Starting phenix.real_space_refine on Sat Aug 8 06:55:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ehf_28146/08_2026/8ehf_28146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehf_28146/08_2026/8ehf_28146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ehf_28146/08_2026/8ehf_28146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehf_28146/08_2026/8ehf_28146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ehf_28146/08_2026/8ehf_28146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehf_28146/08_2026/8ehf_28146.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ehf_28146/08_2026/8ehf_28146.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ehf_28146/08_2026/8ehf_28146.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 62 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16178 2.51 5 N 4612 2.21 5 O 5149 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26110 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "B" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 608 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'4QM': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15499 SG CYS J 70 105.183 99.479 87.898 1.00 89.24 S ATOM 15513 SG CYS J 72 105.602 103.235 88.164 1.00 89.72 S ATOM 15621 SG CYS J 85 107.567 100.997 90.454 1.00 92.71 S ATOM 15645 SG CYS J 88 103.767 101.285 90.883 1.00 95.20 S ATOM 21333 SG CYS J 814 85.988 36.431 87.533 1.00 42.35 S ATOM 21898 SG CYS J 888 84.442 39.866 87.310 1.00 34.88 S ATOM 21949 SG CYS J 895 85.264 37.996 84.100 1.00 30.26 S ATOM 21970 SG CYS J 898 82.474 36.741 86.233 1.00 33.96 S Time building chain proxies: 5.16, per 1000 atoms: 0.20 Number of scatterers: 26110 At special positions: 0 Unit cell: (137.8, 156, 162.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 62 15.00 Mg 1 11.99 O 5149 8.00 N 4612 7.00 C 16178 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: 2.30 Conformation dependent library (CDL) restraints added in 854.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5852 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 46 sheets defined 37.8% alpha, 17.1% beta 26 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 4.149A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.828A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER H 49 " --> pdb=" O ARG H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.566A pdb=" N LEU H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 removed outlier: 4.029A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 4.083A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.523A pdb=" N GLY I 45 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 42 through 46' Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.680A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.533A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.746A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.690A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.159A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.947A pdb=" N GLU I 461 " --> pdb=" O GLY I 457 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.622A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.902A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.793A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.743A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 Processing helix chain 'I' and resid 704 through 712 removed outlier: 3.763A pdb=" N VAL I 710 " --> pdb=" O ARG I 706 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.548A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 948 Processing helix chain 'I' and resid 949 through 980 removed outlier: 3.687A pdb=" N GLU I 962 " --> pdb=" O LYS I 958 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.722A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.689A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.660A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1271 through 1282 removed outlier: 3.515A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1298 through 1309 removed outlier: 3.668A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET I1304 " --> pdb=" O GLY I1300 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.666A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.589A pdb=" N HIS J 80 " --> pdb=" O ARG J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.745A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU J 100 " --> pdb=" O VAL J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 180 through 192 removed outlier: 3.642A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 removed outlier: 3.541A pdb=" N MET J 330 " --> pdb=" O LEU J 327 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE J 331 " --> pdb=" O ALA J 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 327 through 331' Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.596A pdb=" N GLN J 340 " --> pdb=" O GLY J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.761A pdb=" N LEU J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 386 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 removed outlier: 3.551A pdb=" N ILE J 411 " --> pdb=" O VAL J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.657A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 579 Processing helix chain 'J' and resid 580 through 582 No H-bonds generated for 'chain 'J' and resid 580 through 582' Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.507A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 634 removed outlier: 3.692A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.955A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 805 removed outlier: 3.939A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.691A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1072 removed outlier: 3.505A pdb=" N LYS J1072 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1218 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.706A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.266A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.733A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1310 through 1315 removed outlier: 3.709A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.529A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.777A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1360 through 1372 removed outlier: 3.954A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.696A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 80 removed outlier: 3.718A pdb=" N LEU K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.524A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.642A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLY G 151 " --> pdb=" O PRO G 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.510A pdb=" N ALA G 175 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.871A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 12 through 15 removed outlier: 5.762A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL H 19 " --> pdb=" O HIS H 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 15 removed outlier: 5.762A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.198A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.607A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.504A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.853A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.434A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 158 removed outlier: 4.147A pdb=" N ILE I 176 " --> pdb=" O LEU I 184 