 1057 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8433 (mtmm) REVERT: C 1140 LYS cc_start: 0.8544 (mttp) cc_final: 0.8100 (mtmp) REVERT: C 1170 MET cc_start: 0.8718 (mmm) cc_final: 0.8461 (mmm) REVERT: C 1174 GLU cc_start: 0.8097 (tp30) cc_final: 0.7785 (tp30) REVERT: C 1216 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7806 (mtp180) REVERT: C 1303 LYS cc_start: 0.8613 (mtmp) cc_final: 0.8388 (mttp) REVERT: C 1340 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7590 (mt-10) REVERT: D 69 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7266 (mt-10) REVERT: D 79 LYS cc_start: 0.8669 (pttt) cc_final: 0.8335 (ptmt) REVERT: D 81 ARG cc_start: 0.8320 (ttp80) cc_final: 0.8116 (ttp80) REVERT: D 133 ARG cc_start: 0.8223 (mmt180) cc_final: 0.7860 (tmt170) REVERT: D 155 GLU cc_start: 0.7085 (pm20) cc_final: 0.6840 (pm20) REVERT: D 157 GLN cc_start: 0.8690 (mt0) cc_final: 0.8323 (mt0) REVERT: D 159 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8630 (mm) REVERT: D 161 THR cc_start: 0.8905 (m) cc_final: 0.8554 (p) REVERT: D 171 GLU cc_start: 0.7708 (pt0) cc_final: 0.6918 (pt0) REVERT: D 175 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7171 (tm-30) REVERT: D 177 ASP cc_start: 0.7929 (t0) cc_final: 0.7630 (t70) REVERT: D 197 GLU cc_start: 0.8268 (tp30) cc_final: 0.7971 (mm-30) REVERT: D 202 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.8309 (mtt90) REVERT: D 213 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7678 (mmmt) REVERT: D 215 LYS cc_start: 0.8084 (tttp) cc_final: 0.7725 (tttp) REVERT: D 398 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7987 (mtmt) REVERT: D 547 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8069 (mtt90) REVERT: D 564 VAL cc_start: 0.8895 (t) cc_final: 0.8650 (p) REVERT: D 567 THR cc_start: 0.8874 (t) cc_final: 0.8574 (m) REVERT: D 649 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7850 (mmmm) REVERT: D 652 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: D 667 GLN cc_start: 0.7753 (tt0) cc_final: 0.7512 (tt0) REVERT: D 818 GLU cc_start: 0.7825 (mp0) cc_final: 0.7351 (mp0) REVERT: D 850 LYS cc_start: 0.8238 (tttt) cc_final: 0.7948 (ttmm) REVERT: D 880 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7870 (t) REVERT: D 1025 MET cc_start: 0.7169 (ttp) cc_final: 0.6815 (ttp) REVERT: D 1222 ARG cc_start: 0.8184 (ptt-90) cc_final: 0.7951 (ptt-90) REVERT: D 1231 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7764 (ttm-80) REVERT: D 1268 ASN cc_start: 0.8251 (t0) cc_final: 0.7878 (t0) REVERT: D 1276 GLU cc_start: 0.7955 (mp0) cc_final: 0.7472 (mm-30) REVERT: D 1284 ARG cc_start: 0.8599 (mmt180) cc_final: 0.8364 (mmt180) REVERT: D 1361 THR cc_start: 0.8768 (m) cc_final: 0.8410 (p) REVERT: E 3 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.6848 (ttm-80) REVERT: E 55 GLU cc_start: 0.8056 (tt0) cc_final: 0.7784 (tt0) REVERT: F 68 VAL cc_start: 0.8859 (p) cc_final: 0.8584 (t) REVERT: F 102 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8286 (mmtt) REVERT: F 104 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.5830 (t0) REVERT: F 208 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: F 304 THR cc_start: 0.8356 (m) cc_final: 0.7791 (p) REVERT: F 382 ASP cc_start: 0.8455 (p0) cc_final: 0.8092 (p0) REVERT: F 427 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7462 (ptm160) REVERT: F 432 ASP cc_start: 0.7579 (p0) cc_final: 0.7350 (p0) REVERT: F 580 LYS cc_start: 0.8569 (mttt) cc_final: 0.8274 (mtpp) REVERT: F 637 VAL cc_start: 0.8732 (t) cc_final: 0.8510 (m) REVERT: F 649 GLU cc_start: 0.7973 (pm20) cc_final: 0.7434 (pm20) REVERT: F 650 ASP cc_start: 0.7473 (m-30) cc_final: 0.6889 (m-30) outliers start: 100 outliers final: 51 residues processed: 989 average time/residue: 0.8483 time to fit residues: 977.3291 Evaluate side-chains 985 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 922 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1057 LYS Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1216 ARG Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 1041 ILE Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1283 SER Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 345 LYS Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 427 ARG Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 634 ILE Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 722 MET Chi-restraints excluded: chain F residue 823 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 155 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 406 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 312 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN C 613 ASN C 952 GLN C1134 GLN C1264 GLN D 206 ASN D 232 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS D 739 GLN D 817 HIS D1227 HIS D1235 ASN F 365 HIS F 533 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.153451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.122951 restraints weight = 48252.393| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.04 r_work: 0.3393 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34592 Z= 0.193 Angle : 0.582 11.116 47104 Z= 0.304 Chirality : 0.043 0.237 5318 Planarity : 0.004 0.062 5867 Dihedral : 