Starting phenix.real_space_refine on Sat Mar 7 10:25:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c8h_16476/03_2026/8c8h_16476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c8h_16476/03_2026/8c8h_16476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c8h_16476/03_2026/8c8h_16476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c8h_16476/03_2026/8c8h_16476.map" model { file = "/net/cci-nas-00/data/ceres_data/8c8h_16476/03_2026/8c8h_16476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c8h_16476/03_2026/8c8h_16476.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.061 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 4 6.06 5 P 67 5.49 5 Mg 1 5.21 5 S 191 5.16 5 C 26243 2.51 5 N 6851 2.21 5 O 7939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41296 Number of models: 1 Model: "" Number of chains: 27 Chain: "B" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9091 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 2 Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1192 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 5603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5603 Classifications: {'peptide': 669} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 646} Chain breaks: 3 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "R" Number of atoms: 1056 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 129, 1050 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 129, 1050 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} bond proxies already assigned to first conformer: 1065 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "U" Number of atoms: 1362 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 63, 1339 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 24, 'rna3p_pyr': 25} Link IDs: {'rna2p': 14, 'rna3p': 48} Conformer: "B" Number of residues, atoms: 63, 1339 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 24, 'rna3p_pyr': 25} Link IDs: {'rna2p': 14, 'rna3p': 48} bond proxies already assigned to first conformer: 1468 Chain: "A" Number of atoms: 10188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 10188 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1223} Chain: "Q" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1013 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4347 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 11, 'TRANS': 527} Chain breaks: 2 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2484 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "S" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1311 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 150} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8500 SG CYS B1087 85.709 97.908 101.216 1.00102.55 S ATOM 8523 SG CYS B1090 84.965 94.300 100.234 1.00101.00 S ATOM 8612 SG CYS B1103 83.277 95.829 103.116 1.00102.96 S ATOM 8637 SG CYS B1106 86.922 94.911 103.456 1.00 98.80 S ATOM 14373 SG CYS I 326 51.754 114.296 100.278 1.00118.79 S ATOM 14686 SG CYS I 363 50.713 111.521 97.306 1.00102.22 S ATOM 14710 SG CYS I 366 53.512 114.200 96.871 1.00106.34 S ATOM 22247 SG CYS A 49 68.897 93.362 103.568 1.00119.06 S ATOM 22269 SG CYS A 52 69.622 97.116 103.368 1.00114.14 S ATOM 22321 SG CYS A 59 69.853 95.025 100.227 1.00112.49 S ATOM 22581 SG CYS A 90 106.249 63.550 92.795 1.00130.69 S ATOM 22605 SG CYS A 93 108.056 64.595 96.017 1.00129.42 S ATOM 22903 SG CYS A 130 109.932 63.085 93.113 1.00134.49 S ATOM 22946 SG CYS A 135 107.934 60.850 95.193 1.00140.78 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A G U 36 " occ=0.50 ... (44 atoms not shown) pdb=" C4 B G U 36 " occ=0.50 Time building chain proxies: 9.92, per 1000 atoms: 0.24 Number of scatterers: 41296 At special positions: 0 Unit cell: (154.208, 161.652, 190.367, 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 4 29.99 S 191 16.00 P 67 15.00 Mg 1 11.99 O 7939 8.00 N 6851 7.00 C 26243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS J 39 " distance=2.03 Simple disulfide: pdb=" SG CYS K 372 " - pdb=" SG CYS K 441 " distance=2.03 Simple disulfide: pdb=" SG CYS K 418 " - pdb=" SG CYS K 442 " distance=2.03 Simple disulfide: pdb=" SG CYS K 438 " - pdb=" SG CYS K 456 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" ND1 HIS I 328 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 366 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 326 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 363 " Number of angles added : 18 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9422 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 57 sheets defined 40.1% alpha, 15.5% beta 20 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 5.70 Creating SS restraints... Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 31 through 51 removed outlier: 3.827A pdb=" N THR B 51 " --> pdb=" O HIS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 257 through 278 removed outlier: 4.109A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.873A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 348 removed outlier: 3.528A pdb=" N TYR B 348 " --> pdb=" O THR B 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 345 through 348' Processing helix chain 'B' and resid 361 through 392 removed outlier: 3.536A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.595A pdb=" N ALA B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 498 through 515 removed outlier: 3.650A pdb=" N ASP B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 558 Processing helix chain 'B' and resid 610 through 614 removed outlier: 3.536A pdb=" N ASP B 613 " --> pdb=" O ARG B 610 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET B 614 " --> pdb=" O LEU B 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 610 through 614' Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 643 through 649 Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.555A pdb=" N GLN B 657 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.910A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.743A pdb=" N ALA B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 689 " --> pdb=" O PRO B 685 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.749A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.768A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 941 removed outlier: 3.641A pdb=" N ILE B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.638A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 990 Processing helix chain 'B' and resid 1021 through 