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB9, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AC1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.496A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.060A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.458A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.452A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.756A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.546A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.147A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 841 removed outlier: 6.226A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY I 926 " --> pdb=" O VAL I 877 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD2, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.511A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD5, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.048A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.667A pdb=" N ILE J 147 " --> pdb=" O ASP J 177 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 317 through 319 removed outlier: 4.680A pdb=" N SER J 319 " --> pdb=" O ARG J 322 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG J 322 " --> pdb=" O SER J 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'J' and resid 548 through 556 Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.937A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 949 through 951 removed outlier: 6.671A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.683A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE6, first strand: chain 'J' and resid 1025 through 1026 Processing sheet with id=AE7, first strand: chain 'J' and resid 1077 through 1081 removed outlier: 3.631A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY J1033 " --> pdb=" O ILE J1115 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 4.268A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AF1, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.030A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 999 hydrogen bonds defined for protein. 2784 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 6.57 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.19: 17 1.19 - 1.35: 8784 1.35 - 1.51: 7219 1.51 - 1.66: 10419 1.66 - 1.82: 187 Bond restraints: 26626 Sorted by residual: bond pdb=" C VAL J 803 " pdb=" O VAL J 803 " ideal model delta sigma weight residual 1.236 1.070 0.167 9.70e-03 1.06e+04 2.96e+02 bond pdb=" C VAL J 808 " pdb=" O VAL J 808 " ideal model delta sigma weight residual 1.234 1.051 0.183 1.11e-02 8.12e+03 2.72e+02 bond pdb=" CA GLN J 805 " pdb=" C GLN J 805 " ideal model delta sigma weight residual 1.522 1.302 0.220 1.36e-02 5.41e+03 2.62e+02 bond pdb=" C ALA J 804 " pdb=" O ALA J 804 " ideal model delta sigma weight residual 1.236 1.035 0.202 1.33e-02 5.65e+03 2.30e+02 bond pdb=" C GLN J 805 " pdb=" O GLN J 805 " ideal model delta sigma weight residual 1.236 1.055 0.182 1.25e-02 6.40e+03 2.12e+02 ... (remaining 26621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 36053 3.70 - 7.41: 151 7.41 - 11.11: 20 11.11 - 14.81: 8 14.81 - 18.51: 3 Bond angle restraints: 36235 Sorted by residual: angle pdb=" C ARG I 18 " pdb=" N PRO I 19 " pdb=" CA PRO I 19 " ideal model delta sigma weight residual 119.76 132.27 -12.51 1.03e+00 9.43e-01 1.48e+02 angle pdb=" CA PRO I 19 " pdb=" C PRO I 19 " pdb=" O PRO I 19 " ideal model delta sigma weight residual 121.34 110.24 11.10 1.14e+00 7.69e-01 9.49e+01 angle pdb=" N VAL J 803 " pdb=" CA VAL J 803 " pdb=" CB VAL J 803 " ideal model delta sigma weight residual 110.64 122.17 -11.53 1.20e+00 6.94e-01 9.23e+01 angle pdb=" CG1 VAL J 803 " pdb=" CB VAL J 803 " pdb=" CG2 VAL J 803 " ideal model delta sigma weight residual 110.80 92.89 17.91 2.20e+00 2.07e-01 6.62e+01 angle pdb=" CA VAL J 808 " pdb=" C VAL J 808 " pdb=" N VAL J 809 " ideal model delta sigma weight residual 115.96 127.27 -11.31 1.43e+00 4.89e-01 6.25e+01 ... (remaining 36230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.93: 15359 27.93 - 55.86: 750 55.86 - 83.80: 92 83.80 - 111.73: 9 111.73 - 139.66: 2 Dihedral angle restraints: 16212 sinusoidal: 7115 harmonic: 9097 Sorted by residual: dihedral pdb=" O5' G R 10 " pdb=" C5' G R 10 " pdb=" C4' G R 10 " pdb=" C3' G R 10 " ideal model delta sinusoidal sigma weight residual 60.00 101.16 -41.16 3 6.40e+00 2.44e-02 4.04e+01 dihedral pdb=" N VAL J 803 " pdb=" C VAL J 803 " pdb=" CA VAL J 803 " pdb=" CB VAL J 803 " ideal model delta harmonic sigma weight residual 123.40 137.61 -14.21 0 2.50e+00 1.60e-01 3.23e+01 dihedral pdb=" CA GLY J 852 " pdb=" C GLY J 852 " pdb=" N THR J 853 " pdb=" CA THR J 853 " ideal model delta harmonic sigma weight residual 180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 16209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 4125 0.179 - 0.359: 18 0.359 - 0.538: 3 0.538 - 0.718: 6 0.718 - 0.897: 1 Chirality restraints: 4153 Sorted by residual: chirality pdb=" CA GLN J 805 " pdb=" N GLN J 805 " pdb=" C GLN J 805 " pdb=" CB GLN J 805 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" CA VAL J 803 " pdb=" N VAL J 803 " pdb=" C VAL J 803 " pdb=" CB VAL J 803 " both_signs ideal model delta sigma weight residual False 2.44 1.74 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA ASP J 806 " pdb=" N ASP J 806 " pdb=" C ASP J 806 " pdb=" CB ASP J 806 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 4150 not shown) Planarity restraints: 4520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 18 " 0.079 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO I 19 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO I 19 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO I 19 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 803 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C VAL J 803 " -0.071 2.00e-02 2.50e+03 pdb=" O VAL J 803 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA J 804 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 810 " 0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C THR J 810 " -0.071 2.00e-02 2.50e+03 pdb=" O THR J 810 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU J 811 " 0.024 2.00e-02 2.50e+03 ... (remaining 4517 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 296 2.61 - 3.18: 21760 3.18 - 3.75: 40373 3.75 - 4.33: 56111 4.33 - 4.90: 94309 Nonbonded interactions: 212849 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.037 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.129 2.170 nonbonded pdb=" NH2 ARG I1223 " pdb=" O PHE J 719 " model vdw 2.218 3.120 nonbonded pdb=" OD1 ASN J1268 " pdb=" OG1 THR J1301 " model vdw 2.224 3.040 nonbonded pdb=" O TYR I 810 " pdb=" OG SER I1077 " model vdw 2.232 3.040 ... (remaining 212844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 231)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 231)) } 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: 1.570 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.650 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.287 26634 Z= 0.523 Angle : 0.781 18.513 36247 Z= 0.480 Chirality : 0.056 0.897 4153 Planarity : 0.005 0.117 4520 Dihedral : 15.680 139.662 10360 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.82 % Allowed : 10.01 % Favored : 86.17 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 3.10 % 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: -1.52 (0.14), residues: 3150 helix: 0.08 (0.16), residues: 1073 sheet: -1.05 (0.26), residues: 376 loop : -1.75 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 18 TYR 0.020 0.001 TYR G 177 PHE 0.022 0.002 PHE I 15 TRP 0.005 0.001 TRP J 409 HIS 0.006 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00894 / 0.52 (26626) covalent geometry : angle 0.78102 / 0.48 (36235) hydrogen bonds : bond 0.15637 / 17.52 ( 1052) hydrogen bonds : angle 6.62942 / 7.35 ( 2914) metal coordination : bond 0.00665 / 0.66 ( 8) metal coordination : angle 1.51992 / 2.