14.054 175.409 5507 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.97 % Allowed : 19.38 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 1.29 (0.13), residues: 4066 helix: 2.02 (0.13), residues: 1472 sheet: 0.66 (0.21), residues: 634 loop : 0.09 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 271 TYR 0.022 0.001 TYR F 20 PHE 0.013 0.001 PHE C 514 TRP 0.027 0.002 TRP F 395 HIS 0.007 0.001 HIS C 628 Details of bonding type rmsd covalent geometry : bond 0.00444 (34572) covalent geometry : angle 0.57588 (47074) hydrogen bonds : bond 0.04117 ( 1604) hydrogen bonds : angle 4.39896 ( 4429) metal coordination : bond 0.00913 ( 20) metal coordination : angle 3.49369 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 936 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8745 (mt) cc_final: 0.8491 (mt) REVERT: A 25 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8382 (mtpp) REVERT: A 60 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 76 GLU cc_start: 0.8130 (mp0) cc_final: 0.7548 (mp0) REVERT: A 170 ARG cc_start: 0.8534 (ttm170) cc_final: 0.8303 (ttm-80) REVERT: A 174 ASP cc_start: 0.8577 (m-30) cc_final: 0.8299 (m-30) REVERT: A 215 GLU cc_start: 0.8127 (tt0) cc_final: 0.7823 (tt0) REVERT: A 234 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7551 (pt) REVERT: B 7 GLU cc_start: 0.8096 (tt0) cc_final: 0.7784 (tt0) REVERT: B 60 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 97 GLU cc_start: 0.8095 (tt0) cc_final: 0.7801 (tt0) REVERT: B 101 THR cc_start: 0.8578 (m) cc_final: 0.8216 (p) REVERT: B 110 VAL cc_start: 0.8418 (t) cc_final: 0.8046 (p) REVERT: B 120 ASP cc_start: 0.8023 (m-30) cc_final: 0.7736 (m-30) REVERT: B 143 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7563 (mtm110) REVERT: B 144 ILE cc_start: 0.8619 (pt) cc_final: 0.8092 (pp) REVERT: B 174 ASP cc_start: 0.7859 (m-30) cc_final: 0.7510 (m-30) REVERT: B 200 LYS cc_start: 0.8764 (ttpp) cc_final: 0.8342 (ttpp) REVERT: B 205 MET cc_start: 0.8647 (tpp) cc_final: 0.8250 (ttp) REVERT: B 212 ASP cc_start: 0.7404 (p0) cc_final: 0.6958 (p0) REVERT: B 214 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7557 (mp0) REVERT: B 215 GLU cc_start: 0.8061 (tp30) cc_final: 0.7566 (tp30) REVERT: C 101 ARG cc_start: 0.8362 (ttm110) cc_final: 0.8097 (ttm110) REVERT: C 115 LYS cc_start: 0.8729 (pttt) cc_final: 0.8281 (ptmt) REVERT: C 119 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7239 (mt-10) REVERT: C 122 VAL cc_start: 0.8850 (t) cc_final: 0.8621 (p) REVERT: C 197 ARG cc_start: 0.8295 (ptp-110) cc_final: 0.7922 (ptp90) REVERT: C 227 LYS cc_start: 0.8027 (mttt) cc_final: 0.7741 (mttp) REVERT: C 295 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7333 (mmtm) REVERT: C 299 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8170 (ttpp) REVERT: C 315 MET cc_start: 0.7498 (mtp) cc_final: 0.7065 (mtp) REVERT: C 316 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: C 321 LEU cc_start: 0.9127 (mt) cc_final: 0.8759 (mt) REVERT: C 324 LYS cc_start: 0.9055 (mttt) cc_final: 0.8801 (mttt) REVERT: C 407 ARG cc_start: 0.8416 (mmt180) cc_final: 0.7954 (mmt180) REVERT: C 413 GLU cc_start: 0.7917 (mp0) cc_final: 0.7623 (mp0) REVERT: C 490 GLN cc_start: 0.8492 (tp40) cc_final: 0.8252 (tp40) REVERT: C 549 ASP cc_start: 0.8116 (t70) cc_final: 0.7767 (t0) REVERT: C 595 THR cc_start: 0.8501 (m) cc_final: 0.8211 (p) REVERT: C 681 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8604 (mtm) REVERT: C 778 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8031 (mm-30) REVERT: C 854 ILE cc_start: 0.8782 (mt) cc_final: 0.8507 (mm) REVERT: C 859 GLU cc_start: 0.7666 (tp30) cc_final: 0.7310 (tp30) REVERT: C 862 LEU cc_start: 0.8499 (mp) cc_final: 0.8225 (mm) REVERT: C 878 THR cc_start: 0.8744 (t) cc_final: 0.8508 (p) REVERT: C 914 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7716 (ttpp) REVERT: C 949 GLU cc_start: 0.8240 (tt0) cc_final: 0.7932 (tt0) REVERT: C 1032 LYS cc_start: 0.8428 (tttp) cc_final: 0.8110 (tppp) REVERT: C 1057 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8443 (mtmm) REVERT: C 1140 LYS cc_start: 0.8527 (mttp) cc_final: 0.8044 (mtmm) REVERT: C 1170 MET cc_start: 0.8755 (mmm) cc_final: 0.8490 (mmm) REVERT: C 1174 GLU cc_start: 0.8132 (tp30) cc_final: 0.7837 (tp30) REVERT: C 1216 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7855 (mtp180) REVERT: C 1340 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7659 (mt-10) REVERT: D 69 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7328 (mt-10) REVERT: D 79 LYS cc_start: 0.8672 (pttt) cc_final: 0.8360 (ptmt) REVERT: D 133 ARG cc_start: 0.8265 (mmt180) cc_final: 0.7931 (tmt170) REVERT: D 137 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.8027 (ttp80) REVERT: D 157 GLN cc_start: 0.8703 (mt0) cc_final: 0.8312 (mt0) REVERT: D 159 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8663 (mm) REVERT: D 161 THR cc_start: 0.8910 (m) cc_final: 0.8596 (p) REVERT: D 172 PHE cc_start: 0.8009 (m-10) cc_final: 0.7650 (m-10) REVERT: D 175 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7139 (tm-30) REVERT: D 177 ASP cc_start: 0.7899 (t0) cc_final: 0.7642 (t70) REVERT: D 197 GLU cc_start: 0.8295 (tp30) cc_final: 0.8006 (mm-30) REVERT: D 202 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8285 (mtt90) REVERT: D 213 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7711 (mmmt) REVERT: D 215 LYS cc_start: 0.8175 (tttp) cc_final: 0.7820 (tttp) REVERT: D 278 ARG cc_start: 0.8470 (ttm170) cc_final: 0.8258 (ttm170) REVERT: D 295 GLU cc_start: 0.8303 (tp30) cc_final: 0.8050 (tp30) REVERT: D 330 MET cc_start: 0.8528 (mmm) cc_final: 0.8203 (mmm) REVERT: D 398 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8048 (mtmt) REVERT: D 547 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8119 (mtt90) REVERT: D 564 VAL cc_start: 0.8923 (t) cc_final: 0.8682 (p) REVERT: D 567 THR cc_start: 0.8887 (t) cc_final: 0.8598 (m) REVERT: D 649 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7864 (mmmm) REVERT: D 652 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: D 667 GLN cc_start: 0.7818 (tt0) cc_final: 0.7572 (tt0) REVERT: D 818 GLU cc_start: 0.7869 (mp0) cc_final: 0.7383 (mp0) REVERT: D 850 LYS cc_start: 0.8244 (tttt) cc_final: 0.7961 (ttmm) REVERT: D 880 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8095 (t) REVERT: D 1025 MET cc_start: 0.7145 (ttp) cc_final: 0.6806 (ttp) REVERT: D 1222 ARG cc_start: 0.8204 (ptt-90) cc_final: 0.7889 (ptt-90) REVERT: D 1268 ASN cc_start: 0.8265 (t0) cc_final: 0.7894 (t0) REVERT: D 1276 GLU cc_start: 0.7966 (mp0) cc_final: 0.7496 (mm-30) REVERT: E 3 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.6876 (ttm-80) REVERT: E 55 GLU cc_start: 0.8068 (tt0) cc_final: 0.7786 (tt0) REVERT: F 68 VAL cc_start: 0.8856 (p) cc_final: 0.8589 (t) REVERT: F 102 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8270 (mmtt) REVERT: F 104 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.5751 (t0) REVERT: F 208 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: F 304 THR cc_start: 0.8338 (m) cc_final: 0.7781 (p) REVERT: F 382 ASP cc_start: 0.8460 (p0) cc_final: 0.8090 (p0) REVERT: F 427 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7449 (ptm160) REVERT: F 432 ASP cc_start: 0.7680 (p0) cc_final: 0.7379 (p0) REVERT: F 568 PHE cc_start: 0.8736 (t80) cc_final: 0.8521 (t80) REVERT: F 637 VAL cc_start: 0.8730 (t) cc_final: 0.8527 (m) REVERT: F 649 GLU cc_start: 0.7951 (pm20) cc_final: 0.7390 (pm20) REVERT: F 650 ASP cc_start: 0.7508 (m-30) cc_final: 0.6936 (m-30) outliers start: 103 outliers final: 63 residues processed: 976 average time/residue: 0.8281 time to fit residues: 939.1940 Evaluate side-chains 990 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 914 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1057 LYS Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1216 ARG Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1283 SER Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 345 LYS Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 427 ARG Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 722 MET Chi-restraints excluded: chain F residue 823 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 198 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 294 optimal weight: 0.0170 chunk 106 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN C 613 ASN C 952 GLN C1134 GLN C1264 GLN D 232 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS D1235 ASN F 365 HIS F 533 ASN F 574 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.153836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123776 restraints weight = 48174.085| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.07 r_work: 0.3416 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34592 Z= 0.166 Angle : 0.577 11.678 47104 Z= 0.300 Chirality : 0.042 0.217 5318 Planarity : 0.004 0.070 5867 Dihedral : 14.038 176.441 5507 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.74 % Allowed : 19.96 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 1.33 (0.13), residues: 4066 helix: 2.06 (0.13), residues: 1475 sheet: 0.70 (0.21), residues: 619 loop : 0.11 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 271 TYR 0.022 0.001 TYR F 20 PHE 0.018 0.001 PHE C 337 TRP 0.029 0.002 TRP F 860 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00383 (34572) covalent geometry : angle 0.57136 (47074) hydrogen bonds : bond 0.03952 ( 1604) hydrogen bonds : angle 4.37906 ( 4429) metal coordination : bond 0.00717 ( 20) metal coordination : angle 3.36251 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 930 time to evaluate : 1.280 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: A 9 LEU cc_start: 0.8733 (mt) cc_final: 0.8490 (mt) REVERT: A 25 LYS cc_start: 0.8737 (mtpp) cc_final: 0.8352 (mtpp) REVERT: A 60 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8001 (mt-10) REVERT: A 76 GLU cc_start: 0.8114 (mp0) cc_final: 0.7597 (mp0) REVERT: A 170 ARG cc_start: 0.8514 (ttm170) cc_final: 0.8223 (ttm-80) REVERT: A 174 ASP cc_start: 0.8551 (m-30) cc_final: 0.8316 (m-30) REVERT: A 200 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8186 (ttpp) REVERT: A 215 GLU cc_start: 0.8092 (tt0) cc_final: 0.7809 (tt0) REVERT: A 234 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7470 (pt) REVERT: B 7 GLU cc_start: 0.8079 (tt0) cc_final: 0.7774 (tt0) REVERT: B 15 ASP cc_start: 0.7460 (t0) cc_final: 0.7252 (t70) REVERT: B 58 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7909 (mt-10) REVERT: B 60 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7713 (mt-10) REVERT: B 97 GLU cc_start: 0.8066 (tt0) cc_final: 0.7756 (tt0) REVERT: B 101 THR cc_start: 0.8535 (m) cc_final: 0.8168 (p) REVERT: B 110 VAL cc_start: 0.8390 (t) cc_final: 0.8025 (p) REVERT: B 120 ASP cc_start: 0.7999 (m-30) cc_final: 0.7710 (m-30) REVERT: B 143 ARG cc_start: 0.8038 (mtm110) cc_final: 0.7524 (mtm110) REVERT: B 144 ILE cc_start: 0.8606 (pt) cc_final: 0.8104 (pp) REVERT: B 174 ASP cc_start: 0.7835 (m-30) cc_final: 0.7472 (m-30) REVERT: B 200 LYS cc_start: 0.8767 (ttpp) cc_final: 0.8425 (ttpp) REVERT: B 205 MET cc_start: 0.8628 (tpp) cc_final: 0.8225 (ttp) REVERT: B 212 ASP cc_start: 0.7338 (p0) cc_final: 0.6881 (p0) REVERT: B 214 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7514 (mp0) REVERT: B 215 GLU cc_start: 0.8036 (tp30) cc_final: 0.7539 (tp30) REVERT: C 101 ARG cc_start: 0.8298 (ttm110) cc_final: 0.8028 (ttm110) REVERT: C 115 LYS cc_start: 0.8716 (pttt) cc_final: 0.8253 (ptmt) REVERT: C 119 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7181 (mt-10) REVERT: C 122 VAL cc_start: 0.8828 (t) cc_final: 0.8588 (p) REVERT: C 197 ARG cc_start: 0.8276 (ptp-110) cc_final: 0.7893 (ptp90) REVERT: C 227 LYS cc_start: 0.8037 (mttt) cc_final: 0.7708 (mttp) REVERT: C 295 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7214 (mmtm) REVERT: C 299 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8150 (ttpp) REVERT: C 315 MET cc_start: 0.7480 (mtp) cc_final: 0.7033 (mtp) REVERT: C 316 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: C 321 LEU cc_start: 0.9109 (mt) cc_final: 0.8724 (mt) REVERT: C 324 LYS cc_start: 0.9077 (mttt) cc_final: 0.8826 (mttt) REVERT: C 407 ARG cc_start: 0.8408 (mmt180) cc_final: 0.7948 (mmt180) REVERT: C 413 GLU cc_start: 0.7863 (mp0) cc_final: 0.7570 (mp0) REVERT: C 490 GLN cc_start: 0.8473 (tp40) cc_final: 0.8235 (tp40) REVERT: C 549 ASP cc_start: 0.8115 (t70) cc_final: 0.7718 (t0) REVERT: C 595 THR cc_start: 0.8489 (m) cc_final: 0.8207 (p) REVERT: C 778 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7986 (mm-30) REVERT: C 854 ILE cc_start: 0.8785 (mt) cc_final: 0.8495 (mm) REVERT: C 859 GLU cc_start: 0.7639 (tp30) cc_final: 0.7285 (tp30) REVERT: C 862 LEU cc_start: 0.8505 (mp) cc_final: 0.8236 (mm) REVERT: C 878 THR cc_start: 0.8723 (t) cc_final: 0.8484 (p) REVERT: C 914 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7686 (ttpp) REVERT: C 949 GLU cc_start: 0.8217 (tt0) cc_final: 0.7886 (tt0) REVERT: C 1032 LYS cc_start: 0.8423 (tttp) cc_final: 0.8133 (tppp) REVERT: C 1140 LYS cc_start: 0.8480 (mttp) cc_final: 0.8085 (mtmm) REVERT: C 1170 MET cc_start: 0.8737 (mmm) cc_final: 0.8495 (mmm) REVERT: C 1174 GLU cc_start: 0.8103 (tp30) cc_final: 0.7804 (tp30) REVERT: C 1216 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7817 (mtp180) REVERT: C 1340 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7625 (mt-10) REVERT: D 69 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7328 (mt-10) REVERT: D 79 LYS cc_start: 0.8665 (pttt) cc_final: 0.8343 (ptmt) REVERT: D 133 ARG cc_start: 0.8217 (mmt180) cc_final: 0.7849 (tmt170) REVERT: D 161 THR cc_start: 0.8916 (m) cc_final: 0.8598 (p) REVERT: D 172 PHE cc_start: 0.7951 (m-10) cc_final: 0.7661 (m-10) REVERT: D 175 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7066 (tm-30) REVERT: D 197 GLU cc_start: 0.8277 (tp30) cc_final: 0.7979 (mm-30) REVERT: D 202 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8302 (mtt90) REVERT: D 213 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7667 (mmmt) REVERT: D 215 LYS cc_start: 0.8121 (tttp) cc_final: 0.7767 (tttp) REVERT: D 278 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8220 (ttm170) REVERT: D 295 GLU cc_start: 0.8330 (tp30) cc_final: 0.8017 (tp30) REVERT: D 357 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8552 (p) REVERT: D 398 LYS cc_start: 0.8424 (mtmt) cc_final: 0.8027 (mtmt) REVERT: D 547 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8083 (mtt90) REVERT: D 564 VAL cc_start: 0.8918 (t) cc_final: 0.8681 (p) REVERT: D 567 THR cc_start: 0.8878 (t) cc_final: 0.8583 (m) REVERT: D 649 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7817 (mmmm) REVERT: D 652 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: D 667 GLN cc_start: 0.7762 (tt0) cc_final: 0.7523 (tt0) REVERT: D 818 GLU cc_start: 0.7858 (mp0) cc_final: 0.7366 (mp0) REVERT: D 850 LYS cc_start: 0.8229 (tttt) cc_final: 0.7950 (ttmm) REVERT: D 1025 MET cc_start: 0.7163 (ttp) cc_final: 0.6817 (ttp) REVERT: D 1040 MET cc_start: 0.5552 (pmm) cc_final: 0.3881 (pmt) REVERT: D 1268 ASN cc_start: 0.8247 (t0) cc_final: 0.7872 (t0) REVERT: D 1276 GLU cc_start: 0.7928 (mp0) cc_final: 0.7464 (mm-30) REVERT: D 1361 THR cc_start: 0.8769 (m) cc_final: 0.8395 (p) REVERT: E 3 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.6868 (ttm-80) REVERT: E 55 GLU cc_start: 0.8059 (tt0) cc_final: 0.7733 (tt0) REVERT: F 68 VAL cc_start: 0.8858 (p) cc_final: 0.8591 (t) REVERT: F 102 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8263 (mmtt) REVERT: F 104 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.5615 (t0) REVERT: F 208 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: F 304 THR cc_start: 0.8368 (m) cc_final: 0.7798 (p) REVERT: F 382 ASP cc_start: 0.8448 (p0) cc_final: 0.8074 (p0) REVERT: F 427 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7438 (ptm160) REVERT: F 432 ASP cc_start: 0.7619 (p0) cc_final: 0.7410 (p0) REVERT: F 568 PHE cc_start: 0.8738 (t80) cc_final: 0.8530 (t80) REVERT: F 637 VAL cc_start: 0.8737 (t) cc_final: 0.8510 (m) REVERT: F 647 GLU cc_start: 0.8028 (tp30) cc_final: 0.7570 (tp30) REVERT: F 649 GLU cc_start: 0.7962 (pm20) cc_final: 0.7416 (pm20) REVERT: F 650 ASP cc_start: 0.7517 (m-30) cc_final: 0.6953 (m-30) REVERT: F 729 MET cc_start: 0.7704 (mpp) cc_final: 0.7329 (mmm) outliers start: 95 outliers final: 59 residues processed: 966 average time/residue: 0.8466 time to fit residues: 947.4704 Evaluate side-chains 984 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 914 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1216 ARG Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1283 SER Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 345 LYS Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 427 ARG Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 722 MET Chi-restraints excluded: chain F residue 823 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 55 optimal weight: 3.9990 chunk 390 optimal weight: 3.9990 chunk 274 optimal weight: 20.0000 chunk 297 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN C 69 GLN C 518 ASN C 613 ASN C 952 GLN C1134 GLN C1236 ASN C1264 GLN D 80 HIS D 232 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS D1235 ASN F 329 GLN F 365 HIS F 533 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.151371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120253 restraints weight = 47814.069| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.94 r_work: 0.3359 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.111 34592 Z= 0.375 Angle : 0.694 11.172 47104 Z= 0.362 Chirality : 0.049 0.244 5318 Planarity : 0.005 0.067 5867 Dihedral : 14.209 171.847 5507 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.00 % Allowed : 20.13 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: 0.96 (0.13), residues: 4066 helix: 1.69 (0.13), residues: 1467 sheet: 0.47 (0.21), residues: 635 loop : -0.03 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 271 TYR 0.028 0.002 TYR F 20 PHE 0.023 0.002 PHE F 170 TRP 0.035 0.003 TRP F 860 HIS 0.010 0.002 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00861 (34572) covalent geometry : angle 0.68236 (47074) hydrogen bonds : bond 0.05122 ( 1604) hydrogen bonds : angle 4.68992 ( 4429) metal coordination : bond 0.01778 ( 20) metal coordination : angle 4.97931 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 949 time to evaluate : 1.183 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: A 9 LEU cc_start: 0.8771 (mt) cc_final: 0.8515 (mt) REVERT: A 76 GLU cc_start: 0.8128 (mp0) cc_final: 0.7602 (mp0) REVERT: A 170 ARG cc_start: 0.8558 (ttm170) cc_final: 0.8357 (ttm-80) REVERT: A 174 ASP cc_start: 0.8566 (m-30) cc_final: 0.8268 (m-30) REVERT: A 200 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8190 (ttpp) REVERT: A 215 GLU cc_start: 0.8093 (tt0) cc_final: 0.7799 (tt0) REVERT: B 7 GLU cc_start: 0.8075 (tt0) cc_final: 0.7762 (tt0) REVERT: B 58 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7769 (mt-10) REVERT: B 60 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7662 (mt-10) REVERT: B 76 GLU cc_start: 0.7599 (mp0) cc_final: 0.7347 (mp0) REVERT: B 97 GLU cc_start: 0.8064 (tt0) cc_final: 0.7754 (tt0) REVERT: B 110 VAL cc_start: 0.8463 (t) cc_final: 0.8018 (p) REVERT: B 120 ASP cc_start: 0.8020 (m-30) cc_final: 0.7724 (m-30) REVERT: B 143 ARG cc_start: 0.7953 (mtm110) cc_final: 0.7405 (mtm110) REVERT: B 144 ILE cc_start: 0.8588 (pt) cc_final: 0.8100 (pp) REVERT: B 174 ASP cc_start: 0.7859 (m-30) cc_final: 0.7506 (m-30) REVERT: B 200 LYS cc_start: 0.8752 (ttpp) cc_final: 0.8395 (ttpp) REVERT: B 205 MET cc_start: 0.8685 (tpp) cc_final: 0.8162 (ttp) REVERT: B 212 ASP cc_start: 0.7516 (p0) cc_final: 0.7073 (p0) REVERT: B 214 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7515 (mp0) REVERT: B 215 GLU cc_start: 0.8074 (tp30) cc_final: 0.7572 (tp30) REVERT: C 101 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8064 (ttm110) REVERT: C 115 LYS cc_start: 0.8737 (pttt) cc_final: 0.8269 (ptmt) REVERT: C 119 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7243 (mt-10) REVERT: C 122 VAL cc_start: 0.8847 (t) cc_final: 0.8602 (p) REVERT: C 197 ARG cc_start: 0.8277 (ptp-110) cc_final: 0.7836 (ptp90) REVERT: C 227 LYS cc_start: 0.8103 (mttt) cc_final: 0.7785 (mttp) REVERT: C 295 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7167 (mmtm) REVERT: C 299 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8137 (ttpp) REVERT: C 315 MET cc_start: 0.7507 (mtp) cc_final: 0.7057 (mtp) REVERT: C 316 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7233 (mm-30) REVERT: C 321 LEU cc_start: 0.9118 (mt) cc_final: 0.8842 (mt) REVERT: C 324 LYS cc_start: 0.9106 (mttt) cc_final: 0.8850 (mttt) REVERT: C 396 ASP cc_start: 0.8018 (t0) cc_final: 0.7620 (t0) REVERT: C 407 ARG cc_start: 0.8355 (mmt180) cc_final: 0.7910 (mmt180) REVERT: C 413 GLU cc_start: 0.7945 (mp0) cc_final: 0.7648 (mp0) REVERT: C 479 LEU cc_start: 0.8937 (mt) cc_final: 0.8691 (mm) REVERT: C 490 GLN cc_start: 0.8498 (tp40) cc_final: 0.8264 (tp40) REVERT: C 595 THR cc_start: 0.8520 (m) cc_final: 0.8204 (p) REVERT: C 778 GLU cc_start: 0.8214 (mm-30) cc_final: 0.8013 (mm-30) REVERT: C 854 ILE cc_start: 0.8781 (mt) cc_final: 0.8486 (mm) REVERT: C 859 GLU cc_start: 0.7634 (tp30) cc_final: 0.7200 (tp30) REVERT: C 862 LEU cc_start: 0.8565 (mp) cc_final: 0.8352 (mm) REVERT: C 878 THR cc_start: 0.8708 (t) cc_final: 0.8458 (p) REVERT: C 914 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7688 (ttpp) REVERT: C 949 GLU cc_start: 0.8165 (tt0) cc_final: 0.7843 (tt0) REVERT: C 1032 LYS cc_start: 0.8423 (tttp) cc_final: 0.8102 (tppp) REVERT: C 1140 LYS cc_start: 0.8616 (mttp) cc_final: 0.8191 (mtmm) REVERT: C 1170 MET cc_start: 0.8760 (mmm) cc_final: 0.8509 (mmm) REVERT: C 1174 GLU cc_start: 0.8091 (tp30) cc_final: 0.7847 (tp30) REVERT: C 1217 THR cc_start: 0.8941 (p) cc_final: 0.8657 (m) REVERT: C 1340 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7642 (mt-10) REVERT: D 69 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7461 (mt-10) REVERT: D 76 LYS cc_start: 0.8330 (mttm) cc_final: 0.7993 (mmmt) REVERT: D 79 LYS cc_start: 0.8677 (pttt) cc_final: 0.8358 (ptmt) REVERT: D 161 THR cc_start: 0.8936 (m) cc_final: 0.8642 (p) REVERT: D 171 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6956 (pp20) REVERT: D 175 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6970 (tm-30) REVERT: D 197 GLU cc_start: 0.8321 (tp30) cc_final: 0.8038 (mm-30) REVERT: D 202 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.8319 (mtt90) REVERT: D 215 LYS cc_start: 0.8173 (tttp) cc_final: 0.7942 (tttp) REVERT: D 278 ARG cc_start: 0.8439 (ttm170) cc_final: 0.8217 (ttm170) REVERT: D 281 ARG cc_start: 0.8611 (ttt90) cc_final: 0.8371 (ttt90) REVERT: D 295 GLU cc_start: 0.8312 (tp30) cc_final: 0.8018 (tp30) REVERT: D 330 MET cc_start: 0.8621 (mmm) cc_final: 0.8317 (mpp) REVERT: D 398 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8056 (mtmt) REVERT: D 403 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7625 (mtm-85) REVERT: D 547 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8193 (mtt90) REVERT: D 564 VAL cc_start: 0.8923 (t) cc_final: 0.8667 (p) REVERT: D 567 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8600 (m) REVERT: D 649 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7795 (mmmm) REVERT: D 652 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: D 667 GLN cc_start: 0.7844 (tt0) cc_final: 0.7600 (tt0) REVERT: D 669 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7781 (mm-40) REVERT: D 818 GLU cc_start: 0.7902 (mp0) cc_final: 0.7409 (mp0) REVERT: D 832 LYS cc_start: 0.8600 (mttp) cc_final: 0.8213 (mttp) REVERT: D 850 LYS cc_start: 0.8226 (tttt) cc_final: 0.7948 (ttmm) REVERT: D 1025 MET cc_start: 0.7151 (ttp) cc_final: 0.6844 (ttp) REVERT: D 1040 MET cc_start: 0.5745 (pmm) cc_final: 0.4188 (pmt) REVERT: D 1268 ASN cc_start: 0.8316 (t0) cc_final: 0.7931 (t0) REVERT: D 1276 GLU cc_start: 0.7932 (mp0) cc_final: 0.7504 (mm-30) REVERT: E 3 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.6862 (ttm-80) REVERT: E 55 GLU cc_start: 0.8034 (tt0) cc_final: 0.7726 (tt0) REVERT: F 68 VAL cc_start: 0.8855 (p) cc_final: 0.8602 (t) REVERT: F 69 ASN cc_start: 0.8028 (t0) cc_final: 0.7759 (t0) REVERT: F 104 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.5897 (t0) REVERT: F 186 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8206 (mptt) REVERT: F 208 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7708 (tp30) REVERT: F 303 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8041 (tttt) REVERT: F 304 THR cc_start: 0.8431 (m) cc_final: 0.7765 (p) REVERT: F 382 ASP cc_start: 0.8400 (p0) cc_final: 0.8036 (p0) REVERT: F 432 ASP cc_start: 0.7850 (p0) cc_final: 0.7536 (p0) REVERT: F 647 GLU cc_start: 0.8101 (tp30) cc_final: 0.7782 (tp30) REVERT: F 649 GLU cc_start: 0.7950 (pm20) cc_final: 0.7403 (pm20) REVERT: F 650 ASP cc_start: 0.7650 (m-30) cc_final: 0.7088 (m-30) outliers start: 104 outliers final: 59 residues processed: 996 average time/residue: 0.7979 time to fit residues: 926.1914 Evaluate side-chains 1003 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 934 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 399 LYS Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1283 SER Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 303 LYS Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 722 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 403 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 373 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 276 optimal weight: 10.0000 chunk 383 optimal weight: 0.9980 chunk 407 optimal weight: 3.9990 chunk 317 optimal weight: 0.0970 chunk 131 optimal weight: 0.0040 chunk 110 optimal weight: 0.2980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN C 214 ASN C 518 ASN C 613 ASN C 952 GLN C1264 GLN D 232 ASN D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS D1235 ASN F 365 HIS F 388 GLN F 533 ASN