Starting phenix.real_space_refine on Sun May 25 07:45:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ehf_28146/05_2025/8ehf_28146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehf_28146/05_2025/8ehf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ehf_28146/05_2025/8ehf_28146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehf_28146/05_2025/8ehf_28146.map" model { file = "/net/cci-nas-00/data/ceres_data/8ehf_28146/05_2025/8ehf_28146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehf_28146/05_2025/8ehf_28146.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'RNA': 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: 14.97, per 1000 atoms: 0.57 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: 6.82 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 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: 8.33 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: 11.79 Time building geometry restraints manager: 7.71 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: 36058 3.70 - 7.41: 146 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: 15441 27.93 - 55.86: 759 55.86 - 83.80: 112 83.80 - 111.73: 11 111.73 - 139.66: 2 Dihedral angle restraints: 16325 sinusoidal: 7228 harmonic: 9097 Sorted by residual: 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 dihedral pdb=" CA SER J 503 " pdb=" C SER J 503 " pdb=" N GLN J 504 " pdb=" CA GLN J 504 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 16322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 4134 0.179 - 0.359: 9 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 68.630 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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= 0.501 Angle : 0.766 18.513 36247 Z= 0.443 Chirality : 0.055 0.897 4153 Planarity : 0.005 0.117 4520 Dihedral : 15.973 139.662 10473 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP J 409 HIS 0.006 0.001 HIS G 23 PHE 0.022 0.002 PHE I 15 TYR 0.020 0.001 TYR G 177 ARG 0.008 0.000 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.15637 ( 1052) hydrogen bonds : angle 6.62942 ( 2914) metal coordination : bond 0.00665 ( 8) metal coordination : angle 1.51992 ( 12) covalent geometry : bond 0.00885 (26626) covalent geometry : angle 0.76537 (36235) *********************** 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 : 2.942 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: 0.7849 (p0) REVERT: H 145 LYS cc_start: 0.8807 (tttm) cc_final: 0.8592 (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: 0.8042 (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: 0.3732 time to fit residues: 288.2682 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 : 2.780 ------------------------------------------------------------------------------- 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 270 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 chunk 82 optimal weight: 8.9990 chunk 163 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 250 optimal weight: 0.9990 chunk 97 optimal weight: 0.0570 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 290 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 673 HIS I 798 GLN I 955 GLN J 94 GLN J 229 GLN J 489 ASN J 805 GLN J1218 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.167974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122447 restraints weight = 30816.875| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.62 r_work: 0.2946 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26634 Z= 0.120 Angle : 0.550 7.835 36247 Z= 0.291 Chirality : 0.042 0.214 4153 Planarity : 0.004 0.057 4520 Dihedral : 14.984 140.954 4381 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.63 % Allowed : 12.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3150 helix: 0.62 (0.16), residues: 1112 sheet: -0.58 (0.28), residues: 361 loop : -1.60 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 33 HIS 0.004 0.001 HIS I 551 PHE 0.023 0.001 PHE I 337 TYR 0.012 0.001 TYR G 177 ARG 0.008 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 1052) hydrogen bonds : angle 4.83034 ( 2914) metal coordination : bond 0.00606 ( 8) metal coordination : angle 1.78380 ( 12) covalent geometry : bond 0.00269 (26626) covalent geometry : angle 0.54958 (36235) *********************** 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 486 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 388 time to evaluate : 2.642 Fit side-chains REVERT: G 12 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7811 (mtm110) REVERT: G 18 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8187 (mm-40) REVERT: G 185 TYR cc_start: 0.8830 (p90) cc_final: 0.8447 (p90) REVERT: H 17 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7613 (tm-30) REVERT: H 66 HIS cc_start: 0.7614 (t-90) cc_final: 0.7414 (t-90) REVERT: H 77 ASP cc_start: 0.6329 (t70) cc_final: 0.6032 (t0) REVERT: H 103 ASN cc_start: 0.8430 (m-40) cc_final: 0.7982 (p0) REVERT: H 172 LEU cc_start: 0.8827 (mt) cc_final: 0.8543 (mt) REVERT: H 206 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7788 (tt0) REVERT: I 17 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8314 (mmtm) REVERT: I 72 SER cc_start: 0.8820 (t) cc_final: 0.8537 (p) REVERT: I 189 ASP cc_start: 0.8238 (m-30) cc_final: 0.7744 (m-30) REVERT: I 191 LYS cc_start: 0.8721 (mptt) cc_final: 0.8502 (mmtp) REVERT: I 195 PHE cc_start: 0.8948 (m-80) cc_final: 0.8636 (m-80) REVERT: I 214 ASN cc_start: 0.8358 (t0) cc_final: 0.8073 (t0) REVERT: I 376 PRO cc_start: 0.8695 (Cg_endo) cc_final: 0.8421 (Cg_exo) REVERT: I 490 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7543 (tp40) REVERT: I 524 ILE cc_start: 0.9054 (tp) cc_final: 0.8637 (tp) REVERT: I 538 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9026 (pt) REVERT: I 1085 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8729 (mmm) REVERT: I 1188 ASP cc_start: 0.8689 (t0) cc_final: 0.8283 (t0) REVERT: I 1310 ASP cc_start: 0.7725 (t0) cc_final: 0.7132 (t0) REVERT: J 94 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8010 (mm110) REVERT: J 192 MET cc_start: 0.8419 (ttp) cc_final: 0.8120 (ttp) REVERT: J 195 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7392 (mm-30) REVERT: J 197 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7725 (mm-30) REVERT: J 248 ASP cc_start: 0.8480 (m-30) cc_final: 0.8009 (t0) REVERT: J 591 ILE cc_start: 0.8574 (tp) cc_final: 0.8260 (pt) REVERT: J 765 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7673 (pp20) REVERT: J 889 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: J 913 GLU cc_start: 0.7531 (pt0) cc_final: 0.7186 (tt0) REVERT: J 996 LYS cc_start: 0.7905 (tptt) cc_final: 0.7616 (mptt) REVERT: J 999 TYR cc_start: 0.7183 (t80) cc_final: 0.6849 (t80) REVERT: J 1025 MET cc_start: 0.6199 (mtm) cc_final: 0.5921 (mtm) REVERT: J 1174 ARG cc_start: 0.7668 (mtp85) cc_final: 0.7411 (mtp85) REVERT: J 1189 MET cc_start: 0.7379 (mmt) cc_final: 0.6641 (tmm) REVERT: J 1238 GLN cc_start: 0.8810 (tp40) cc_final: 0.7876 (tp40) REVERT: K 35 LYS cc_start: 0.8527 (mmtp) cc_final: 0.8262 (mptt) outliers start: 98 outliers final: 58 residues processed: 459 average time/residue: 0.3711 time to fit residues: 267.7922 Evaluate side-chains 409 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 346 time to evaluate : 2.961 ------------------------------------------------------------------------------- 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 176 CYS 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 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 503 LYS 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 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 1085 MET 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 176 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 424 ASN 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 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 974 VAL Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1267 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 150 optimal weight: 0.7980 chunk 189 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 272 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 319 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN J 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.162811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116897 restraints weight = 30792.436| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.81 r_work: 0.2870 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 0.067 26634 Z= 0.248 Angle : 0.625 8.158 36247 Z= 0.326 Chirality : 0.045 0.218 4153 Planarity : 0.004 0.055 4520 Dihedral : 14.931 139.707 4349 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.38 % Allowed : 13.90 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3150 helix: 0.65 (0.16), residues: 1106 sheet: -0.72 (0.27), residues: 384 loop : -1.55 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 409 HIS 0.008 0.001 HIS G 23 PHE 0.023 0.002 PHE I 337 TYR 0.018 0.002 TYR G 177 ARG 0.011 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 1052) hydrogen bonds : angle 4.76214 ( 2914) metal coordination : bond 0.00952 ( 8) metal coordination : angle 1.69914 ( 12) covalent geometry : bond 0.00597 (26626) covalent geometry : angle 0.62418 (36235) *********************** 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 476 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 358 time to evaluate : 3.084 Fit side-chains REVERT: G 18 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8380 (mm-40) REVERT: G 185 TYR cc_start: 0.8952 (p90) cc_final: 0.8542 (p90) REVERT: H 17 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7795 (tm-30) REVERT: H 77 ASP cc_start: 0.6362 (t70) cc_final: 0.6144 (t0) REVERT: H 103 ASN cc_start: 0.8479 (m-40) cc_final: 0.8032 (p0) REVERT: H 145 LYS cc_start: 0.8705 (tttm) cc_final: 0.8496 (tttm) REVERT: H 172 LEU cc_start: 0.8821 (mt) cc_final: 0.8534 (mt) REVERT: H 206 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7796 (tt0) REVERT: I 17 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8688 (mmtp) REVERT: I 33 ASP cc_start: 0.8330 (m-30) cc_final: 0.7964 (m-30) REVERT: I 72 SER cc_start: 0.8913 (t) cc_final: 0.8671 (p) REVERT: I 189 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: I 191 LYS cc_start: 0.8753 (mptt) cc_final: 0.8516 (mmtp) REVERT: I 214 ASN cc_start: 0.8463 (t0) cc_final: 0.8025 (t0) REVERT: I 231 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7158 (mm-30) REVERT: I 239 MET cc_start: 0.2921 (OUTLIER) cc_final: 0.2708 (tmm) REVERT: I 490 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7684 (tp40) REVERT: I 524 ILE cc_start: 0.9083 (tp) cc_final: 0.8725 (tp) REVERT: I 538 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9042 (pt) REVERT: I 1188 ASP cc_start: 0.8931 (t0) cc_final: 0.8680 (t0) REVERT: J 197 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7765 (mm-30) REVERT: J 248 ASP cc_start: 0.8452 (m-30) cc_final: 0.7842 (t0) REVERT: J 352 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8676 (ptm160) REVERT: J 725 MET cc_start: 0.9526 (ptp) cc_final: 0.8353 (mtm) REVERT: J 765 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: J 889 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: J 895 CYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8549 (p) REVERT: J 913 GLU cc_start: 0.7887 (pt0) cc_final: 0.7322 (tt0) REVERT: J 954 ASN cc_start: 0.7373 (m-40) cc_final: 0.7132 (m-40) REVERT: J 999 TYR cc_start: 0.7245 (t80) cc_final: 0.6939 (t80) REVERT: J 1025 MET cc_start: 0.6165 (mtm) cc_final: 0.5951 (mtm) REVERT: J 1174 ARG cc_start: 0.7601 (mtp85) cc_final: 0.7151 (mtp85) REVERT: J 1189 MET cc_start: 0.7387 (mmt) cc_final: 0.6605 (tmm) REVERT: K 35 LYS cc_start: 0.8570 (mmtp) cc_final: 0.8286 (mptt) REVERT: K 55 GLU cc_start: 0.7784 (tt0) cc_final: 0.7401 (tt0) outliers start: 118 outliers final: 85 residues processed: 442 average time/residue: 0.3717 time to fit residues: 258.2779 Evaluate side-chains 425 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 332 time to evaluate : 2.935 ------------------------------------------------------------------------------- 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 70 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 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 377 THR 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 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 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 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 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 401 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 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 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 1146 GLU Chi-restraints excluded: chain J residue 1162 ILE 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 58 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 313 optimal weight: 0.6980 chunk 272 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 226 optimal weight: 0.5980 chunk 297 optimal weight: 5.9990 chunk 277 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 132 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 = 0.3873 r_free = 0.3873 target = 0.170538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126028 restraints weight = 30819.487| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.62 r_work: 0.2935 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26634 Z= 0.120 Angle : 0.534 8.311 36247 Z= 0.280 Chirality : 0.041 0.211 4153 Planarity : 0.004 0.053 4520 Dihedral : 14.716 140.519 4343 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.82 % Allowed : 15.