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 404 time to evaluate : 0.807 Fit side-chains REVERT: H 17 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7391 (tt0) REVERT: H 103 ASN cc_start: 0.8165 (m-40) cc_final: 0.7848 (p0) REVERT: H 145 LYS cc_start: 0.8807 (tttm) cc_final: 0.8593 (tttm) REVERT: I 33 ASP cc_start: 0.7659 (m-30) cc_final: 0.7430 (m-30) REVERT: I 70 TYR cc_start: 0.8516 (t80) cc_final: 0.8300 (t80) REVERT: I 191 LYS cc_start: 0.8672 (mptt) cc_final: 0.8287 (mtmt) REVERT: I 214 ASN cc_start: 0.8296 (t0) cc_final: 0.8029 (t0) REVERT: I 370 MET cc_start: 0.9031 (mmm) cc_final: 0.8714 (mmm) REVERT: I 470 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7666 (mtt180) REVERT: I 490 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7486 (tp-100) REVERT: I 518 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7843 (p0) REVERT: I 524 ILE cc_start: 0.8968 (tp) cc_final: 0.8496 (tp) REVERT: I 538 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8926 (pt) REVERT: I 681 MET cc_start: 0.8418 (mtt) cc_final: 0.8078 (mtp) REVERT: I 850 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8426 (mm) REVERT: I 1085 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8783 (mmm) REVERT: I 1119 MET cc_start: 0.8043 (tpt) cc_final: 0.7309 (ttt) REVERT: I 1154 ASP cc_start: 0.7727 (p0) cc_final: 0.6801 (p0) REVERT: I 1170 MET cc_start: 0.8761 (mmt) cc_final: 0.8408 (mmt) REVERT: I 1188 ASP cc_start: 0.8405 (t0) cc_final: 0.8010 (t0) REVERT: I 1273 MET cc_start: 0.8918 (mtp) cc_final: 0.8660 (mtp) REVERT: I 1310 ASP cc_start: 0.7201 (t0) cc_final: 0.6816 (t0) REVERT: J 765 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7238 (pp20) REVERT: J 847 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7900 (p0) REVERT: J 889 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: J 895 CYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7792 (p) REVERT: J 954 ASN cc_start: 0.6745 (m-40) cc_final: 0.6513 (m-40) REVERT: J 996 LYS cc_start: 0.8031 (tptt) cc_final: 0.7750 (mptt) REVERT: J 999 TYR cc_start: 0.6739 (t80) cc_final: 0.6531 (t80) REVERT: J 1025 MET cc_start: 0.5698 (mtm) cc_final: 0.5295 (mtm) REVERT: J 1189 MET cc_start: 0.7233 (mmt) cc_final: 0.6877 (tmm) REVERT: K 35 LYS cc_start: 0.8389 (mmtp) cc_final: 0.8131 (mptt) outliers start: 103 outliers final: 55 residues processed: 490 average time/residue: 0.1645 time to fit residues: 128.0617 Evaluate side-chains 397 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 334 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.0570 chunk 298 optimal weight: 3.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN J 94 GLN J 229 GLN J 805 GLN J1218 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.166779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121706 restraints weight = 30868.382| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.65 r_work: 0.2916 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26634 Z= 0.132 Angle : 0.593 8.112 36247 Z= 0.313 Chirality : 0.044 0.251 4153 Planarity : 0.004 0.057 4520 Dihedral : 14.885 145.044 4268 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.60 % Allowed : 12.61 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -1.07 (0.15), residues: 3150 helix: 0.54 (0.16), residues: 1110 sheet: -0.66 (0.28), residues: 355 loop : -1.62 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 368 TYR 0.014 0.001 TYR G 177 PHE 0.021 0.001 PHE I 337 TRP 0.007 0.001 TRP J 33 HIS 0.005 0.001 HIS J 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (26626) covalent geometry : angle 0.59196 / 0.31 (36235) hydrogen bonds : bond 0.04318 / 4.70 ( 1052) hydrogen bonds : angle 5.01983 / 5.47 ( 2914) metal coordination : bond 0.00576 / 0.59 ( 8) metal coordination : angle 2.17599 / 3.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 367 time to evaluate : 0.862 Fit side-chains REVERT: G 18 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8305 (mm-40) REVERT: G 185 TYR cc_start: 0.8857 (p90) cc_final: 0.8483 (p90) REVERT: H 17 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7478 (tm-30) REVERT: H 103 ASN cc_start: 0.8430 (m-40) cc_final: 0.8021 (p0) REVERT: H 145 LYS cc_start: 0.8810 (tttm) cc_final: 0.8456 (tttm) REVERT: H 172 LEU cc_start: 0.8828 (mt) cc_final: 0.8547 (mt) REVERT: H 206 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7776 (tt0) REVERT: I 17 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8508 (mmtm) REVERT: I 70 TYR cc_start: 0.8597 (t80) cc_final: 0.8389 (t80) REVERT: I 189 ASP cc_start: 0.8225 (m-30) cc_final: 0.7756 (m-30) REVERT: I 191 LYS cc_start: 0.8739 (mptt) cc_final: 0.8531 (mmtp) REVERT: I 214 ASN cc_start: 0.8403 (t0) cc_final: 0.8088 (t0) REVERT: I 461 GLU cc_start: 0.8350 (tt0) cc_final: 0.8141 (tt0) REVERT: I 490 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7446 (tp-100) REVERT: I 538 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9045 (pt) REVERT: I 633 LEU cc_start: 0.7021 (pp) cc_final: 0.6802 (pp) REVERT: I 1119 MET cc_start: 0.8682 (tpt) cc_final: 0.7903 (ttt) REVERT: I 1154 ASP cc_start: 0.7896 (p0) cc_final: 0.7036 (p0) REVERT: I 1188 ASP cc_start: 0.8802 (t0) cc_final: 0.8406 (t0) REVERT: I 1310 ASP cc_start: 0.7746 (t0) cc_final: 0.7161 (t0) REVERT: J 94 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8011 (mm110) REVERT: J 130 MET cc_start: 0.8495 (mtp) cc_final: 0.8209 (mtm) REVERT: J 192 MET cc_start: 0.8303 (ttp) cc_final: 0.8018 (ttp) REVERT: J 195 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7505 (mm-30) REVERT: J 248 ASP cc_start: 0.8504 (m-30) cc_final: 0.8025 (t0) REVERT: J 625 MET cc_start: 0.9173 (ttp) cc_final: 0.8969 (ttp) REVERT: J 703 THR cc_start: 0.7389 (m) cc_final: 0.6892 (t) REVERT: J 725 MET cc_start: 0.9445 (ptp) cc_final: 0.8322 (mtm) REVERT: J 765 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7765 (pp20) REVERT: J 847 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7862 (p0) REVERT: J 889 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8229 (m-30) REVERT: J 913 GLU cc_start: 0.7694 (pt0) cc_final: 0.7426 (tt0) REVERT: J 954 ASN cc_start: 0.7310 (m-40) cc_final: 0.7085 (m-40) REVERT: J 996 LYS cc_start: 0.7899 (tptt) cc_final: 0.7571 (mptt) REVERT: J 999 TYR cc_start: 0.7167 (t80) cc_final: 0.6832 (t80) REVERT: J 1025 MET cc_start: 0.6210 (mtm) cc_final: 0.5920 (mtm) REVERT: J 1040 MET cc_start: 0.6479 (mmm) cc_final: 0.6038 (tpp) REVERT: J 1095 MET cc_start: 0.6145 (ptm) cc_final: 0.5265 (ppp) REVERT: J 1174 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7401 (mtp85) REVERT: J 1189 MET cc_start: 0.7675 (mmt) cc_final: 0.6585 (tmm) REVERT: K 29 GLN cc_start: 0.9016 (mt0) cc_final: 0.8679 (mt0) REVERT: K 35 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8312 (mptt) outliers start: 97 outliers final: 60 residues processed: 438 average time/residue: 0.1556 time to fit residues: 108.3980 Evaluate side-chains 405 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 340 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 89 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 281 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 673 HIS J 229 GLN J 489 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.160641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.114329 restraints weight = 31154.071| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.84 r_work: 0.2857 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 26634 Z= 0.257 Angle : 0.642 8.396 36247 Z= 0.335 Chirality : 0.046 0.268 4153 Planarity : 0.005 0.060 4520 Dihedral : 14.801 143.292 4237 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.45 % Allowed : 13.50 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -1.04 (0.15), residues: 3150 helix: 0.58 (0.16), residues: 1102 sheet: -0.68 (0.27), residues: 367 loop : -1.60 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 133 TYR 0.019 0.002 TYR I 123 PHE 0.012 0.002 PHE I 389 TRP 0.010 0.001 TRP J 409 HIS 0.008 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.26 (26626) covalent geometry : angle 0.64160 / 0.33 (36235) hydrogen bonds : bond 0.04706 / 5.04 ( 1052) hydrogen bonds : angle 4.90855 / 5.37 ( 2914) metal coordination : bond 0.01014 / 1.00 ( 8) metal coordination : angle 1.80974 / 3.