1025 Processing helix chain 'B' and resid 1054 through 1064 Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.710A pdb=" N TYR B1081 " --> pdb=" O GLU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1134 Processing helix chain 'E' and resid 4 through 22 removed outlier: 4.035A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 removed outlier: 3.645A pdb=" N LEU E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'F' and resid 63 through 75 Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 112 through 124 Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.610A pdb=" N LEU G 36 " --> pdb=" O TYR G 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 170 through 186 removed outlier: 6.424A pdb=" N ASP I 180 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 192 Processing helix chain 'I' and resid 254 through 264 removed outlier: 3.828A pdb=" N ASP I 258 " --> pdb=" O ASN I 254 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 326 through 336 removed outlier: 4.357A pdb=" N ILE I 330 " --> pdb=" O CYS I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 353 Processing helix chain 'I' and resid 370 through 374 removed outlier: 3.622A pdb=" N ASN I 374 " --> pdb=" O PRO I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 421 removed outlier: 4.231A pdb=" N PHE I 409 " --> pdb=" O HIS I 405 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN I 412 " --> pdb=" O ARG I 408 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE I 413 " --> pdb=" O PHE I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 427 No H-bonds generated for 'chain 'I' and resid 425 through 427' Processing helix chain 'I' and resid 428 through 446 Processing helix chain 'I' and resid 446 through 454 removed outlier: 3.756A pdb=" N LYS I 452 " --> pdb=" O GLN I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 454 through 459 Processing helix chain 'I' and resid 482 through 501 Processing helix chain 'I' and resid 503 through 514 removed outlier: 4.093A pdb=" N ILE I 507 " --> pdb=" O SER I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 522 through 538 Processing helix chain 'I' and resid 545 through 557 Processing helix chain 'I' and resid 561 through 581 removed outlier: 3.753A pdb=" N VAL I 579 " --> pdb=" O LEU I 575 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 Processing helix chain 'I' and resid 756 through 770 removed outlier: 3.656A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 793 removed outlier: 5.890A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 20 removed outlier: 3.651A pdb=" N LYS J 20 " --> pdb=" O HIS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 36 removed outlier: 4.559A pdb=" N SER J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS J 36 " --> pdb=" O LEU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 46 Processing helix chain 'R' and resid 26 through 42 removed outlier: 4.125A pdb=" N LEU R 30 " --> pdb=" O CYS R 26 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN R 32 " --> pdb=" O SER R 28 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS R 33 " --> pdb=" O GLU R 29 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 46 removed outlier: 3.743A pdb=" N GLN R 46 " --> pdb=" O HIS R 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 43 through 46' Processing helix chain 'K' and resid 450 through 458 removed outlier: 3.653A pdb=" N SER K 454 " --> pdb=" O ARG K 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 78 through 89 Processing helix chain 'A' and resid 113 through 127 removed outlier: 4.587A pdb=" N LYS A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.792A pdb=" N ILE A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 236 through 249 Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 267 removed outlier: 4.236A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 267 " --> pdb=" O TYR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.886A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 488 removed outlier: 4.311A pdb=" N ARG A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.750A pdb=" N ILE A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.637A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 572 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 585 through 615 Processing helix chain 'A' and resid 622 through 656 Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 727 through 763 Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.895A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.657A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.668A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 943 Processing helix chain 'A' and resid 944 through 946 No H-bonds generated for 'chain 'A' and resid 944 through 946' Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.779A pdb=" N PHE A 964 " --> pdb=" O GLY A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.386A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 removed outlier: 3.589A pdb=" N ASN A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1001 through 1004' Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1035 through 1046 Processing helix chain 'A' and resid 1077 through 1093 Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1129 through 1136 removed outlier: 4.386A pdb=" N GLU A1132 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1155 Processing helix chain 'A' and resid 1155 through 1172 removed outlier: 3.755A pdb=" N GLY A1172 " --> pdb=" O LEU A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1235 through 1241 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.838A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'Q' and resid 29 through 42 Processing helix chain 'Q' and resid 43 through 46 removed outlier: 3.726A pdb=" N GLN Q 46 " --> pdb=" O HIS Q 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 43 through 46' Processing helix chain 'Y' and resid 4 through 16 removed outlier: 4.284A pdb=" N TYR Y 8 " --> pdb=" O SER Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 45 Processing helix chain 'Y' and resid 60 through 71 Processing helix chain 'Y' and resid 72 through 75 Processing helix chain 'Y' and resid 86 through 90 removed outlier: 3.617A pdb=" N ILE Y 90 " --> pdb=" O LYS Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 102 Processing helix chain 'Y' and resid 103 through 106 removed outlier: 3.857A pdb=" N THR Y 106 " --> pdb=" O PRO Y 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 103 through 106' Processing