F 574 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.154984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123814 restraints weight = 47985.883| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.06 r_work: 0.3429 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 34592 Z= 0.131 Angle : 0.617 16.160 47104 Z= 0.317 Chirality : 0.042 0.210 5318 Planarity : 0.005 0.077 5867 Dihedral : 14.113 175.241 5507 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.98 % Rotamer: Outliers : 1.96 % Allowed : 21.89 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.13), residues: 4066 helix: 1.96 (0.13), residues: 1466 sheet: 0.49 (0.21), residues: 621 loop : 0.00 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 271 TYR 0.041 0.001 TYR F 622 PHE 0.027 0.001 PHE F 170 TRP 0.038 0.002 TRP F 860 HIS 0.006 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00301 (34572) covalent geometry : angle 0.61078 (47074) hydrogen bonds : bond 0.03844 ( 1604) hydrogen bonds : angle 4.44384 ( 4429) metal coordination : bond 0.00502 ( 20) metal coordination : angle 3.39699 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 944 time to evaluate : 1.316 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: A 9 LEU cc_start: 0.8730 (mt) cc_final: 0.8462 (mt) REVERT: A 25 LYS cc_start: 0.8750 (mtpp) cc_final: 0.8348 (mtpp) REVERT: A 60 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7988 (mt-10) REVERT: A 76 GLU cc_start: 0.8138 (mp0) cc_final: 0.7658 (mp0) REVERT: A 170 ARG cc_start: 0.8538 (ttm170) cc_final: 0.8284 (ttm-80) REVERT: A 174 ASP cc_start: 0.8544 (m-30) cc_final: 0.8324 (m-30) REVERT: A 200 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8160 (ptmm) REVERT: A 215 GLU cc_start: 0.8053 (tt0) cc_final: 0.7782 (tt0) REVERT: B 7 GLU cc_start: 0.8081 (tt0) cc_final: 0.7786 (tt0) REVERT: B 15 ASP cc_start: 0.7431 (t0) cc_final: 0.7225 (t70) REVERT: B 58 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7724 (mt-10) REVERT: B 60 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 76 GLU cc_start: 0.7541 (mp0) cc_final: 0.7299 (mp0) REVERT: B 97 GLU cc_start: 0.8022 (tt0) cc_final: 0.7698 (tt0) REVERT: B 101 THR cc_start: 0.8736 (m) cc_final: 0.8411 (p) REVERT: B 110 VAL cc_start: 0.8428 (t) cc_final: 0.8013 (p) REVERT: B 120 ASP cc_start: 0.8013 (m-30) cc_final: 0.7721 (m-30) REVERT: B 143 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7557 (mtm110) REVERT: B 144 ILE cc_start: 0.8623 (pt) cc_final: 0.8130 (pp) REVERT: B 148 ARG cc_start: 0.8572 (ttm110) cc_final: 0.8228 (ttp-110) REVERT: B 174 ASP cc_start: 0.7839 (m-30) cc_final: 0.7476 (m-30) REVERT: B 200 LYS cc_start: 0.8724 (ttpp) cc_final: 0.8424 (ttpp) REVERT: B 205 MET cc_start: 0.8640 (tpp) cc_final: 0.8197 (ttp) REVERT: B 212 ASP cc_start: 0.7276 (p0) cc_final: 0.6816 (p0) REVERT: B 214 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7477 (mp0) REVERT: B 215 GLU cc_start: 0.7991 (tp30) cc_final: 0.7477 (tp30) REVERT: C 57 PHE cc_start: 0.8651 (m-80) cc_final: 0.8424 (m-80) REVERT: C 101 ARG cc_start: 0.8307 (ttm110) cc_final: 0.7938 (ttm110) REVERT: C 115 LYS cc_start: 0.8737 (pttt) cc_final: 0.8264 (ptmt) REVERT: C 119 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7111 (mt-10) REVERT: C 122 VAL cc_start: 0.8824 (t) cc_final: 0.8569 (p) REVERT: C 175 ARG cc_start: 0.8320 (ttm110) cc_final: 0.8000 (ttm-80) REVERT: C 197 ARG cc_start: 0.8269 (ptp-110) cc_final: 0.7846 (ptp90) REVERT: C 227 LYS cc_start: 0.8028 (mttt) cc_final: 0.7695 (mttp) REVERT: C 263 VAL cc_start: 0.6135 (OUTLIER) cc_final: 0.5747 (m) REVERT: C 295 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7249 (mmtm) REVERT: C 299 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8161 (ttpp) REVERT: C 315 MET cc_start: 0.7521 (mtp) cc_final: 0.7087 (mtp) REVERT: C 316 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: C 321 LEU cc_start: 0.9158 (mt) cc_final: 0.8791 (mt) REVERT: C 324 LYS cc_start: 0.9071 (mttt) cc_final: 0.8831 (mttt) REVERT: C 407 ARG cc_start: 0.8372 (mmt180) cc_final: 0.7917 (mmt180) REVERT: C 413 GLU cc_start: 0.7873 (mp0) cc_final: 0.7573 (mp0) REVERT: C 479 LEU cc_start: 0.8909 (mt) cc_final: 0.8673 (mm) REVERT: C 490 GLN cc_start: 0.8466 (tp40) cc_final: 0.8243 (tp40) REVERT: C 595 THR cc_start: 0.8496 (m) cc_final: 0.8192 (p) REVERT: C 778 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7966 (mm-30) REVERT: C 854 ILE cc_start: 0.8792 (mt) cc_final: 0.8513 (mm) REVERT: C 859 GLU cc_start: 0.7619 (tp30) cc_final: 0.7244 (tp30) REVERT: C 862 LEU cc_start: 0.8504 (mp) cc_final: 0.8226 (mm) REVERT: C 878 THR cc_start: 0.8729 (t) cc_final: 0.8502 (p) REVERT: C 914 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7731 (ttpp) REVERT: C 949 GLU cc_start: 0.8196 (tt0) cc_final: 0.7855 (tt0) REVERT: C 952 GLN cc_start: 0.8540 (mt0) cc_final: 0.8325 (mt0) REVERT: C 1032 LYS cc_start: 0.8429 (tttp) cc_final: 0.8135 (tppp) REVERT: C 1140 LYS cc_start: 0.8450 (mttp) cc_final: 0.8065 (mtmm) REVERT: C 1170 MET cc_start: 0.8727 (mmm) cc_final: 0.8444 (mmm) REVERT: C 1174 GLU cc_start: 0.8143 (tp30) cc_final: 0.7870 (tp30) REVERT: C 1340 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7581 (mt-10) REVERT: D 69 