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 355 time to evaluate : 0.884 Fit side-chains REVERT: G 18 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8413 (mm-40) REVERT: G 93 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7151 (mm-40) REVERT: G 185 TYR cc_start: 0.8978 (p90) cc_final: 0.8635 (p90) REVERT: H 17 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7661 (tm-30) REVERT: H 145 LYS cc_start: 0.8897 (tttm) cc_final: 0.8529 (tttm) REVERT: H 172 LEU cc_start: 0.8842 (mt) cc_final: 0.8521 (mt) REVERT: H 206 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7785 (tt0) REVERT: I 17 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8425 (mmtm) REVERT: I 33 ASP cc_start: 0.8371 (m-30) cc_final: 0.7980 (m-30) REVERT: I 72 SER cc_start: 0.8828 (t) cc_final: 0.8545 (p) REVERT: I 189 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: I 191 LYS cc_start: 0.8757 (mptt) cc_final: 0.8523 (mmtp) REVERT: I 214 ASN cc_start: 0.8458 (t0) cc_final: 0.8198 (t0) REVERT: I 231 GLU cc_start: 0.7564 (mm-30) cc_final: 0.6386 (tp30) REVERT: I 461 GLU cc_start: 0.8397 (tt0) cc_final: 0.8178 (tt0) REVERT: I 490 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7609 (tp40) REVERT: I 524 ILE cc_start: 0.9096 (tp) cc_final: 0.8731 (tp) REVERT: I 538 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9066 (pt) REVERT: I 1085 MET cc_start: 0.9186 (mmm) cc_final: 0.8913 (mmm) REVERT: I 1154 ASP cc_start: 0.7959 (p0) cc_final: 0.7126 (p0) REVERT: I 1188 ASP cc_start: 0.8934 (t0) cc_final: 0.8654 (t0) REVERT: I 1310 ASP cc_start: 0.7922 (t0) cc_final: 0.7179 (t0) REVERT: J 68 TYR cc_start: 0.8332 (m-80) cc_final: 0.8087 (m-80) REVERT: J 94 GLN cc_start: 0.8267 (mm-40) cc_final: 0.8062 (mm110) REVERT: J 130 MET cc_start: 0.8492 (mtp) cc_final: 0.8180 (mtm) REVERT: J 192 MET cc_start: 0.8362 (ttp) cc_final: 0.7931 (ttp) REVERT: J 248 ASP cc_start: 0.8508 (m-30) cc_final: 0.8080 (t0) REVERT: J 352 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8601 (ptm160) REVERT: J 725 MET cc_start: 0.9516 (ptp) cc_final: 0.8324 (mtm) REVERT: J 765 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8425 (pp20) REVERT: J 889 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8215 (m-30) REVERT: J 895 CYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8490 (p) REVERT: J 913 GLU cc_start: 0.7941 (pt0) cc_final: 0.7418 (tt0) REVERT: J 954 ASN cc_start: 0.7356 (m-40) cc_final: 0.7122 (m-40) REVERT: J 996 LYS cc_start: 0.7914 (tptt) cc_final: 0.7669 (mptt) REVERT: J 999 TYR cc_start: 0.7123 (t80) cc_final: 0.6830 (t80) REVERT: J 1025 MET cc_start: 0.6200 (mtm) cc_final: 0.5574 (mtm) REVERT: J 1040 MET cc_start: 0.6521 (mmm) cc_final: 0.6132 (tpp) REVERT: J 1174 ARG cc_start: 0.7637 (mtp85) cc_final: 0.7180 (mtp85) REVERT: J 1189 MET cc_start: 0.7282 (mmt) cc_final: 0.6581 (tmm) REVERT: K 35 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8308 (mptt) outliers start: 120 outliers final: 83 residues processed: 443 average time/residue: 0.1711 time to fit residues: 120.2344 Evaluate side-chains 425 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 335 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 33 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 294 optimal weight: 9.9990 chunk 301 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 317 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN H 103 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN J 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.162489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.116277 restraints weight = 30884.021| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.75 r_work: 0.2798 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 26634 Z= 0.257 Angle : 0.643 9.538 36247 Z= 0.334 Chirality : 0.046 0.267 4153 Planarity : 0.004 0.058 4520 Dihedral : 14.779 143.405 4234 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.56 % Allowed : 14.61 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -1.03 (0.15), residues: 3150 helix: 0.58 (0.16), residues: 1105 sheet: -0.77 (0.27), residues: 386 loop : -1.58 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 133 TYR 0.019 0.001 TYR G 177 PHE 0.012 0.002 PHE I 389 TRP 0.010 0.001 TRP J 409 HIS 0.008 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.26 (26626) covalent geometry : angle 0.64229 / 0.33 (36235) hydrogen bonds : bond 0.04547 / 4.86 ( 1052) hydrogen bonds : angle 4.82579 / 5.30 ( 2914) metal coordination : bond 0.00948 / 0.94 ( 8) metal coordination : angle 1.81916 / 3.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 351 time to evaluate : 0.827 Fit side-chains REVERT: G 18 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8562 (mm-40) REVERT: G 93 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7202 (mm-40) REVERT: G 185 TYR cc_start: 0.9126 (p90) cc_final: 0.8814 (p90) REVERT: H 17 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7736 (tm-30) REVERT: H 66 HIS cc_start: 0.7586 (t-90) cc_final: 0.7305 (t-90) REVERT: H 77 ASP cc_start: 0.6374 (t70) cc_final: 0.6071 (t0) REVERT: H 103 ASN cc_start: 0.8522 (m110) cc_final: 0.8069 (p0) REVERT: H 145 LYS cc_start: 0.8823 (tttm) cc_final: 0.8437 (tttm) REVERT: H 172 LEU cc_start: 0.8797 (mt) cc_final: 0.8453 (mt) REVERT: H 206 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7975 (tt0) REVERT: I 33 ASP cc_start: 0.8617 (m-30) cc_final: 0.8250 (m-30) REVERT: I 72 SER cc_start: 0.8867 (t) cc_final: 0.8596 (p) REVERT: I 189 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: I 191 LYS cc_start: 0.8732 (mptt) cc_final: 0.8444 (mmtp) REVERT: I 201 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.7545 (mtt-85) REVERT: I 214 ASN cc_start: 0.8555 (t0) cc_final: 0.8098 (t0) REVERT: I 231 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6381 (tp30) REVERT: I 370 MET cc_start: 0.8939 (mmm) cc_final: 0.8711 (mmm) REVERT: I 461 GLU cc_start: 0.8610 (tt0) cc_final: 0.8381 (tt0) REVERT: I 490 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7549 (tp40) REVERT: I 524 ILE cc_start: 0.9154 (tp) cc_final: 0.8799 (tp) REVERT: I 538 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9088 (pt) REVERT: I 814 ASP cc_start: 0.8713 (m-30) cc_final: 0.8474 (m-30) REVERT: I 850 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8341 (mm) REVERT: I 1085 MET cc_start: 0.9316 (mmm) cc_final: 0.8899 (mmm) REVERT: I 1154 ASP cc_start: 0.8077 (p0) cc_final: 0.7291 (p0) REVERT: I 1188 ASP cc_start: 0.9069 (t0) cc_final: 0.8781 (t0) REVERT: I 1223 ARG cc_start: 0.9027 (mtt-85) cc_final: 0.8773 (mtt-85) REVERT: I 1310 ASP cc_start: 0.8169 (t0) cc_final: 0.7969 (t0) REVERT: J 68 TYR cc_start: 0.8389 (m-80) cc_final: 0.8115 (m-80) REVERT: J 94 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8085 (mm110) REVERT: J 248 ASP cc_start: 0.8707 (m-30) cc_final: 0.8203 (t0) REVERT: J 352 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8672 (ptm160) REVERT: J 464 