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3150 helix: 0.97 (0.16), residues: 1105 sheet: -0.32 (0.28), residues: 353 loop : -1.46 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 868 HIS 0.003 0.001 HIS G 23 PHE 0.024 0.001 PHE I 337 TYR 0.019 0.001 TYR I 123 ARG 0.008 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 1052) hydrogen bonds : angle 4.48383 ( 2914) metal coordination : bond 0.00482 ( 8) metal coordination : angle 1.53379 ( 12) covalent geometry : bond 0.00275 (26626) covalent geometry : angle 0.53354 (36235) *********************** 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 473 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 370 time to evaluate : 2.786 Fit side-chains revert: symmetry clash REVERT: G 18 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8269 (mm-40) REVERT: G 185 TYR cc_start: 0.8888 (p90) cc_final: 0.8491 (p90) REVERT: H 17 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7676 (tm-30) REVERT: H 77 ASP cc_start: 0.6495 (t70) cc_final: 0.6234 (t0) REVERT: H 103 ASN cc_start: 0.8383 (m-40) cc_final: 0.8033 (p0) REVERT: H 172 LEU cc_start: 0.8769 (mt) cc_final: 0.8521 (mt) REVERT: H 206 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8011 (tt0) REVERT: I 189 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8071 (m-30) REVERT: I 191 LYS cc_start: 0.8697 (mptt) cc_final: 0.8455 (mmtp) REVERT: I 214 ASN cc_start: 0.8363 (t0) cc_final: 0.7942 (t0) REVERT: I 231 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6418 (tp30) REVERT: I 490 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7511 (tp-100) REVERT: I 524 ILE cc_start: 0.9048 (tp) cc_final: 0.8660 (tp) REVERT: I 538 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9059 (pt) REVERT: I 1085 MET cc_start: 0.9200 (mmm) cc_final: 0.8983 (mmm) REVERT: I 1170 MET cc_start: 0.9010 (tpp) cc_final: 0.8803 (mmp) REVERT: I 1253 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8791 (mp) REVERT: J 81 ARG cc_start: 0.7835 (tmm-80) cc_final: 0.7520 (ttp-170) REVERT: J 197 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7779 (mm-30) REVERT: J 248 ASP cc_start: 0.8440 (m-30) cc_final: 0.7891 (t0) REVERT: J 625 MET cc_start: 0.9266 (ttp) cc_final: 0.9054 (ttp) REVERT: J 722 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8566 (mt) REVERT: J 765 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.7668 (pp20) REVERT: J 889 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8248 (m-30) REVERT: J 913 GLU cc_start: 0.7638 (pt0) cc_final: 0.7140 (tt0) REVERT: J 999 TYR cc_start: 0.7137 (t80) cc_final: 0.6739 (t80) REVERT: J 1025 MET cc_start: 0.6145 (mtm) cc_final: 0.5851 (mtm) REVERT: J 1174 ARG cc_start: 0.7669 (mtp85) cc_final: 0.7441 (mtp85) REVERT: J 1189 MET cc_start: 0.7320 (mmt) cc_final: 0.6583 (tmm) REVERT: J 1258 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8576 (ttt90) REVERT: J 1290 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7527 (mtp180) REVERT: J 1307 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9074 (mp) REVERT: K 59 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8235 (tt) outliers start: 103 outliers final: 66 residues processed: 442 average time/residue: 0.3747 time to fit residues: 261.7919 Evaluate side-chains 407 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 332 time to evaluate : 2.773 ------------------------------------------------------------------------------- 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 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 104 ILE 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 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 635 THR Chi-restraints excluded: chain I residue 650 VAL 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 1092 THR 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 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 416 ILE Chi-restraints excluded: chain J residue 424 ASN 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 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 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 1146 GLU Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1267 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 144 optimal weight: 7.9990 chunk 301 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 183 optimal weight: 0.0030 chunk 228 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 180 optimal weight: 0.5980 chunk 249 optimal weight: 0.0070 chunk 62 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN J 229 GLN J1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.172985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.128267 restraints weight = 30598.739| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.56 r_work: 0.2971 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1662 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= 0.103 Angle : 0.512 8.458 36247 Z= 0.268 Chirality : 0.041 0.209 4153 Planarity : 0.004 0.051 4520 Dihedral : 14.548 140.739 4335 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.30 % Allowed : 16.31 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3150 helix: 1.23 (0.16), residues: 1103 sheet: -0.27 (0.27), residues: 373 loop : -1.38 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I1276 HIS 0.004 0.001 HIS H 66 PHE 0.022 0.001 PHE I 337 TYR 0.019 0.001 TYR I 123 ARG 0.009 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 1052) hydrogen bonds : angle 4.29668 ( 2914) metal coordination : bond 0.00352 ( 8) metal coordination : angle 1.25474 ( 12) covalent geometry : bond 0.00227 (26626) covalent geometry : angle 0.51146 (36235) *********************** 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 456 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 367 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8854 (p90) cc_final: 0.8578 (p90) REVERT: H 17 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7522 (tm-30) REVERT: H 75 GLN cc_start: 0.7532 (tm-30) cc_final: 0.7198 (tm-30) REVERT: H 77 ASP cc_start: 0.6540 (t70) cc_final: 0.6231 (t0) REVERT: H 95 LYS cc_start: 0.8400 (pttt) cc_final: 0.8176 (pttt) REVERT: H 172 LEU cc_start: 0.8718 (mt) cc_final: 0.8509 (mt) REVERT: H 206 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7980 (tt0) REVERT: I 80 PHE cc_start: 0.8005 (m-80) cc_final: 0.7198 (m-80) REVERT: I 189 