helix chain 'Y' and resid 118 through 129 removed outlier: 3.669A pdb=" N THR Y 129 " --> pdb=" O THR Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 152 removed outlier: 3.795A pdb=" N PHE Y 146 " --> pdb=" O GLU Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 161 through 175 removed outlier: 3.890A pdb=" N LYS Y 170 " --> pdb=" O ASN Y 166 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA Y 173 " --> pdb=" O SER Y 169 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 202 removed outlier: 3.664A pdb=" N THR Y 195 " --> pdb=" O VAL Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 219 through 227 Processing helix chain 'Y' and resid 264 through 282 Processing helix chain 'Y' and resid 287 through 296 removed outlier: 3.566A pdb=" N PHE Y 296 " --> pdb=" O MET Y 292 " (cutoff:3.500A) Processing helix chain 'Y' and resid 322 through 328 Processing helix chain 'Y' and resid 334 through 342 Processing helix chain 'Y' and resid 351 through 365 Processing helix chain 'Y' and resid 365 through 378 Processing helix chain 'Y' and resid 392 through 405 removed outlier: 4.075A pdb=" N ILE Y 396 " --> pdb=" O SER Y 392 " (cutoff:3.500A) Processing helix chain 'Y' and resid 418 through 427 Processing helix chain 'Y' and resid 466 through 478 Processing helix chain 'Y' and resid 479 through 484 removed outlier: 3.622A pdb=" N VAL Y 484 " --> pdb=" O ASN Y 481 " (cutoff:3.500A) Processing helix chain 'Y' and resid 508 through 534 removed outlier: 3.869A pdb=" N PHE Y 514 " --> pdb=" O ASP Y 510 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN Y 526 " --> pdb=" O LYS Y 522 " (cutoff:3.500A) Processing helix chain 'Y' and resid 535 through 543 Processing helix chain 'Y' and resid 554 through 560 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 58 through 59 No H-bonds generated for 'chain 'C' and resid 58 through 59' Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.712A pdb=" N LYS C 63 " --> pdb=" O PRO C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 117 through 123 removed outlier: 3.532A pdb=" N THR C 123 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 177 Processing helix chain 'C' and resid 207 through 229 removed outlier: 4.126A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 283 through 302 Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 72 through 80 Processing helix chain 'S' and resid 81 through 85 removed outlier: 3.736A pdb=" N ASN S 84 " --> pdb=" O ASP S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 108 Processing helix chain 'S' and resid 112 through 131 removed outlier: 3.968A pdb=" N GLU S 116 " --> pdb=" O GLY S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 217 removed outlier: 3.689A pdb=" N GLU S 217 " --> pdb=" O GLU S 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 54 through 59 removed outlier: 6.519A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 59 removed outlier: 6.519A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 360 Processing sheet with id=AA5, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.585A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AA7, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AA8, first strand: chain 'B' and resid 535 through 540 removed outlier: 5.431A pdb=" N LEU B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 532 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 538 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.812A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 870 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG B 856 " --> pdb=" O LEU B 870 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N GLU B 874 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N SER B 852 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.812A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 870 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG B 856 " --> pdb=" O LEU B 870 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N GLU B 874 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N SER B 852 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AB3, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.791A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL B 913 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 743 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE B 915 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA B 745 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1027 through 1028 removed outlier: 3.525A pdb=" N SER A 288 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AB6, first strand: chain 'B' and resid 1095 through 1097 removed outlier: 3.511A pdb=" N ILE B1097 " --> pdb=" O ILE B1100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1136 through 1142 Processing sheet with id=AB8, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB9, first strand: chain 'E' and resid 63 through 65 Processing sheet with id=AC1, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.303A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 136 through 137 removed outlier: 3.914A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 3 through 14 removed outlier: 6.990A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 84 through 91 removed outlier: 5.213A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 124 through 126 Processing sheet with id=AC6, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.115A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 162 through 166 removed outlier: 6.081A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 210 through 217 Processing sheet with id=AC9, first strand: chain 'I' and resid 307 through 308 removed outlier: 7.245A pdb=" N ILE I 307 " --> pdb=" O GLU A1265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 354 through 357 Processing sheet with id=AD2, first strand: chain 'I' and resid 656 through 658 Processing sheet with id=AD3, first strand: chain 'I' and resid 668 through 670 Processing sheet with id=AD4, first strand: chain 'R' and resid 14 through 18 removed outlier: 11.501A pdb=" N VAL R 15 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N ASN R 5 " --> pdb=" O VAL R 15 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE R 17 " --> pdb=" O LEU R 3 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU R 2 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS R 54 " --> pdb=" O GLU R 2 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL R 52 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE R 6 " --> pdb=" O TYR R 50 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N TYR R 50 " --> pdb=" O ILE R 6 " (cutoff:3.500A) removed outlier: 16.366A pdb=" N LEU R 8 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 19.225A pdb=" N GLU R 48 " --> pdb=" O LEU R 8 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 14 through 18 removed outlier: 11.501A pdb=" N VAL R 15 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N ASN R 5 " --> pdb=" O VAL R 15 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE R 17 " --> pdb=" O LEU R 3 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN R 5 " --> pdb=" O ILE R 97 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS Q 104 " --> pdb=" O SER R 116 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 104 through 106 removed outlier: 3.933A pdb=" N CYS R 104 " --> pdb=" O SER Q 116 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 383 through 385 removed outlier: 4.060A pdb=" N MET K 415 " --> pdb=" O ILE K 385 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 427 through 431 removed outlier: 3.831A pdb=" N LYS K 427 " --> pdb=" O PHE K 443 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE K 439 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 22 through 24 removed outlier: 4.279A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AE2, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.196A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 158 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 312 through 316 removed outlier: 6.999A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AE5, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AE6, first strand: chain 'A' and resid 767 through 768 removed outlier: 6.636A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AE8, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AE9, first strand: chain 'A' and resid 1125 through 1127 Processing sheet with id=AF1, first strand: chain 'A' and resid 998 through 999 removed outlier: 3.576A pdb=" N VAL A 998 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 1008 through 1012 removed outlier: 3.690A pdb=" N LYS A1015 " --> pdb=" O GLU A1012 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 17 through 18 removed outlier: 4.520A pdb=" N PHE Q 17 " --> pdb=" O LEU Q 3 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 14 through 15 removed outlier: 5.817A pdb=" N ARG Q 14 " --> pdb=" O VAL Q 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF6, first strand: chain 'Y' and resid 109 through 113 removed outlier: 8.379A pdb=" N ILE Y 110 " --> pdb=" O TRP Y 79 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE Y 81 " --> pdb=" O ILE Y 110 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE Y 112 " --> pdb=" O ILE Y 81 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU Y 83 " --> pdb=" O ILE Y 112 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE Y 136 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE Y 180 " --> pdb=" O ILE Y 136 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL Y 138 " --> pdb=" O ILE Y 180 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU Y 182 " --> pdb=" O VAL Y 138 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE Y 140 " --> pdb=" O LEU Y 182 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N SER Y 232 " --> pdb=" O SER Y 50 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU Y 52 " --> pdb=" O SER Y 232 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE Y 234 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE Y 54 " --> pdb=" O ILE Y 234 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 253 through 262 removed outlier: 5.955A pdb=" N LYS Y 253 " --> pdb=" O VAL Y 493 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL Y 495 " --> pdb=" O LYS Y 253 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR Y 255 " --> pdb=" O VAL Y 495 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE Y 497 " --> pdb=" O THR Y 255 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU Y 257 " --> pdb=" O PHE Y 497 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N MET Y 499 " --> pdb=" O LEU Y 257 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG Y 259 " --> pdb=" O MET Y 499 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG Y 501 " --> pdb=" O ARG Y 259 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL Y 261 " --> pdb=" O ARG Y 501 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN Y 456 " --> pdb=" O ASN Y 494 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N HIS Y 496 " --> pdb=" O ASN Y 456 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE Y 458 " --> pdb=" O HIS Y 496 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE Y 498 " --> pdb=" O ILE Y 458 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE Y 460 " --> pdb=" O ILE Y 498 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA Y 500 " --> pdb=" O ILE Y 460 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS Y 381 " --> pdb=" O ASP Y 457 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N PHE Y 459 " --> pdb=" O LYS Y 381 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU Y 383 " --> pdb=" O PHE Y 459 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N CYS Y 382 " --> pdb=" O CYS Y 440 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE Y 442 " --> pdb=" O CYS Y 382 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL Y 384 " --> pdb=" O PHE Y 442 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 5 through 13 Processing sheet with id=AF9, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AG1, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.502A pdb=" N ILE C 37 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU C 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AG3, first strand: chain 'C' and resid 251 through 253 1625 hydrogen bonds defined for protein. 