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7323 (mt-10) REVERT: D 79 LYS cc_start: 0.8670 (pttt) cc_final: 0.8337 (ptmt) REVERT: D 161 THR cc_start: 0.8910 (m) cc_final: 0.8597 (p) REVERT: D 175 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7164 (tm-30) REVERT: D 197 GLU cc_start: 0.8294 (tp30) cc_final: 0.7978 (mm-30) REVERT: D 202 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8276 (mtt90) REVERT: D 213 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7671 (mmmt) REVERT: D 215 LYS cc_start: 0.8156 (tttp) cc_final: 0.7917 (tttp) REVERT: D 271 ARG cc_start: 0.8424 (ttm110) cc_final: 0.7907 (mtp-110) REVERT: D 278 ARG cc_start: 0.8420 (ttm170) cc_final: 0.8182 (ttm170) REVERT: D 295 GLU cc_start: 0.8310 (tp30) cc_final: 0.7996 (tp30) REVERT: D 330 MET cc_start: 0.8534 (mmm) cc_final: 0.8211 (mpp) REVERT: D 398 LYS cc_start: 0.8420 (mtmt) cc_final: 0.8012 (mtmt) REVERT: D 547 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8036 (mtt90) REVERT: D 564 VAL cc_start: 0.8903 (t) cc_final: 0.8658 (p) REVERT: D 567 THR cc_start: 0.8894 (t) cc_final: 0.8586 (m) REVERT: D 649 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7809 (mmmm) REVERT: D 652 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: D 667 GLN cc_start: 0.7762 (tt0) cc_final: 0.7539 (tt0) REVERT: D 714 GLU cc_start: 0.8190 (tt0) cc_final: 0.7961 (tt0) REVERT: D 818 GLU cc_start: 0.7944 (mp0) cc_final: 0.7465 (mp0) REVERT: D 832 LYS cc_start: 0.8570 (mttp) cc_final: 0.8351 (mtpp) REVERT: D 850 LYS cc_start: 0.8244 (tttt) cc_final: 0.7962 (ttmm) REVERT: D 876 SER cc_start: 0.8679 (m) cc_final: 0.8133 (p) REVERT: D 1025 MET cc_start: 0.7178 (ttp) cc_final: 0.6835 (ttp) REVERT: D 1040 MET cc_start: 0.5458 (pmm) cc_final: 0.3894 (pmt) REVERT: D 1268 ASN cc_start: 0.8271 (t0) cc_final: 0.7882 (t0) REVERT: D 1276 GLU cc_start: 0.7933 (mp0) cc_final: 0.7475 (mm-30) REVERT: D 1361 THR cc_start: 0.8726 (m) cc_final: 0.8364 (p) REVERT: E 3 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.6924 (ttm-80) REVERT: E 55 GLU cc_start: 0.8061 (tt0) cc_final: 0.7778 (tt0) REVERT: F 68 VAL cc_start: 0.8849 (p) cc_final: 0.8609 (t) REVERT: F 69 ASN cc_start: 0.7987 (t0) cc_final: 0.7715 (t0) REVERT: F 104 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.6021 (t70) REVERT: F 186 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7980 (mptt) REVERT: F 208 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: F 274 LYS cc_start: 0.8300 (mppt) cc_final: 0.8076 (mppt) REVERT: F 303 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7815 (tttt) REVERT: F 304 THR cc_start: 0.8274 (m) cc_final: 0.7696 (p) REVERT: F 382 ASP cc_start: 0.8390 (p0) cc_final: 0.8033 (p0) REVERT: F 432 ASP cc_start: 0.7627 (p0) cc_final: 0.7386 (p0) REVERT: F 568 PHE cc_start: 0.8719 (t80) cc_final: 0.8503 (t80) REVERT: F 647 GLU cc_start: 0.8047 (tp30) cc_final: 0.7669 (tp30) REVERT: F 649 GLU cc_start: 0.7943 (pm20) cc_final: 0.7368 (pm20) REVERT: F 650 ASP cc_start: 0.7500 (m-30) cc_final: 0.6985 (m-30) REVERT: F 729 MET cc_start: 0.7633 (mpp) cc_final: 0.7288 (mmm) outliers start: 68 outliers final: 46 residues processed: 973 average time/residue: 0.7931 time to fit residues: 900.5729 Evaluate side-chains 978 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 923 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1368 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 303 LYS Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 722 MET Chi-restraints excluded: chain F residue 823 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 8 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 404 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 340 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 1 optimal weight: 8.9990 chunk 295 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN C 69 GLN C 214 ASN C 613 ASN C1134 GLN C1135 GLN C1264 GLN D 157 GLN D 232 ASN D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS D1235 ASN F 329 GLN F 365 HIS F 388 GLN F 533 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.153841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123279 restraints weight = 47826.069| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.96 r_work: 0.3411 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34592 Z= 0.170 Angle : 0.628 13.247 47104 Z= 0.324 Chirality : 0.043 0.216 5318 Planarity : 0.005 0.071 5867 Dihedral : 14.073 175.961 5507 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.87 % Allowed : 22.26 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.13), residues: 4066 helix: 1.96 (0.13), residues: 1471 sheet: 0.59 (0.21), residues: 622 loop : 0.06 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 271 TYR 0.030 0.002 TYR D 144 PHE 0.019 0.001 PHE C 337 TRP 0.043 0.002 TRP F 860 HIS 0.006 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00396 (34572) covalent geometry : angle 0.62143 (47074) hydrogen bonds : bond 0.03990 ( 1604) hydrogen bonds : angle 4.41403 ( 4429) metal coordination : bond 0.00670 ( 20) metal coordination : angle 3.52041 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21762.57 seconds wall clock time: 368 minutes 8.58 seconds (22088.58 seconds total)