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8333 (m-30) REVERT: I 191 LYS cc_start: 0.8670 (mptt) cc_final: 0.8328 (mmtp) REVERT: I 214 ASN cc_start: 0.8359 (t0) cc_final: 0.7891 (t0) REVERT: I 231 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6849 (mm-30) REVERT: I 364 VAL cc_start: 0.8746 (t) cc_final: 0.8355 (p) REVERT: I 490 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7561 (tp40) REVERT: I 524 ILE cc_start: 0.9114 (tp) cc_final: 0.8792 (tp) REVERT: I 538 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9030 (pt) REVERT: I 1085 MET cc_start: 0.9182 (mmm) cc_final: 0.8883 (mmm) REVERT: I 1134 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7027 (pp30) REVERT: I 1253 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8741 (mp) REVERT: I 1340 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8177 (mm-30) REVERT: J 81 ARG cc_start: 0.7766 (tmm-80) cc_final: 0.7451 (ttp-170) REVERT: J 197 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7750 (mm-30) REVERT: J 248 ASP cc_start: 0.8402 (m-30) cc_final: 0.7876 (t0) REVERT: J 497 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7675 (mt-10) REVERT: J 765 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7667 (pp20) REVERT: J 889 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: J 895 CYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8498 (p) REVERT: J 913 GLU cc_start: 0.7468 (pt0) cc_final: 0.7032 (tt0) REVERT: J 999 TYR cc_start: 0.7100 (t80) cc_final: 0.6656 (t80) REVERT: J 1025 MET cc_start: 0.6128 (mtm) cc_final: 0.5813 (mtm) REVERT: J 1174 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7444 (mtp85) REVERT: J 1189 MET cc_start: 0.7459 (mmt) cc_final: 0.6693 (tmm) REVERT: J 1258 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8605 (ttt-90) REVERT: J 1290 ARG cc_start: 0.7840 (mtm110) cc_final: 0.7544 (mtp180) REVERT: J 1307 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9051 (mp) REVERT: K 55 GLU cc_start: 0.7940 (tt0) cc_final: 0.7698 (tt0) REVERT: K 59 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8120 (tt) REVERT: K 74 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6644 (mt-10) outliers start: 89 outliers final: 63 residues processed: 433 average time/residue: 0.3762 time to fit residues: 256.2829 Evaluate side-chains 405 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 332 time to evaluate : 2.961 ------------------------------------------------------------------------------- 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 28 LEU Chi-restraints excluded: chain I residue 104 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 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 503 LYS 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 697 LYS Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 989 LEU Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1134 GLN 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 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 416 ILE 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 706 VAL 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 952 VAL 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 1146 GLU Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1267 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 110 optimal weight: 0.2980 chunk 166 optimal weight: 2.9990 chunk 93 optimal weight: 0.0270 chunk 165 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN J 954 ASN J1366 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.173219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.128444 restraints weight = 30614.377| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.50 r_work: 0.2999 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 26634 Z= 0.107 Angle : 0.510 8.799 36247 Z= 0.266 Chirality : 0.041 0.208 4153 Planarity : 0.003 0.051 4520 Dihedral : 14.422 141.386 4331 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.63 % Allowed : 16.94 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3150 helix: 1.36 (0.16), residues: 1101 sheet: -0.20 (0.27), residues: 378 loop : -1.30 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J1193 HIS 0.003 0.001 HIS J 865 PHE 0.021 0.001 PHE I 337 TYR 0.017 0.001 TYR I 123 ARG 0.013 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 1052) hydrogen bonds : angle 4.19979 ( 2914) metal coordination : bond 0.00361 ( 8) metal coordination : angle 1.16486 ( 12) covalent geometry : bond 0.00243 (26626) covalent geometry : angle 0.51013 (36235) *********************** 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 457 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 359 time to evaluate : 2.616 Fit side-chains REVERT: G 185 TYR cc_start: 0.8843 (p90) cc_final: 0.8577 (p90) REVERT: H 17 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7488 (tm-30) REVERT: H 75 GLN cc_start: 0.7419 (tm-30) cc_final: 0.7029 (tm-30) REVERT: H 77 ASP cc_start: 0.6680 (t70) cc_final: 0.6398 (t0) REVERT: H 95 LYS cc_start: 0.8416 (pttt) cc_final: 0.8191 (pttt) REVERT: H 97 GLU cc_start: 0.8450 (pp20) cc_final: 0.8203 (pp20) REVERT: H 103 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7676 (p0) REVERT: H 206 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8002 (tt0) REVERT: I 80 PHE cc_start: 0.7988 (m-80) cc_final: 0.7205 (m-80) REVERT: I 173 ASN cc_start: 0.8551 (p0) cc_final: 0.8070 (p0) REVERT: I 189 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: I 191 LYS cc_start: 0.8666 (mptt) cc_final: 0.8325 (mmtp) REVERT: I 201 ARG cc_start: 0.7758 (mtt-85) cc_final: 0.7462 (mtp85) REVERT: I 214 ASN cc_start: 0.8306 (t0) cc_final: 0.7851 (t0) REVERT: I 231 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6726 (mm-30) REVERT: I 321 LEU cc_start: 0.7449 (mp) cc_final: 0.7164 (tp) REVERT: I 364 VAL cc_start: 0.8847 (t) cc_final: 0.8482 (p) REVERT: I 490 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7542 (tp40) REVERT: I 524 ILE cc_start: 0.9095 (tp) cc_final: 0.8801 (tp) REVERT: I 538 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9108 (pt) REVERT: I 1085 MET cc_start: 0.9163 (mmm) cc_final: 0.8866 (mmm) REVERT: I 1134 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7075 (pp30) REVERT: I 1340 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8186 (mm-30) REVERT: J 81 ARG cc_start: 0.7684 (tmm-80) cc_final: 0.7425 (ttp-170) REVERT: J 197 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7762 (mm-30) REVERT: J 222 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8618 (mtmt) REVERT: J 248 ASP cc_start: 0.8411 (m-30) cc_final: 0.7891 (t0) REVERT: J 352 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8552 (ptm160) REVERT: J 462 ASP cc_start: 0.8969 (p0) cc_final: 0.8685 (p0) REVERT: J 497 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7676 (mt-10) REVERT: J 765 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7747 (pp20) REVERT: J 889 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: J 895 CYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8506 (p) REVERT: J 913 GLU cc_start: 0.7516 (pt0) cc_final: 0.7121 (tt0) REVERT: J 999 TYR cc_start: 0.7104 (t80) cc_final: 0.6603 (t80) REVERT: J 1025 MET cc_start: 0.6092 (mtm) cc_final: 0.5743 (mtm) REVERT: J 1066 GLU cc_start: 0.2816 (OUTLIER) cc_final: 0.2535 (pm20) REVERT: J 1168 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.5157 (mt-10) REVERT: J 1189 MET cc_start: 0.7469 (mmt) cc_final: 0.6723 (tmm) REVERT: J 1258 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8626 (ttt-90) REVERT: J 1290 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7530 (mtp180) REVERT: J 1307 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9046 (mp) REVERT: K 55 GLU cc_start: 0.7955 (tt0) cc_final: 0.7670 (tt0) outliers start: 98 outliers final: 68 residues processed: 430 average time/residue: 0.3839 time to fit residues: 259.7404 Evaluate side-chains 409 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 329 time to evaluate : 2.849 ------------------------------------------------------------------------------- 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 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 103 ASN 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 28 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL 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 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 503 LYS 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 697 LYS Chi-restraints excluded: chain I residue 765 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 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 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1310 ASP 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 416 ILE 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 706 VAL Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 849 LEU 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 952 VAL 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 1066 GLU Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1267 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 44 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 271 optimal weight: 0.2980 chunk 157 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN I 554 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 = 0.3884 r_free = 0.3884 target = 0.171551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126624 restraints weight = 30685.923| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.61 r_work: 0.2949 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26634 Z= 0.140 Angle : 0.532 8.838 36247 Z= 0.276 Chirality : 0.042 0.208 4153 Planarity : 0.004 0.050 4520 Dihedral : 14.401 141.461 4327 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.67 % Allowed : 17.06 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3150 helix: 1.28 (0.16), residues: 1110 sheet: -0.24 (0.27), residues: 386 loop : -1.26 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 409 HIS 0.003 0.001 HIS G 23 PHE 0.019 0.001 PHE I 337 TYR 0.013 0.001 TYR I 123 ARG 0.013 0.000 ARG J1371 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 1052) hydrogen bonds : angle 4.22023 ( 2914) metal coordination : bond 0.00523 ( 8) metal coordination : angle 1.05930 ( 12) covalent geometry : bond 0.00329 (26626) covalent geometry : angle 0.53147 (36235) *********************** 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 444 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 345 time to evaluate : 2.963 Fit side-chains revert: symmetry clash REVERT: G 93 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7372 (mm-40) REVERT: G 185 TYR cc_start: 0.8875 (p90) cc_final: 0.8585 (p90) REVERT: H 75 GLN cc_start: 0.7443 (tm-30) cc_final: 0.7032 (tm-30) REVERT: H 77 ASP cc_start: 0.6823 (t70) cc_final: 0.6504 (t0) REVERT: H 95 LYS cc_start: 0.8417 (pttt) cc_final: 0.8174 (pttt) REVERT: H 97 GLU cc_start: 0.8424 (pp20) cc_final: 0.8178 (pp20) REVERT: H 103 ASN cc_start: 0.8355 (m110) cc_final: 0.7859 (p0) REVERT: H 206 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7937 (tt0) REVERT: I 80 PHE cc_start: 0.7992 (m-80) cc_final: 0.7168 (m-80) REVERT: I 189 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: I 191 LYS cc_start: 0.8681 (mptt) cc_final: 0.8336 (mmtp) REVERT: I 214 ASN cc_start: 0.8440 (t0) cc_final: 0.7989 (t0) REVERT: I 231 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6763 (mm-30) REVERT: I 364 VAL cc_start: 0.8771 (t) cc_final: 0.8369 (p) REVERT: I 387 ASN cc_start: 0.8680 (m-40) cc_final: 0.8328 (m-40) REVERT: I 490 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7554 (tp40) REVERT: I 524 ILE cc_start: 0.9135 (tp) cc_final: 0.8860 (tp) REVERT: I 538 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9098 (pt) REVERT: I 1085 MET cc_start: 0.9198 (mmm) cc_final: 0.8875 (mmm) REVERT: I 1134 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7012 (pp30) REVERT: J 81 ARG cc_start: 0.7713 (tmm-80) cc_final: 0.7417 (ttp-170) REVERT: J 197 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7758 (mm-30) REVERT: J 222 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8625 (mtmt) REVERT: J 248 ASP cc_start: 0.8452 (m-30) cc_final: 0.7932 (t0) REVERT: J 352 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8695 (ptm160) REVERT: J 462 ASP cc_start: 0.8940 (p0) cc_final: 0.8645 (p0) REVERT: J 731 ARG cc_start: 0.8644 (tpt-90) cc_final: 0.8429 (tpt-90) REVERT: J 765 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.7699 (pp20) REVERT: J 889 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8248 (m-30) REVERT: J 895 CYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8360 (p) REVERT: J 913 GLU cc_start: 0.7629 (pt0) cc_final: 0.7212 (tt0) REVERT: J 999 TYR cc_start: 0.7107 (t80) cc_final: 0.6606 (t80) REVERT: J 1025 MET cc_start: 0.6110 (mtm) cc_final: 0.5842 (mtm) REVERT: J 1066 GLU cc_start: 0.3120 (OUTLIER) cc_final: 0.2773 (pm20) REVERT: J 1168 GLU cc_start: 0.5906 (OUTLIER) cc_final: 0.5305 (mt-10) REVERT: J 1174 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7264 (mtp-110) REVERT: J 1189 MET cc_start: 0.7363 (mmt) cc_final: 0.6566 (tmm) REVERT: J 1258 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8706 (ttt-90) REVERT: J 1290 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7489 (mtp180) REVERT: J 1307 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9070 (mp) REVERT: K 55 GLU cc_start: 0.7978 (tt0) cc_final: 0.7708 (tt0) outliers start: 99 outliers final: 71 residues processed: 416 average time/residue: 0.3867 time to fit residues: 252.4786 Evaluate side-chains 413 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 331 time to evaluate : 2.592 ------------------------------------------------------------------------------- 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 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 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 122 VAL 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 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 516 ASP 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 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 839 VAL 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 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP 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 124 ILE 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 416 ILE 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 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN 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 952 VAL 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 1066 GLU Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1267 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 90 optimal weight: 2.9990 chunk 250 optimal weight: 0.3980 chunk 272 optimal weight: 0.2980 chunk 178 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3903 r_free = 0.3903 target = 0.173328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128626 restraints weight = 30587.275| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.61 r_work: 0.2993 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 26634 Z= 0.110 Angle : 0.514 9.353 36247 Z= 0.268 Chirality : 0.041 0.206 4153 Planarity : 0.004 0.050 4520 Dihedral : 14.343 141.746 4327 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.15 % Allowed : 17.65 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3150 helix: 1.36 (0.16), residues: 1111 sheet: -0.13 (0.27), residues: 382 loop : -1.21 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J1193 HIS 0.003 0.000 HIS J 865 PHE 0.017 0.001 PHE I 337 TYR 0.013 0.001 TYR I 123 ARG 0.010 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03107 ( 1052) hydrogen bonds : angle 4.15212 ( 2914) metal coordination : bond 0.00374 ( 8) metal coordination : angle 1.05172 ( 12) covalent geometry : bond 0.00257 (26626) covalent geometry : angle 0.51395 (36235) *********************** 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 438 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 353 time to evaluate : 2.642 Fit side-chains revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8865 (p90) cc_final: 0.8577 (p90) REVERT: H 75 GLN cc_start: 0.7375 (tm-30) cc_final: 0.6961 (tm-30) REVERT: H 77 ASP cc_start: 0.6784 (t70) cc_final: 0.6488 (t0) REVERT: H 95 LYS cc_start: 0.8340 (pttt) cc_final: 0.8125 (pttt) REVERT: H 97 GLU cc_start: 0.8444 (pp20) cc_final: 0.8162 (pp20) REVERT: H 103 ASN cc_start: 0.8328 (m110) cc_final: 0.7911 (p0) REVERT: H 206 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7879 (tt0) REVERT: I 80 PHE cc_start: 0.7976 (m-80) cc_final: 0.7176 (m-80) REVERT: I 173 ASN cc_start: 0.8568 (p0) cc_final: 0.8086 (p0) REVERT: I 189 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8311 (m-30) REVERT: I 191 LYS cc_start: 0.8669 (mptt) cc_final: 0.8336 (mmtp) REVERT: I 201 ARG cc_start: 0.7621 (mtt-85) cc_final: 0.7282 (mtp85) REVERT: I 214 ASN cc_start: 0.8419 (t0) cc_final: 0.7985 (t0) REVERT: I 321 LEU cc_start: 0.7641 (mp) cc_final: 0.7335 (tt) REVERT: I 364 VAL cc_start: 0.8828 (t) cc_final: 0.8449 (p) REVERT: I 383 SER cc_start: 0.7960 (t) cc_final: 0.7516 (p) REVERT: I 387 ASN cc_start: 0.8683 (m-40) cc_final: 0.8390 (m-40) REVERT: I 490 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7515 (tp40) REVERT: I 524 ILE cc_start: 0.9107 (tp) cc_final: 0.8814 (tp) REVERT: I 538 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9111 (pt) REVERT: I 1085 MET cc_start: 0.9165 (mmm) cc_final: 0.8830 (mmm) REVERT: I 1134 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7008 (pp30) REVERT: J 81 ARG cc_start: 0.7592 (tmm-80) cc_final: 0.7354 (ttp-170) REVERT: J 197 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7767 (mm-30) REVERT: J 222 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8571 (mtmt) REVERT: J 248 ASP cc_start: 0.8434 (m-30) cc_final: 0.7926 (t0) REVERT: J 352 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8548 (ptm160) REVERT: J 462 ASP cc_start: 0.8877 (p0) cc_final: 0.8571 (p0) REVERT: J 765 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7729 (pp20) REVERT: J 889 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: J 895 CYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8352 (p) REVERT: J 913 GLU cc_start: 0.7507 (pt0) cc_final: 0.7129 (tt0) REVERT: J 1025 MET cc_start: 0.6090 (mtm) cc_final: 0.5810 (mtm) REVERT: J 1040 MET cc_start: 0.5935 (tpp) cc_final: 0.5673 (tpp) REVERT: J 1066 GLU cc_start: 0.3110 (OUTLIER) cc_final: 0.2770 (pm20) REVERT: J 1168 GLU cc_start: 0.5789 (OUTLIER) cc_final: 0.5199 (mt-10) REVERT: J 1174 ARG cc_start: 0.7597 (mtp85) cc_final: 0.7086 (mtp-110) REVERT: J 1189 MET cc_start: 0.7520 (mmt) cc_final: 0.6736 (tmm) REVERT: J 1258 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8675 (ttt-90) REVERT: J 1281 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: J 1290 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7470 (mtp180) REVERT: J 1307 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9054 (mp) REVERT: J 1317 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7377 (mt-10) REVERT: K 3 ARG cc_start: 0.8544 (tpp-160) cc_final: 0.8259 (tpp-160) REVERT: K 55 GLU cc_start: 0.7981 (tt0) cc_final: 0.7679 (tt0) outliers start: 85 outliers final: 62 residues processed: 415 average time/residue: 0.3845 time to fit residues: 248.6563 Evaluate side-chains 419 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 345 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 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 90 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 11 ILE 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 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 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 516 ASP 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 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 924 VAL 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 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 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1298 