4572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 11.84 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12924 1.34 - 1.46: 10086 1.46 - 1.59: 18755 1.59 - 1.71: 139 1.71 - 1.83: 299 Bond restraints: 42203 Sorted by residual: bond pdb=" C3' U U 20 " pdb=" C2' U U 20 " ideal model delta sigma weight residual 1.525 1.544 -0.019 1.50e-02 4.44e+03 1.63e+00 bond pdb=" C4' G U 18 " pdb=" C3' G U 18 " ideal model delta sigma weight residual 1.527 1.510 0.017 1.50e-02 4.44e+03 1.36e+00 bond pdb=" O4' U U 20 " pdb=" C1' U U 20 " ideal model delta sigma weight residual 1.415 1.398 0.017 1.50e-02 4.44e+03 1.25e+00 bond pdb=" CA THR A1109 " pdb=" CB THR A1109 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.15e+00 bond pdb=" C VAL C 173 " pdb=" O VAL C 173 " ideal model delta sigma weight residual 1.236 1.223 0.014 1.35e-02 5.49e+03 1.05e+00 ... (remaining 42198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 57077 2.78 - 5.56: 251 5.56 - 8.34: 15 8.34 - 11.13: 2 11.13 - 13.91: 1 Bond angle restraints: 57346 Sorted by residual: angle pdb=" N CYS E 14 " pdb=" CA CYS E 14 " pdb=" C CYS E 14 " ideal model delta sigma weight residual 113.18 104.94 8.24 1.33e+00 5.65e-01 3.84e+01 angle pdb=" C2' A U 31 " pdb=" C1' A U 31 " pdb=" N9 A U 31 " ideal model delta sigma weight residual 112.00 117.32 -5.32 1.50e+00 4.44e-01 1.26e+01 angle pdb=" C THR A 695 " pdb=" N ARG A 696 " pdb=" CA ARG A 696 " ideal model delta sigma weight residual 122.15 112.96 9.19 2.83e+00 1.25e-01 1.05e+01 angle pdb=" C4' G U 18 " pdb=" C3' G U 18 " pdb=" C2' G U 18 " ideal model delta sigma weight residual 102.60 99.44 3.16 1.00e+00 1.00e+00 9.96e+00 angle pdb=" O4' G U 18 " pdb=" C4' G U 18 " pdb=" C3' G U 18 " ideal model delta sigma weight residual 106.10 103.07 3.03 1.00e+00 1.00e+00 9.18e+00 ... (remaining 57341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.18: 24657 29.18 - 58.36: 918 58.36 - 87.54: 123 87.54 - 116.72: 4 116.72 - 145.90: 1 Dihedral angle restraints: 25703 sinusoidal: 11151 harmonic: 14552 Sorted by residual: dihedral pdb=" CB CYS J 7 " pdb=" SG CYS J 7 " pdb=" SG CYS J 39 " pdb=" CB CYS J 39 " ideal model delta sinusoidal sigma weight residual -86.00 -158.84 72.84 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" O4' U U 19 " pdb=" C1' U U 19 " pdb=" N1 U U 19 " pdb=" C2 U U 19 " ideal model delta sinusoidal sigma weight residual 232.00 86.10 145.90 1 1.70e+01 3.46e-03 6.07e+01 dihedral pdb=" O4' U U 16 " pdb=" C1' U U 16 " pdb=" N1 U U 16 " pdb=" C2 U U 16 " ideal model delta sinusoidal sigma weight residual -160.00 -68.93 -91.07 1 1.50e+01 4.44e-03 4.35e+01 ... (remaining 25700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4962 0.046 - 0.091: 1187 0.091 - 0.137: 391 0.137 - 0.182: 10 0.182 - 0.228: 2 Chirality restraints: 6552 Sorted by residual: chirality pdb=" C1' C U 23 " pdb=" O4' C U 23 " pdb=" C2' C U 23 " pdb=" N1 C U 23 " both_signs ideal model delta sigma weight residual False 2.45 2.22 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1' C U 44 " pdb=" O4' C U 44 " pdb=" C2' C U 44 " pdb=" N1 C U 44 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA THR E 136 " pdb=" N THR E 136 " pdb=" C THR E 136 " pdb=" CB THR E 136 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 6549 not shown) Planarity restraints: 7012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 42 " 0.024 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C ILE B 42 " -0.082 2.00e-02 2.50e+03 pdb=" O ILE B 42 " 0.031 2.00e-02 2.50e+03 pdb=" N LEU B 43 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G U 18 " 0.040 2.00e-02 2.50e+03 2.52e-02 1.91e+01 pdb=" N9 G U 18 " -0.071 2.00e-02 2.50e+03 pdb=" C8 G U 18 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G U 18 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G U 18 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G U 18 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G U 18 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G U 18 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G U 18 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G U 18 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G U 18 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G U 18 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C U 44 " -0.035 2.00e-02 2.50e+03 2.41e-02 1.30e+01 pdb=" N1 C U 44 " 0.059 2.00e-02 2.50e+03 pdb=" C2 C U 44 " -0.021 2.00e-02 2.50e+03 pdb=" O2 C U 44 " 0.008 2.00e-02 2.50e+03 pdb=" N3 C U 44 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C U 44 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C U 44 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C U 44 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C U 44 " 0.001 2.00e-02 2.50e+03 ... (remaining 7009 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 745 2.66 - 3.22: 37068 3.22 - 3.78: 65225 3.78 - 4.34: 93930 4.34 - 4.90: 150584 Nonbonded interactions: 347552 Sorted by model distance: nonbonded pdb=" OD1 ASP A 419 " pdb="MG MG A1301 " model vdw 2.105 2.170 nonbonded pdb=" OH TYR A 606 " pdb=" OE2 GLU A 626 " model vdw 2.147 3.040 nonbonded pdb=" O VAL A 619 " pdb=" OH TYR S 144 " model vdw 2.173 3.040 nonbonded pdb=" O GLU I 398 " pdb=" OG SER Y 547 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR B 208 " pdb=" O PHE B 315 " model vdw 2.179 3.040 ... (remaining 347547 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 'Q' and (resid 1 through 15 or resid 17 through 124)) selection = (chain 'R' and (resid 1 through 15 or resid 17 through 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 124)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.050 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 51.180 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.002 0.039 42223 Z= 0.115 Angle : 0.564 16.801 57372 Z= 0.315 Chirality : 0.042 0.228 6552 Planarity : 0.006 0.073 7012 Dihedral : 14.853 145.902 16269 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.29 % Allowed : 7.66 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.10), residues: 4859 helix: -2.18 (0.09), residues: 1813 sheet: -1.64 (0.18), residues: 712 loop : -2.37 (0.11), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG I 317 TYR 0.025 0.001 TYR C 170 PHE 0.037 0.001 PHE A 938 TRP 0.015 0.001 TRP I 777 HIS 0.007 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00230 (42203) covalent geometry : angle 0.55673 (57346) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.85209 ( 8) hydrogen bonds : bond 0.13526 ( 1645) hydrogen bonds : angle 6.37067 ( 4666) metal coordination : bond 0.01432 ( 16) metal coordination : angle 5.14530 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 1240 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 TYR cc_start: 0.7888 (t80) cc_final: 0.7500 (t80) REVERT: B 209 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7947 (tttt) REVERT: B 237 SER cc_start: 0.9036 (m) cc_final: 0.8596 (t) REVERT: B 307 PHE cc_start: 0.7801 (t80) cc_final: 0.7361 (t80) REVERT: B 474 ASP cc_start: 0.8102 (t70) cc_final: 0.7716 (t0) REVERT: B 614 MET cc_start: 0.7332 (mtm) cc_final: 0.7120 (mtm) REVERT: B 627 