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8200 (p0) REVERT: J 625 MET cc_start: 0.9293 (ttp) cc_final: 0.9061 (ttp) REVERT: J 703 THR cc_start: 0.7672 (m) cc_final: 0.7068 (t) REVERT: J 889 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: J 895 CYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8708 (p) REVERT: J 913 GLU cc_start: 0.8237 (pt0) cc_final: 0.7707 (tt0) REVERT: J 954 ASN cc_start: 0.7424 (m-40) cc_final: 0.7204 (m-40) REVERT: J 999 TYR cc_start: 0.7281 (t80) cc_final: 0.6999 (t80) REVERT: J 1025 MET cc_start: 0.6253 (mtm) cc_final: 0.6030 (mtm) REVERT: J 1040 MET cc_start: 0.6756 (mmm) cc_final: 0.6458 (tpp) REVERT: J 1174 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7145 (mtp85) REVERT: J 1189 MET cc_start: 0.7438 (mmt) cc_final: 0.6622 (tmm) REVERT: K 35 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8351 (mptt) REVERT: K 36 ASP cc_start: 0.8192 (p0) cc_final: 0.7990 (p0) outliers start: 123 outliers final: 93 residues processed: 441 average time/residue: 0.1493 time to fit residues: 105.4133 Evaluate side-chains 440 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 340 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 547 ARG Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 18 optimal weight: 1.9990 chunk 268 optimal weight: 0.7980 chunk 300 optimal weight: 0.9980 chunk 252 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 236 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN H 66 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN J 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.167658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.122614 restraints weight = 30589.133| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.43 r_work: 0.2779 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26634 Z= 0.120 Angle : 0.555 7.995 36247 Z= 0.291 Chirality : 0.043 0.261 4153 Planarity : 0.004 0.059 4520 Dihedral : 14.636 143.816 4234 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.89 % Allowed : 16.02 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.73 (0.15), residues: 3150 helix: 0.88 (0.16), residues: 1106 sheet: -0.49 (0.27), residues: 364 loop : -1.46 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 133 TYR 0.019 0.001 TYR I 123 PHE 0.009 0.001 PHE J 437 TRP 0.007 0.001 TRP J 33 HIS 0.003 0.001 HIS J 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (26626) covalent geometry : angle 0.55397 / 0.29 (36235) hydrogen bonds : bond 0.03786 / 4.09 ( 1052) hydrogen bonds : angle 4.60322 / 5.08 ( 2914) metal coordination : bond 0.00482 / 0.49 ( 8) metal coordination : angle 1.72404 / 3.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 368 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: G 18 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8498 (mm-40) REVERT: G 185 TYR cc_start: 0.9106 (p90) cc_final: 0.8586 (p90) REVERT: H 17 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7607 (tm-30) REVERT: H 77 ASP cc_start: 0.6255 (t70) cc_final: 0.5972 (t0) REVERT: H 103 ASN cc_start: 0.8458 (m110) cc_final: 0.8023 (p0) REVERT: H 172 LEU cc_start: 0.8694 (mt) cc_final: 0.8372 (mt) REVERT: H 206 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7912 (tt0) REVERT: I 17 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8576 (mmtp) REVERT: I 72 SER cc_start: 0.8856 (t) cc_final: 0.8576 (p) REVERT: I 185 ASP cc_start: 0.8164 (t0) cc_final: 0.7922 (t0) REVERT: I 189 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: I 191 LYS cc_start: 0.8664 (mptt) cc_final: 0.8380 (mmtp) REVERT: I 214 ASN cc_start: 0.8571 (t0) cc_final: 0.8100 (t0) REVERT: I 231 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6364 (tp30) REVERT: I 490 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7592 (tp40) REVERT: I 524 ILE cc_start: 0.9063 (tp) cc_final: 0.8665 (tp) REVERT: I 538 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9045 (pt) REVERT: I 850 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8269 (mm) REVERT: I 1085 MET cc_start: 0.9396 (mmm) cc_final: 0.8939 (mmm) REVERT: I 1154 ASP cc_start: 0.7940 (p0) cc_final: 0.7205 (p0) REVERT: I 1188 ASP cc_start: 0.8894 (t0) cc_final: 0.8536 (t0) REVERT: I 1289 GLU cc_start: 0.8970 (pt0) cc_final: 0.8717 (pt0) REVERT: J 81 ARG cc_start: 0.7859 (tmm-80) cc_final: 0.7493 (ttp-170) REVERT: J 248 ASP cc_start: 0.8685 (m-30) cc_final: 0.7921 (t0) REVERT: J 625 MET cc_start: 0.9203 (ttp) cc_final: 0.8984 (ttp) REVERT: J 765 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.7879 (pp20) REVERT: J 889 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: J 895 CYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8672 (p) REVERT: J 913 GLU cc_start: 0.8090 (pt0) cc_final: 0.7604 (tt0) REVERT: J 954 ASN cc_start: 0.7640 (m-40) cc_final: 0.7434 (m-40) REVERT: J 999 TYR cc_start: 0.7145 (t80) cc_final: 0.6830 (t80) REVERT: J 1025 MET cc_start: 0.6366 (mtm) cc_final: 0.6097 (mtm) REVERT: J 1040 MET cc_start: 0.6729 (mmm) cc_final: 0.6457 (tpp) REVERT: J 1174 ARG cc_start: 0.7633 (mtp85) cc_final: 0.7374 (mtp85) REVERT: J 1189 MET cc_start: 0.7526 (mmt) cc_final: 0.6690 (tmm) REVERT: J 1307 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8982 (mp) outliers start: 105 outliers final: 74 residues processed: 450 average time/residue: 0.1602 time to fit residues: 115.6874 Evaluate side-chains 420 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 338 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 547 ARG Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 218 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 319 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 167 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 554 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN J 94 GLN J 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.167276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.121545 restraints weight = 30780.561| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.63 r_work: 0.2831 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26634 Z= 0.134 Angle : 0.555 8.048 36247 Z= 0.290 Chirality : 0.043 0.265 4153 Planarity : 0.004 0.062 4520 Dihedral : 14.542 142.983 4232 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.19 % Allowed : 16.13 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.61 (0.15), residues: 3150 helix: 1.01 (0.16), residues: 1106 sheet: -0.48 (0.27), residues: 366 loop : -1.40 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 133 TYR 0.019 0.001 TYR I 123 PHE 0.009 0.001 PHE J 35 TRP 0.006 0.001 TRP J 409 HIS 0.004 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (26626) covalent geometry : angle 0.55483 / 0.29 (36235) hydrogen bonds : bond 0.03743 / 4.05 ( 1052) hydrogen bonds : angle 4.50294 / 4.97 ( 2914) metal coordination : bond 0.00546 / 0.55 ( 8) metal coordination : angle 1.46474 / 2.