VAL 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 416 ILE 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 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN 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 952 VAL 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 1066 GLU Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1258 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 299 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 280 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3875 r_free = 0.3875 target = 0.170732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125404 restraints weight = 30711.684| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.68 r_work: 0.2943 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 26634 Z= 0.157 Angle : 0.546 9.475 36247 Z= 0.283 Chirality : 0.042 0.208 4153 Planarity : 0.004 0.050 4520 Dihedral : 14.340 141.804 4323 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.67 % Allowed : 17.17 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3150 helix: 1.29 (0.16), residues: 1107 sheet: -0.17 (0.27), residues: 383 loop : -1.24 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 409 HIS 0.003 0.001 HIS G 23 PHE 0.018 0.001 PHE I 337 TYR 0.015 0.001 TYR I 123 ARG 0.014 0.000 ARG J1371 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 1052) hydrogen bonds : angle 4.23127 ( 2914) metal coordination : bond 0.00558 ( 8) metal coordination : angle 1.16169 ( 12) covalent geometry : bond 0.00378 (26626) covalent geometry : angle 0.54601 (36235) *********************** 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 448 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 349 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8895 (p90) cc_final: 0.8655 (p90) REVERT: H 17 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7758 (tm-30) REVERT: H 77 ASP cc_start: 0.6815 (t70) cc_final: 0.6509 (t0) REVERT: H 95 LYS cc_start: 0.8358 (pttt) cc_final: 0.8129 (pttt) REVERT: H 97 GLU cc_start: 0.8449 (pp20) cc_final: 0.8176 (pp20) REVERT: H 102 LEU cc_start: 0.9012 (tp) cc_final: 0.8788 (tp) REVERT: H 206 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7836 (tt0) REVERT: I 80 PHE cc_start: 0.7979 (m-80) cc_final: 0.7139 (m-80) REVERT: I 189 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: I 191 LYS cc_start: 0.8698 (mptt) cc_final: 0.8356 (mmtp) REVERT: I 201 ARG cc_start: 0.7730 (mtt-85) cc_final: 0.7199 (mtp85) REVERT: I 214 ASN cc_start: 0.8502 (t0) cc_final: 0.8105 (t0) REVERT: I 321 LEU cc_start: 0.7630 (mp) cc_final: 0.7356 (tt) REVERT: I 364 VAL cc_start: 0.8867 (t) cc_final: 0.8513 (p) REVERT: I 383 SER cc_start: 0.7995 (t) cc_final: 0.7525 (p) REVERT: I 387 ASN cc_start: 0.8685 (m-40) cc_final: 0.8378 (m-40) REVERT: I 490 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7546 (tp40) REVERT: I 524 ILE cc_start: 0.9112 (tp) cc_final: 0.8846 (tp) REVERT: I 538 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9099 (pt) REVERT: I 580 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8340 (mt0) REVERT: I 850 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8319 (mm) REVERT: I 1085 MET cc_start: 0.9190 (mmm) cc_final: 0.8846 (mmm) REVERT: I 1134 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7076 (pp30) REVERT: J 197 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7532 (mm-30) REVERT: J 222 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8585 (mtmt) REVERT: J 248 ASP cc_start: 0.8520 (m-30) cc_final: 0.8028 (t0) REVERT: J 352 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8701 (ptm160) REVERT: J 462 ASP cc_start: 0.8897 (p0) cc_final: 0.8606 (p0) REVERT: J 765 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.7672 (pp20) REVERT: J 889 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: J 895 CYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8362 (p) REVERT: J 913 GLU cc_start: 0.7708 (pt0) cc_final: 0.7258 (tt0) REVERT: J 1025 MET cc_start: 0.6022 (mtm) cc_final: 0.5774 (mtm) REVERT: J 1040 MET cc_start: 0.5984 (tpp) cc_final: 0.5716 (tpp) REVERT: J 1066 GLU cc_start: 0.3535 (OUTLIER) cc_final: 0.3044 (pm20) REVERT: J 1168 GLU cc_start: 0.5906 (OUTLIER) cc_final: 0.5297 (mt-10) REVERT: J 1174 ARG cc_start: 0.7673 (mtp85) cc_final: 0.7192 (mtp-110) REVERT: J 1189 MET cc_start: 0.7425 (mmt) cc_final: 0.6580 (tmm) REVERT: J 1258 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8751 (ttt-90) REVERT: J 1281 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: J 1290 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7489 (mtp180) REVERT: J 1307 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9071 (mp) REVERT: K 55 GLU cc_start: 0.7967 (tt0) cc_final: 0.7633 (tt0) outliers start: 99 outliers final: 75 residues processed: 422 average time/residue: 0.3795 time to fit residues: 249.7934 Evaluate side-chains 433 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 344 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL 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 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR 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 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 503 LYS 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 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 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 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 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP 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 124 ILE 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 180 MET 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 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 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN 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 952 VAL 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 1066 GLU Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1258 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 130 optimal weight: 0.3980 chunk 174 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 303 optimal weight: 10.0000 chunk 268 optimal weight: 0.0040 chunk 166 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN H 147 GLN ** 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 = 0.3907 r_free = 0.3907 target = 0.173699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128945 restraints weight = 30472.517| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.55 r_work: 0.2992 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 26634 Z= 0.112 Angle : 0.519 9.807 36247 Z= 0.270 Chirality : 0.041 0.205 4153 Planarity : 0.004 0.050 4520 Dihedral : 14.269 141.903 4323 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.19 % Allowed : 17.61 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3150 helix: 1.39 (0.16), residues: 1109 sheet: -0.03 (0.27), residues: 376 loop : -1.19 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 409 HIS 0.003 0.001 HIS G 23 PHE 0.017 0.001 PHE I 337 TYR 0.016 0.001 TYR I 123 ARG 0.014 0.000 ARG J1371 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 1052) hydrogen bonds : angle 4.15982 ( 2914) metal coordination : bond 0.00329 ( 8) metal coordination : angle 1.22518 ( 12) covalent geometry : bond 0.00264 (26626) covalent geometry : angle 0.51893 (36235) ********************** 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 442 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 356 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8871 (p90) cc_final: 0.8572 (p90) REVERT: H 75 GLN cc_start: 0.7343 (tm-30) cc_final: 0.7048 (tm-30) REVERT: H 77 ASP cc_start: 0.6793 (t70) cc_final: 0.6502 (t0) REVERT: H 95 LYS cc_start: 0.8375 (pttt) cc_final: 0.8159 (pttt) REVERT: H 97 GLU cc_start: 0.8469 (pp20) cc_final: 0.8143 (pp20) REVERT: H 145 LYS cc_start: 0.8542 (tmtt) cc_final: 0.8320 (tmtt) REVERT: H 206 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8016 (tt0) REVERT: I 80 PHE cc_start: 0.7965 (m-80) cc_final: 0.7230 (m-80) REVERT: I 189 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8034 (m-30) REVERT: I 191 LYS cc_start: 0.8674 (mptt) cc_final: 0.8337 (mmtp) REVERT: I 201 ARG cc_start: 0.7666 (mtt-85) cc_final: 0.7303 (mtp85) REVERT: I 214 ASN cc_start: 0.8523 (t0) cc_final: 0.8121 (t0) REVERT: I 321 LEU cc_start: 0.7602 (mp) cc_final: 0.7331 (tt) REVERT: I 364 VAL cc_start: 0.8819 (t) cc_final: 0.8307 (p) REVERT: I 368 ARG cc_start: 0.8369 (ttm110) cc_final: 0.7474 (mmt90) REVERT: I 387 ASN cc_start: 0.8667 (m-40) cc_final: 0.8298 (m-40) REVERT: I 490 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7497 (tp40) REVERT: I 524 ILE cc_start: 0.9109 (tp) cc_final: 0.8823 (tp) REVERT: I 538 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9096 (pt) REVERT: I 580 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: I 850 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8316 (mm) REVERT: I 1085 MET cc_start: 0.9180 (mmm) cc_final: 0.8853 (mmm) REVERT: I 1134 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7058 (pp30) REVERT: I 1216 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8671 (ptt180) REVERT: J 197 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7544 (mm-30) REVERT: J 248 ASP cc_start: 0.8483 (m-30) cc_final: 0.7986 (t0) REVERT: J 352 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8540 (ptm160) REVERT: J 462 ASP cc_start: 0.8856 (p0) cc_final: 0.8554 (p0) REVERT: J 765 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7717 (pp20) REVERT: J 889 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8195 (m-30) REVERT: J 895 CYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8348 (p) REVERT: J 913 GLU cc_start: 0.7551 (pt0) cc_final: 0.7158 (tt0) REVERT: J 1025 MET cc_start: 0.5980 (mtm) cc_final: 0.5751 (mtm) REVERT: J 1040 MET cc_start: 0.5932 (tpp) cc_final: 0.5690 (tpp) REVERT: J 1066 GLU cc_start: 0.3114 (OUTLIER) cc_final: 0.2727 (pm20) REVERT: J 1168 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5175 (mt-10) REVERT: J 1174 ARG cc_start: 0.7585 (mtp85) cc_final: 0.7124 (mtp-110) REVERT: J 1189 MET cc_start: 0.7532 (mmt) cc_final: 0.6762 (tmm) REVERT: J 1258 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8688 (ttt-90) REVERT: J 1281 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: J 1284 ARG cc_start: 0.8639 (tpp-160) cc_final: 0.8208 (mmt-90) REVERT: J 1290 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7456 (mtp180) REVERT: J 1307 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9050 (mp) REVERT: K 3 ARG cc_start: 0.8542 (tpp-160) cc_final: 0.8283 (tpp-160) REVERT: K 55 GLU cc_start: 0.8012 (tt0) cc_final: 0.7594 (tt0) outliers start: 86 outliers final: 66 residues processed: 421 average time/residue: 0.3817 time to fit residues: 251.4257 Evaluate side-chains 419 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 338 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 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 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 11 ILE 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 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 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 503 LYS 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 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 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 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 1298 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 124 ILE 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 180 MET 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 416 ILE 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 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 805 GLN 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 952 VAL 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 1066 GLU Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1258 ARG 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 K residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 207 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 220 optimal weight: 0.4980 chunk 271 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3902 r_free = 0.3902 target = 0.173205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128157 restraints weight = 30718.897| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.62 r_work: 0.2984 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 26634 Z= 0.164 Angle : 0.655 59.200 36247 Z= 0.365 Chirality : 0.042 0.229 4153 Planarity : 0.004 0.050 4520 Dihedral : 14.271 141.921 4323 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.37 % Allowed : 17.58 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3150 helix: 1.37 (0.16), residues: 1109 sheet: -0.03 (0.27), residues: 376 loop : -1.19 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 409 HIS 0.011 0.001 HIS H 66 PHE 0.017 0.001 PHE I 337 TYR 0.014 0.001 TYR I 123 ARG 0.012 0.000 ARG J1371 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 1052) hydrogen bonds : angle 4.15480 ( 2914) metal coordination : bond 0.00453 ( 8) metal coordination : angle 1.20848 ( 12) covalent geometry : bond 0.00383 (26626) covalent geometry : angle 0.65436 (36235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12135.55 seconds wall clock time: 210 minutes 51.02 seconds (12651.02 seconds total)