ILE cc_start: 0.9067 (mt) cc_final: 0.8864 (tp) REVERT: B 680 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.6833 (p0) REVERT: B 704 ASP cc_start: 0.7246 (m-30) cc_final: 0.6839 (m-30) REVERT: B 719 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7155 (mt-10) REVERT: B 721 PRO cc_start: 0.8827 (Cg_endo) cc_final: 0.8241 (Cg_exo) REVERT: B 777 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8438 (ttmt) REVERT: B 785 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: B 790 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7398 (ptpp) REVERT: B 794 ARG cc_start: 0.6427 (mtm110) cc_final: 0.6193 (mmt180) REVERT: B 1014 TYR cc_start: 0.7983 (t80) cc_final: 0.6202 (t80) REVERT: B 1085 TYR cc_start: 0.8723 (m-80) cc_final: 0.8271 (m-80) REVERT: B 1131 MET cc_start: 0.8744 (mmt) cc_final: 0.8449 (mmp) REVERT: B 1141 ASP cc_start: 0.8044 (m-30) cc_final: 0.7823 (m-30) REVERT: E 51 ARG cc_start: 0.8596 (ttm170) cc_final: 0.8359 (tmt-80) REVERT: E 152 LEU cc_start: 0.8719 (mt) cc_final: 0.7345 (mt) REVERT: F 94 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8608 (mm-40) REVERT: F 147 LEU cc_start: 0.9151 (tp) cc_final: 0.8949 (tt) REVERT: F 152 ASP cc_start: 0.7922 (m-30) cc_final: 0.7634 (m-30) REVERT: G 83 ASP cc_start: 0.7003 (m-30) cc_final: 0.6724 (m-30) REVERT: G 103 ASP cc_start: 0.7858 (p0) cc_final: 0.6689 (m-30) REVERT: G 104 LEU cc_start: 0.9108 (tp) cc_final: 0.8880 (tp) REVERT: G 125 PHE cc_start: 0.8442 (t80) cc_final: 0.8090 (t80) REVERT: I 205 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8020 (tttt) REVERT: I 214 LEU cc_start: 0.8276 (tp) cc_final: 0.7540 (pt) REVERT: I 376 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7472 (t70) REVERT: I 384 THR cc_start: 0.3823 (OUTLIER) cc_final: 0.2615 (m) REVERT: I 487 MET cc_start: 0.6754 (mmp) cc_final: 0.6386 (mmm) REVERT: I 646 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8739 (mmmt) REVERT: J 10 CYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7631 (p) REVERT: A 73 ILE cc_start: 0.9179 (mm) cc_final: 0.8966 (mm) REVERT: A 105 ASP cc_start: 0.8088 (m-30) cc_final: 0.7572 (p0) REVERT: A 151 PHE cc_start: 0.8167 (m-80) cc_final: 0.7917 (m-80) REVERT: A 266 THR cc_start: 0.8786 (p) cc_final: 0.8479 (p) REVERT: A 287 ARG cc_start: 0.8533 (ttp-170) cc_final: 0.8209 (ttm-80) REVERT: A 389 VAL cc_start: 0.8460 (t) cc_final: 0.8221 (p) REVERT: A 423 MET cc_start: 0.8540 (mtt) cc_final: 0.8299 (mtt) REVERT: A 530 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8615 (t) REVERT: A 545 LEU cc_start: 0.8685 (mt) cc_final: 0.8443 (tp) REVERT: A 675 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 765 ASP cc_start: 0.7389 (m-30) cc_final: 0.7002 (m-30) REVERT: A 836 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9146 (p) REVERT: A 998 VAL cc_start: 0.8534 (t) cc_final: 0.8271 (p) REVERT: A 1068 PHE cc_start: 0.9094 (m-80) cc_final: 0.8722 (m-80) REVERT: A 1199 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8138 (m-40) REVERT: A 1234 ASP cc_start: 0.7983 (m-30) cc_final: 0.7761 (m-30) REVERT: A 1241 PHE cc_start: 0.9031 (m-80) cc_final: 0.8742 (m-80) REVERT: A 1242 SER cc_start: 0.8966 (m) cc_final: 0.8573 (p) REVERT: Y 182 LEU cc_start: 0.8447 (mp) cc_final: 0.8179 (mt) REVERT: Y 218 VAL cc_start: 0.6361 (OUTLIER) cc_final: 0.5273 (m) REVERT: Y 258 MET cc_start: 0.2983 (mtt) cc_final: 0.2612 (mmm) REVERT: Y 565 LEU cc_start: 0.6610 (mt) cc_final: 0.5976 (mp) REVERT: C 29 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8541 (mt) REVERT: C 31 LYS cc_start: 0.8233 (mtmt) cc_final: 0.8012 (mtmm) REVERT: C 42 SER cc_start: 0.7819 (t) cc_final: 0.7135 (p) REVERT: C 98 ASP cc_start: 0.7645 (m-30) cc_final: 0.7155 (t0) REVERT: C 101 TYR cc_start: 0.8723 (m-80) cc_final: 0.8419 (m-10) REVERT: C 151 ASN cc_start: 0.8831 (p0) cc_final: 0.8297 (p0) REVERT: C 239 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6624 (mm-30) REVERT: C 244 TYR cc_start: 0.7760 (t80) cc_final: 0.7066 (t80) REVERT: C 250 MET cc_start: 0.8601 (tpp) cc_final: 0.8171 (tpt) REVERT: S 78 TYR cc_start: 0.7500 (t80) cc_final: 0.7253 (t80) REVERT: S 118 LEU cc_start: 0.7554 (mt) cc_final: 0.7079 (mp) REVERT: S 125 ILE cc_start: 0.7640 (mt) cc_final: 0.7412 (tt) outliers start: 194 outliers final: 24 residues processed: 1374 average time/residue: 0.2696 time to fit residues: 600.0144 Evaluate side-chains 656 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 619 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 376 ASP Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain I residue 558 SER Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 218 VAL Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain S residue 107 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 470 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 ASN B 169 ASN B 288 ASN ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 344 HIS B 387 ASN ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN B 681 HIS ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 HIS B 789 ASN B 971 GLN B1040 GLN B1101 ASN B1132 ASN E 30 ASN E 129 GLN F 115 HIS ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN G 100 GLN G 133 ASN I 246 ASN I 253 ASN I 348 ASN I 419 ASN I 448 GLN I 489 ASN I 567 HIS I 703 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 728 GLN I 735 ASN I 753 ASN J 51 GLN J 53 ASN K 373 GLN K 374 ASN ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 167 GLN ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 255 ASN A 309 ASN A 318 ASN A 359 HIS A 385 HIS ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS A 589 ASN A 611 ASN A 636 ASN A 641 ASN A 741 GLN A 865 HIS A 994 ASN A1065 ASN A1094 ASN A1116 GLN A1142 ASN A1149 ASN A1169 ASN A1199 ASN A1226 HIS ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 ASN Y 144 HIS Y 145 ASN Y 166 ASN Y 189 ASN Y 272 GLN Y 391 GLN Y 408 ASN Y 472 GLN C 2 GLN C 24 GLN C 27 ASN C 129 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN C 171 ASN S 58 ASN S 72 ASN S 135 ASN S 225 ASN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.113062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.087615 restraints weight = 250893.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090868 restraints weight = 111898.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.091018 restraints weight = 55236.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.091273 restraints weight = 51606.