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 348 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: G 18 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8525 (mm-40) REVERT: G 93 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7219 (mm-40) REVERT: G 185 TYR cc_start: 0.9069 (p90) cc_final: 0.8728 (p90) REVERT: H 17 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8054 (tm-30) REVERT: H 77 ASP cc_start: 0.6303 (t70) cc_final: 0.6043 (t0) REVERT: H 103 ASN cc_start: 0.8459 (m110) cc_final: 0.8027 (p0) REVERT: H 172 LEU cc_start: 0.8738 (mt) cc_final: 0.8428 (mt) REVERT: H 206 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8006 (tt0) REVERT: I 17 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8739 (mmtp) REVERT: I 72 SER cc_start: 0.8950 (t) cc_final: 0.8702 (p) REVERT: I 185 ASP cc_start: 0.8177 (t0) cc_final: 0.7953 (t0) REVERT: I 189 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: I 191 LYS cc_start: 0.8680 (mptt) cc_final: 0.8277 (mmtp) REVERT: I 214 ASN cc_start: 0.8547 (t0) cc_final: 0.8086 (t0) REVERT: I 222 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7828 (t0) REVERT: I 231 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6368 (tp30) REVERT: I 490 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7501 (tp40) REVERT: I 524 ILE cc_start: 0.9118 (tp) cc_final: 0.8714 (tp) REVERT: I 538 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9072 (pt) REVERT: I 644 LEU cc_start: 0.8876 (mp) cc_final: 0.8626 (tp) REVERT: I 850 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8331 (mm) REVERT: I 1085 MET cc_start: 0.9358 (mmm) cc_final: 0.9092 (mmm) REVERT: I 1216 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8744 (ptt180) REVERT: J 68 TYR cc_start: 0.8323 (m-80) cc_final: 0.8093 (m-80) REVERT: J 81 ARG cc_start: 0.7871 (tmm-80) cc_final: 0.7501 (ttp-170) REVERT: J 248 ASP cc_start: 0.8669 (m-30) cc_final: 0.7969 (t0) REVERT: J 352 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8629 (ptm160) REVERT: J 497 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7947 (mm-30) REVERT: J 625 MET cc_start: 0.9263 (ttp) cc_final: 0.9018 (ttp) REVERT: J 765 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.7848 (pp20) REVERT: J 889 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8346 (m-30) REVERT: J 895 CYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8707 (p) REVERT: J 913 GLU cc_start: 0.8059 (pt0) cc_final: 0.7566 (tt0) REVERT: J 954 ASN cc_start: 0.7623 (m-40) cc_final: 0.7419 (m-40) REVERT: J 999 TYR cc_start: 0.7110 (t80) cc_final: 0.6727 (t80) REVERT: J 1025 MET cc_start: 0.6282 (mtm) cc_final: 0.5948 (mtm) REVERT: J 1040 MET cc_start: 0.6716 (mmm) cc_final: 0.6463 (tpp) REVERT: J 1168 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5489 (mt-10) REVERT: J 1174 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7277 (mtp85) REVERT: J 1189 MET cc_start: 0.7430 (mmt) cc_final: 0.6594 (tmm) REVERT: J 1281 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: J 1290 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7594 (mtp180) REVERT: J 1307 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9040 (mp) outliers start: 113 outliers final: 79 residues processed: 431 average time/residue: 0.1660 time to fit residues: 113.4122 Evaluate side-chains 420 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 328 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 547 ARG Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 75 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 175 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 316 optimal weight: 0.0030 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 ASN G 137 ASN H 132 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.165456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118240 restraints weight = 30779.122| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.45 r_work: 0.2866 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26634 Z= 0.195 Angle : 0.590 8.041 36247 Z= 0.307 Chirality : 0.044 0.271 4153 Planarity : 0.004 0.057 4520 Dihedral : 14.537 142.039 4226 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.26 % Allowed : 16.61 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.66 (0.15), residues: 3150 helix: 0.97 (0.16), residues: 1106 sheet: -0.44 (0.28), residues: 361 loop : -1.44 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 133 TYR 0.017 0.001 TYR I 123 PHE 0.012 0.001 PHE I 390 TRP 0.008 0.001 TRP J 409 HIS 0.006 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (26626) covalent geometry : angle 0.58945 / 0.31 (36235) hydrogen bonds : bond 0.04017 / 4.33 ( 1052) hydrogen bonds : angle 4.52418 / 5.00 ( 2914) metal coordination : bond 0.00727 / 0.72 ( 8) metal coordination : angle 1.56594 / 2.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 346 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: G 18 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8410 (mm-40) REVERT: G 93 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7127 (mm-40) REVERT: G 185 TYR cc_start: 0.8955 (p90) cc_final: 0.8708 (p90) REVERT: H 77 ASP cc_start: 0.6308 (t70) cc_final: 0.6074 (t0) REVERT: H 97 GLU cc_start: 0.8503 (pp20) cc_final: 0.8248 (pp20) REVERT: H 103 ASN cc_start: 0.8427 (m110) cc_final: 0.8025 (p0) REVERT: H 172 LEU cc_start: 0.8765 (mt) cc_final: 0.8489 (mt) REVERT: H 206 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7805 (tt0) REVERT: I 17 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8597 (mmtp) REVERT: I 33 ASP cc_start: 0.8330 (m-30) cc_final: 0.7949 (m-30) REVERT: I 189 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: I 191 LYS cc_start: 0.8736 (mptt) cc_final: 0.8347 (mmtp) REVERT: I 214 ASN cc_start: 0.8579 (t0) cc_final: 0.8159 (t0) REVERT: I 231 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6454 (tp30) REVERT: I 376 PRO cc_start: 0.8564 (Cg_endo) cc_final: 0.8322 (Cg_exo) REVERT: I 490 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7502 (tp40) REVERT: I 524 ILE cc_start: 0.9079 (tp) cc_final: 0.8693 (tp) REVERT: I 525 THR cc_start: 0.9439 (OUTLIER) cc_final: 0.9098 (m) REVERT: I 538 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8990 (pt) REVERT: I 814 ASP cc_start: 0.8328 (m-30) cc_final: 0.8082 (m-30) REVERT: I 850 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8354 (mm) REVERT: I 1134 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7125 (pp30) REVERT: I 1188 ASP cc_start: 0.8776 (t0) cc_final: 0.8508 (t0) REVERT: I 1216 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8733 (ptt180) REVERT: J 81 ARG cc_start: 0.7724 (tmm-80) cc_final: 0.7376 (ttp-110) REVERT: J 248 ASP cc_start: 0.8491 (m-30) cc_final: 0.7869 (t0) REVERT: J 352 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8553 (ptm160) REVERT: J 625 MET cc_start: 0.9172 (ttp) cc_final: 0.8967 (ttp) REVERT: J 765 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.7527 (pp20) REVERT: J 889 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: J 895 CYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8497 (p) REVERT: J 913 GLU cc_start: 0.7813 (pt0) cc_final: 0.7334 (tt0) REVERT: J 954 ASN cc_start: 0.7611 (m-40) cc_final: 0.7394 (m-40) REVERT: J 999 TYR cc_start: 0.7091 (t80) cc_final: 0.6719 (t80) REVERT: J 1025 MET cc_start: 0.6272 (mtm) cc_final: 0.6012 (mtm) REVERT: J 1040 MET cc_start: 0.6738 (mmm) cc_final: 0.6476 (tpp) REVERT: J 1168 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5516 (mt-10) REVERT: J 1189 MET cc_start: 0.7413 (mmt) cc_final: 0.7151 (mmt) REVERT: J 1281 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: J 1290 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7654 (mtp180) REVERT: J 1307 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9068 (mp) REVERT: K 29 GLN cc_start: 0.8954 (mt0) cc_final: 0.8615 (mt0) outliers start: 115 outliers final: 84 residues processed: 432 average time/residue: 0.1607 time to fit residues: 110.2636 Evaluate side-chains 432 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 334 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 547 ARG Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 755 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 264 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 303 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 260 optimal weight: 0.1980 chunk 96 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 293 optimal weight: 0.1980 chunk 245 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 798 GLN J 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.168776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123938 restraints weight = 30826.396| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.58 r_work: 0.2790 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26634 Z= 0.111 Angle : 0.544 8.189 36247 Z= 0.284 Chirality : 0.042 0.264 4153 Planarity : 0.004 0.060 4520 Dihedral : 14.454 142.264 4224 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.49 % Allowed : 17.43 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.45 (0.15), residues: 3150 helix: 1.17 (0.16), residues: 1105 sheet: -0.29 (0.28), residues: 358 loop : -1.35 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 133 TYR 0.019 0.001 TYR I 123 PHE 0.012 0.001 PHE J 17 TRP 0.007 0.001 TRP I1276 HIS 0.003 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (26626) covalent geometry : angle 0.54338 / 0.28 (36235) hydrogen bonds : bond 0.03491 / 3.80 ( 1052) hydrogen bonds : angle 4.39275 / 4.87 ( 2914) metal coordination : bond 0.00392 / 0.40 ( 8) metal coordination : angle 1.50883 / 2.