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.091395 restraints weight = 42276.356| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 42223 Z= 0.345 Angle : 0.860 19.998 57372 Z= 0.444 Chirality : 0.051 0.245 6552 Planarity : 0.006 0.074 7012 Dihedral : 12.127 146.434 6417 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.03 % Allowed : 16.07 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.11), residues: 4859 helix: -0.37 (0.11), residues: 1780 sheet: -1.10 (0.20), residues: 637 loop : -1.84 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG C 184 TYR 0.040 0.003 TYR I 734 PHE 0.028 0.003 PHE Y 531 TRP 0.020 0.002 TRP S 43 HIS 0.012 0.002 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00771 (42203) covalent geometry : angle 0.85321 (57346) SS BOND : bond 0.01004 ( 4) SS BOND : angle 2.08008 ( 8) hydrogen bonds : bond 0.05332 ( 1645) hydrogen bonds : angle 5.46166 ( 4666) metal coordination : bond 0.02250 ( 16) metal coordination : angle 5.96559 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 586 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 SER cc_start: 0.9224 (m) cc_final: 0.8736 (t) REVERT: B 307 PHE cc_start: 0.7671 (t80) cc_final: 0.7330 (t80) REVERT: B 311 MET cc_start: 0.8022 (ttm) cc_final: 0.7790 (ttm) REVERT: B 319 MET cc_start: 0.7355 (mmt) cc_final: 0.6210 (mmm) REVERT: B 474 ASP cc_start: 0.7877 (t70) cc_final: 0.7587 (t0) REVERT: B 482 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8730 (m) REVERT: B 662 ASP cc_start: 0.8296 (t0) cc_final: 0.7662 (t0) REVERT: B 680 ASN cc_start: 0.7479 (OUTLIER) cc_final: 0.6786 (p0) REVERT: B 716 MET cc_start: 0.7715 (mtp) cc_final: 0.7188 (mtp) REVERT: B 771 ASP cc_start: 0.8759 (t0) cc_final: 0.7966 (t0) REVERT: B 777 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8402 (ttmm) REVERT: B 785 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: E 51 ARG cc_start: 0.8575 (ttm170) cc_final: 0.8374 (tmt-80) REVERT: F 152 ASP cc_start: 0.8068 (m-30) cc_final: 0.7822 (m-30) REVERT: G 58 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8771 (mt) REVERT: G 83 ASP cc_start: 0.7753 (m-30) cc_final: 0.7066 (m-30) REVERT: G 103 ASP cc_start: 0.8049 (p0) cc_final: 0.7137 (m-30) REVERT: G 104 LEU cc_start: 0.9236 (tp) cc_final: 0.9034 (tp) REVERT: G 141 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8233 (mp) REVERT: I 168 MET cc_start: 0.8640 (mtp) cc_final: 0.8236 (mmm) REVERT: I 205 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8199 (tttt) REVERT: I 372 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7834 (mm) REVERT: I 415 MET cc_start: 0.7597 (mmm) cc_final: 0.7374 (ttt) REVERT: I 487 MET cc_start: 0.7304 (mmp) cc_final: 0.6730 (mmm) REVERT: I 593 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: I 695 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7909 (p0) REVERT: I 715 MET cc_start: 0.8385 (tpt) cc_final: 0.8098 (tpt) REVERT: R 72 ASN cc_start: 0.8860 (p0) cc_final: 0.8536 (p0) REVERT: A 107 ASN cc_start: 0.7437 (t0) cc_final: 0.6901 (t0) REVERT: A 266 THR cc_start: 0.8688 (p) cc_final: 0.8479 (p) REVERT: A 287 ARG cc_start: 0.8617 (ttp-170) cc_final: 0.8265 (ttm-80) REVERT: A 536 MET cc_start: 0.9125 (mmm) cc_final: 0.8836 (mmt) REVERT: A 633 MET cc_start: 0.8382 (mtp) cc_final: 0.8172 (mtp) REVERT: A 675 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8046 (mm-30) REVERT: A 677 MET cc_start: 0.8477 (ttp) cc_final: 0.8182 (mtp) REVERT: A 781 ILE cc_start: 0.8509 (mm) cc_final: 0.8203 (mm) REVERT: A 1026 TYR cc_start: 0.8176 (m-80) cc_final: 0.7837 (m-80) REVERT: A 1068 PHE cc_start: 0.9077 (m-80) cc_final: 0.8858 (m-80) REVERT: A 1103 ILE cc_start: 0.9077 (mp) cc_final: 0.8745 (mt) REVERT: A 1242 SER cc_start: 0.8940 (m) cc_final: 0.8575 (p) REVERT: Q 16 LYS cc_start: 0.6351 (pttt) cc_final: 0.5665 (mttt) REVERT: Q 102 MET cc_start: 0.6170 (mtp) cc_final: 0.5636 (mpp) REVERT: Q 105 ARG cc_start: 0.7478 (ttt-90) cc_final: 0.6852 (ttp-170) REVERT: Y 63 MET cc_start: 0.8666 (ttp) cc_final: 0.8300 (tmm) REVERT: Y 258 MET cc_start: 0.2702 (mtt) cc_final: 0.2184 (mmt) REVERT: Y 391 GLN cc_start: 0.2776 (OUTLIER) cc_final: 0.2276 (pm20) REVERT: Y 463 MET cc_start: 0.1935 (mmm) cc_final: 0.1589 (mmt) REVERT: Y 531 PHE cc_start: 0.8720 (m-80) cc_final: 0.8146 (m-80) REVERT: C 31 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8058 (mtmm) REVERT: C 98 ASP cc_start: 0.7480 (m-30) cc_final: 0.7135 (t0) REVERT: C 142 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8777 (tp) REVERT: C 170 TYR cc_start: 0.7873 (t80) cc_final: 0.7477 (t80) REVERT: S 77 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7239 (tm-30) outliers start: 182 outliers final: 92 residues processed: 728 average time/residue: 0.2526 time to fit residues: 306.1855 Evaluate side-chains 562 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 459 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 253 ASN Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 395 PHE Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 695 ASN Chi-restraints excluded: chain I residue 752 SER Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 78 ASN Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 391 GLN Chi-restraints excluded: chain Y residue 441 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 150 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 376 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 290 optimal weight: 0.8980 chunk 464 optimal weight: 3.9990 chunk 330 optimal weight: 0.9990 chunk 280 optimal weight: 0.4980 chunk 383 optimal weight: 8.9990 chunk 384 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN B 318 HIS ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 HIS B 789 ASN ** F 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 373 GLN ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 HIS Y 78 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.115951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.090048 restraints weight = 252978.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093386 restraints weight = 114562.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094329 restraints weight = 59402.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095106 restraints weight = 38100.