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 346 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7171 (mm-40) REVERT: G 185 TYR cc_start: 0.9079 (p90) cc_final: 0.8568 (p90) REVERT: H 77 ASP cc_start: 0.6549 (t70) cc_final: 0.6310 (t0) REVERT: H 97 GLU cc_start: 0.8568 (pp20) cc_final: 0.8241 (pp20) REVERT: H 102 LEU cc_start: 0.9022 (tp) cc_final: 0.8808 (tp) REVERT: H 103 ASN cc_start: 0.8418 (m110) cc_final: 0.7983 (p0) REVERT: H 172 LEU cc_start: 0.8691 (mt) cc_final: 0.8454 (mt) REVERT: H 206 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8057 (tt0) REVERT: I 17 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8686 (mmtp) REVERT: I 189 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8148 (m-30) REVERT: I 191 LYS cc_start: 0.8657 (mptt) cc_final: 0.8249 (mmtp) REVERT: I 214 ASN cc_start: 0.8558 (t0) cc_final: 0.8077 (t0) REVERT: I 231 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6276 (tp30) REVERT: I 239 MET cc_start: 0.2866 (OUTLIER) cc_final: 0.2492 (tmm) REVERT: I 321 LEU cc_start: 0.7606 (mp) cc_final: 0.7206 (tt) REVERT: I 376 PRO cc_start: 0.8578 (Cg_endo) cc_final: 0.8285 (Cg_exo) REVERT: I 490 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7378 (tp40) REVERT: I 538 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9054 (pt) REVERT: I 644 LEU cc_start: 0.8862 (mp) cc_final: 0.8603 (tp) REVERT: I 850 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8289 (mm) REVERT: I 1085 MET cc_start: 0.9381 (mmm) cc_final: 0.9102 (mmm) REVERT: I 1134 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7033 (pp30) REVERT: I 1216 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8645 (ptt180) REVERT: J 81 ARG cc_start: 0.7728 (tmm-80) cc_final: 0.7341 (ttp-110) REVERT: J 248 ASP cc_start: 0.8648 (m-30) cc_final: 0.7922 (t0) REVERT: J 352 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8694 (ptm160) REVERT: J 722 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8457 (mt) REVERT: J 765 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.7953 (pp20) REVERT: J 889 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8330 (m-30) REVERT: J 895 CYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8669 (p) REVERT: J 913 GLU cc_start: 0.8027 (pt0) cc_final: 0.7589 (tt0) REVERT: J 999 TYR cc_start: 0.7092 (t80) cc_final: 0.6708 (t80) REVERT: J 1025 MET cc_start: 0.6355 (mtm) cc_final: 0.5737 (mtm) REVERT: J 1040 MET cc_start: 0.6763 (mmm) cc_final: 0.6507 (tpp) REVERT: J 1168 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5431 (mt-10) REVERT: J 1189 MET cc_start: 0.7470 (mmt) cc_final: 0.6605 (tmm) REVERT: J 1281 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: J 1290 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7612 (mtp180) REVERT: J 1307 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8986 (mp) outliers start: 94 outliers final: 67 residues processed: 419 average time/residue: 0.1504 time to fit residues: 100.9222 Evaluate side-chains 410 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 328 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 547 ARG Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 210 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 133 optimal weight: 0.0980 chunk 308 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.166070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121086 restraints weight = 30725.806| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.52 r_work: 0.2879 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 26634 Z= 0.202 Angle : 0.592 8.153 36247 Z= 0.307 Chirality : 0.044 0.272 4153 Planarity : 0.004 0.056 4520 Dihedral : 14.453 141.112 4222 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.74 % Allowed : 17.58 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.55 (0.15), residues: 3150 helix: 1.10 (0.16), residues: 1103 sheet: -0.49 (0.27), residues: 382 loop : -1.38 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 133 TYR 0.016 0.001 TYR I 123 PHE 0.012 0.001 PHE I 390 TRP 0.008 0.001 TRP J 409 HIS 0.005 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (26626) covalent geometry : angle 0.59147 / 0.31 (36235) hydrogen bonds : bond 0.03919 / 4.23 ( 1052) hydrogen bonds : angle 4.43933 / 4.93 ( 2914) metal coordination : bond 0.00699 / 0.70 ( 8) metal coordination : angle 1.45803 / 2.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 343 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: G 18 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8379 (mm-40) REVERT: G 93 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7242 (mm-40) REVERT: G 185 TYR cc_start: 0.8953 (p90) cc_final: 0.8726 (p90) REVERT: H 77 ASP cc_start: 0.6623 (t70) cc_final: 0.6401 (t0) REVERT: H 97 GLU cc_start: 0.8539 (pp20) cc_final: 0.8281 (pp20) REVERT: H 102 LEU cc_start: 0.9057 (tp) cc_final: 0.8817 (tp) REVERT: H 103 ASN cc_start: 0.8384 (m110) cc_final: 0.8011 (p0) REVERT: H 172 LEU cc_start: 0.8805 (mt) cc_final: 0.8603 (mt) REVERT: H 206 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7963 (tt0) REVERT: I 17 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8628 (mmtp) REVERT: I 33 ASP cc_start: 0.8331 (m-30) cc_final: 0.7955 (m-30) REVERT: I 189 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: I 191 LYS cc_start: 0.8741 (mptt) cc_final: 0.8357 (mmtp) REVERT: I 214 ASN cc_start: 0.8512 (t0) cc_final: 0.8079 (t0) REVERT: I 231 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6351 (tp30) REVERT: I 321 LEU cc_start: 0.7592 (mp) cc_final: 0.7182 (tt) REVERT: I 376 PRO cc_start: 0.8537 (Cg_endo) cc_final: 0.8262 (Cg_exo) REVERT: I 490 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7484 (tp40) REVERT: I 524 ILE cc_start: 0.9143 (tp) cc_final: 0.8809 (tp) REVERT: I 538 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9043 (pt) REVERT: I 580 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8331 (mt0) REVERT: I 644 LEU cc_start: 0.8882 (mp) cc_final: 0.8650 (tp) REVERT: I 814 ASP cc_start: 0.8485 (m-30) cc_final: 0.8231 (m-30) REVERT: I 850 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8393 (mm) REVERT: I 957 LYS cc_start: 0.7397 (mtmt) cc_final: 0.6896 (mttm) REVERT: I 1134 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7153 (pp30) REVERT: I 1188 ASP cc_start: 0.8761 (t0) cc_final: 0.8487 (t0) REVERT: I 1216 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8747 (ptt180) REVERT: J 81 ARG cc_start: 0.7727 (tmm-80) cc_final: 0.7369 (ttp-110) REVERT: J 248 ASP cc_start: 0.8513 (m-30) cc_final: 0.7939 (t0) REVERT: J 352 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8576 (ptm160) REVERT: J 532 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: J 722 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8607 (mt) REVERT: J 765 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.7582 (pp20) REVERT: J 889 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: J 895 CYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8554 (p) REVERT: J 913 GLU cc_start: 0.7804 (pt0) cc_final: 0.7313 (tt0) REVERT: J 999 TYR cc_start: 0.7119 (t80) cc_final: 0.6736 (t80) REVERT: J 1025 MET cc_start: 0.6195 (mtm) cc_final: 0.5659 (mtm) REVERT: J 1040 MET cc_start: 0.6697 (mmm) cc_final: 0.6436 (tpp) REVERT: J 1168 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5473 (mt-10) REVERT: J 1189 MET cc_start: 0.7379 (mmt) cc_final: 0.6608 (tmm) REVERT: J 1281 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: J 1290 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7637 (mtp180) REVERT: J 1307 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9062 (mp) REVERT: K 55 GLU cc_start: 0.7961 (tt0) cc_final: 0.7689 (tt0) outliers start: 101 outliers final: 78 residues processed: 422 average time/residue: 0.1570 time to fit residues: 104.6223 Evaluate side-chains 430 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 336 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 547 ARG Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.167355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.120078 restraints weight = 30679.609| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.47 r_work: 0.2920 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 26634 Z= 0.144 Angle : 0.564 8.659 36247 Z= 0.293 Chirality : 0.043 0.269 4153 Planarity : 0.004 0.059 4520 Dihedral : 14.434 141.369 4222 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.56 % Allowed : 17.69 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.47 (0.15), residues: 3150 helix: 1.13 (0.16), residues: 1105 sheet: -0.32 (0.28), residues: 370 loop : -1.35 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 133 TYR 0.017 0.001 TYR I 123 PHE 0.009 0.001 PHE I 405 TRP 0.008 0.001 TRP J 409 HIS 0.003 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (26626) covalent geometry : angle 0.56365 / 0.29 (36235) hydrogen bonds : bond 0.03674 / 3.99 ( 1052) hydrogen bonds : angle 4.40653 / 4.89 ( 2914) metal coordination : bond 0.00520 / 0.53 ( 8) metal coordination : angle 1.49140 / 2.72 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 336 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: G 93 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7275 (mm-40) REVERT: G 185 TYR cc_start: 0.9061 (p90) cc_final: 0.8574 (p90) REVERT: H 75 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7201 (tm-30) REVERT: H 77 ASP cc_start: 0.6757 (t70) cc_final: 0.6466 (t0) REVERT: H 97 GLU cc_start: 0.8503 (pp20) cc_final: 0.8257 (pp20) REVERT: H 102 LEU cc_start: 0.9148 (tp) cc_final: 0.8922 (tp) REVERT: H 103 ASN cc_start: 0.8423 (m110) cc_final: 0.8007 (p0) REVERT: H 206 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8144 (tt0) REVERT: I 17 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8709 (mmtp) REVERT: I 126 GLU cc_start: 0.7901 (tt0) cc_final: 0.7663 (tt0) REVERT: I 189 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: I 191 LYS cc_start: 0.8711 (mptt) cc_final: 0.8318 (mmtp) REVERT: I 214 ASN cc_start: 0.8584 (t0) cc_final: 0.8138 (t0) REVERT: I 231 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6353 (tp30) REVERT: I 239 MET cc_start: 0.2944 (OUTLIER) cc_final: 0.2567 (tmm) REVERT: I 321 LEU cc_start: 0.7660 (mp) cc_final: 0.7237 (tt) REVERT: I 376 PRO cc_start: 0.8633 (Cg_endo) cc_final: 0.8301 (Cg_exo) REVERT: I 490 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7427 (tp40) REVERT: I 524 ILE cc_start: 0.9109 (tp) cc_final: 0.8687 (tp) REVERT: I 538 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9090 (pt) REVERT: I 541 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8600 (pm20) REVERT: I 580 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8407 (mt0) REVERT: I 644 LEU cc_start: 0.8859 (mp) cc_final: 0.8630 (tp) REVERT: I 850 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8382 (mm) REVERT: I 957 LYS cc_start: 0.7395 (mtmt) cc_final: 0.6926 (mtpp) REVERT: I 1085 MET cc_start: 0.9312 (mmm) cc_final: 0.9017 (mmm) REVERT: I 1134 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7134 (pp30) REVERT: I 1216 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8784 (ptt180) REVERT: I 1253 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8828 (mp) REVERT: J 81 ARG cc_start: 0.7735 (tmm-80) cc_final: 0.7373 (ttp-110) REVERT: J 248 ASP cc_start: 0.8661 (m-30) cc_final: 0.8072 (t0) REVERT: J 352 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8630 (ptm160) REVERT: J 532 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: J 722 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8589 (mt) REVERT: J 765 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.7951 (pp20) REVERT: J 889 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8284 (m-30) REVERT: J 895 CYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8673 (p) REVERT: J 913 GLU cc_start: 0.7986 (pt0) cc_final: 0.7483 (tt0) REVERT: J 999 TYR cc_start: 0.7091 (t80) cc_final: 0.6697 (t80) REVERT: J 1025 MET cc_start: 0.6247 (mtm) cc_final: 0.5680 (mtm) REVERT: J 1040 MET cc_start: 0.6743 (mmm) cc_final: 0.6478 (tpp) REVERT: J 1168 GLU cc_start: 0.6036 (OUTLIER) cc_final: 0.5443 (mt-10) REVERT: J 1189 MET cc_start: 0.7444 (mmt) cc_final: 0.6627 (tmm) REVERT: J 1281 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: J 1290 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7669 (mtp180) REVERT: J 1307 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9067 (mp) outliers start: 96 outliers final: 74 residues processed: 409 average time/residue: 0.1549 time to fit residues: 100.6684 Evaluate side-chains 423 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 330 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 547 ARG Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 126 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 312 optimal weight: 0.0270 chunk 266 optimal weight: 0.8980 chunk 299 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 95 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 227 optimal weight: 0.3980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.169578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124042 restraints weight = 30572.570| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.41 r_work: 0.2960 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.105 26634 Z= 0.109 Angle : 0.541 9.162 36247 Z= 0.282 Chirality : 0.042 0.266 4153 Planarity : 0.004 0.056 4520 Dihedral : 14.366 140.997 4222 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.19 % Allowed : 18.21 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.30 (0.15), residues: 3150 helix: 1.27 (0.16), residues: 1110 sheet: -0.21 (0.28), residues: 363 loop : -1.25 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 133 TYR 0.017 0.001 TYR I 123 PHE 0.008 0.001 PHE J 437 TRP 0.008 0.001 TRP I1276 HIS 0.003 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (26626) covalent geometry : angle 0.54070 / 0.28 (36235) hydrogen bonds : bond 0.03354 / 3.67 ( 1052) hydrogen bonds : angle 4.32325 / 4.81 ( 2914) metal coordination : bond 0.00372 / 0.38 ( 8) metal coordination : angle 1.42798 / 2.56 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6108.18 seconds wall clock time: 105 minutes 15.08 seconds (6315.08 seconds total)