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095330 restraints weight = 33618.392| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 42223 Z= 0.169 Angle : 0.655 15.073 57372 Z= 0.339 Chirality : 0.046 0.221 6552 Planarity : 0.004 0.056 7012 Dihedral : 11.673 148.498 6385 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.63 % Allowed : 16.45 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.12), residues: 4859 helix: 0.23 (0.12), residues: 1768 sheet: -0.96 (0.20), residues: 650 loop : -1.62 (0.12), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 681 TYR 0.039 0.002 TYR I 734 PHE 0.032 0.002 PHE I 793 TRP 0.016 0.002 TRP A 365 HIS 0.010 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00377 (42203) covalent geometry : angle 0.64773 (57346) SS BOND : bond 0.01050 ( 4) SS BOND : angle 4.01684 ( 8) hydrogen bonds : bond 0.04377 ( 1645) hydrogen bonds : angle 5.11082 ( 4666) metal coordination : bond 0.01002 ( 16) metal coordination : angle 4.90066 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 547 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 SER cc_start: 0.9147 (m) cc_final: 0.8710 (t) REVERT: B 386 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8142 (mpp) REVERT: B 474 ASP cc_start: 0.7780 (t70) cc_final: 0.7550 (t0) REVERT: B 482 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8682 (m) REVERT: B 662 ASP cc_start: 0.8032 (t0) cc_final: 0.7635 (t0) REVERT: B 680 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6738 (p0) REVERT: B 704 ASP cc_start: 0.7557 (m-30) cc_final: 0.6206 (m-30) REVERT: B 716 MET cc_start: 0.7593 (mtp) cc_final: 0.7141 (mtp) REVERT: B 771 ASP cc_start: 0.8643 (t0) cc_final: 0.7895 (t0) REVERT: B 785 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: B 862 THR cc_start: 0.8479 (m) cc_final: 0.8260 (t) REVERT: F 152 ASP cc_start: 0.7943 (m-30) cc_final: 0.7699 (m-30) REVERT: G 83 ASP cc_start: 0.7749 (m-30) cc_final: 0.6976 (m-30) REVERT: G 103 ASP cc_start: 0.7935 (p0) cc_final: 0.6991 (m-30) REVERT: G 104 LEU cc_start: 0.9186 (tp) cc_final: 0.8980 (tp) REVERT: G 141 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8253 (mp) REVERT: I 168 MET cc_start: 0.8390 (mtp) cc_final: 0.8019 (mmm) REVERT: I 205 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8012 (tttt) REVERT: I 211 TYR cc_start: 0.7141 (m-80) cc_final: 0.6832 (m-80) REVERT: I 259 TRP cc_start: 0.8771 (m-10) cc_final: 0.8470 (m-10) REVERT: I 415 MET cc_start: 0.7549 (mmm) cc_final: 0.7035 (ttt) REVERT: I 487 MET cc_start: 0.7302 (mmp) cc_final: 0.6734 (mmm) REVERT: I 593 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: I 599 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.5173 (pp) REVERT: J 10 CYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7534 (p) REVERT: R 6 ILE cc_start: 0.8788 (mt) cc_final: 0.8577 (mm) REVERT: R 14 ARG cc_start: 0.5830 (OUTLIER) cc_final: 0.5361 (ptm160) REVERT: R 72 ASN cc_start: 0.8524 (p0) cc_final: 0.8158 (p0) REVERT: R 73 ASN cc_start: 0.6749 (m-40) cc_final: 0.6255 (m-40) REVERT: R 127 LEU cc_start: 0.8474 (mt) cc_final: 0.8248 (mp) REVERT: A 105 ASP cc_start: 0.8224 (m-30) cc_final: 0.7605 (p0) REVERT: A 107 ASN cc_start: 0.7092 (t0) cc_final: 0.6593 (t0) REVERT: A 140 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7025 (mm-40) REVERT: A 266 THR cc_start: 0.8609 (p) cc_final: 0.8359 (p) REVERT: A 287 ARG cc_start: 0.8632 (ttp-170) cc_final: 0.8324 (ttm-80) REVERT: A 675 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7849 (mm-30) REVERT: A 687 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6906 (mtt-85) REVERT: A 781 ILE cc_start: 0.8421 (mm) cc_final: 0.8144 (mm) REVERT: A 836 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9090 (p) REVERT: A 934 LEU cc_start: 0.8807 (mt) cc_final: 0.8588 (mt) REVERT: A 1026 TYR cc_start: 0.8081 (m-80) cc_final: 0.7646 (m-80) REVERT: A 1028 LYS cc_start: 0.9345 (ttpp) cc_final: 0.9013 (ttpp) REVERT: A 1063 GLU cc_start: 0.8487 (pt0) cc_final: 0.8201 (tm-30) REVERT: A 1242 SER cc_start: 0.8816 (m) cc_final: 0.8432 (p) REVERT: Q 76 TYR cc_start: 0.5279 (m-80) cc_final: 0.4601 (m-80) REVERT: Q 102 MET cc_start: 0.5751 (mtp) cc_final: 0.5360 (mpp) REVERT: Q 105 ARG cc_start: 0.7575 (ttt-90) cc_final: 0.7001 (ttp-170) REVERT: Y 192 GLN cc_start: 0.8815 (pt0) cc_final: 0.8440 (pt0) REVERT: Y 220 GLU cc_start: 0.8478 (tt0) cc_final: 0.7940 (mm-30) REVERT: Y 258 MET cc_start: 0.2601 (mtt) cc_final: 0.2252 (mmt) REVERT: Y 531 PHE cc_start: 0.8584 (m-80) cc_final: 0.7899 (m-80) REVERT: C 31 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8076 (mtmm) REVERT: C 170 TYR cc_start: 0.7578 (t80) cc_final: 0.7355 (t80) REVERT: C 279 MET cc_start: 0.8072 (mmm) cc_final: 0.7282 (mmt) REVERT: S 39 ASP cc_start: 0.8743 (p0) cc_final: 0.8478 (p0) outliers start: 164 outliers final: 99 residues processed: 670 average time/residue: 0.2489 time to fit residues: 280.4910 Evaluate side-chains 585 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 474 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 318 HIS Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1080 ASP Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 276 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain I residue 599 LEU Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 752 SER Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 687 ARG Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 78 ASN Chi-restraints excluded: chain Y residue 408 ASN Chi-restraints excluded: chain Y residue 445 SER Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 536 LEU Chi-restraints excluded: chain Y residue 547 SER Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 430 optimal weight: 9.9990 chunk 330 optimal weight: 0.7980 chunk 425 optimal weight: 6.9990 chunk 76 optimal weight: 0.0170 chunk 194 optimal weight: 3.9990 chunk 374 optimal weight: 7.9990 chunk 456 optimal weight: 0.8980 chunk 345 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 272 optimal weight: 0.0070 chunk 256 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN B 388 ASN B 436 GLN B 693 GLN E 62 GLN E 125 ASN ** F 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN G 64 ASN I 178 ASN I 253 ASN I 589 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 ASN ** R 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS A 428 ASN A 435 GLN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN Q 43 HIS C 137 GLN C 230 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.117756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092314 restraints weight = 262075.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.096137 restraints weight = 106837.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.096430 restraints weight = 50425.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.096843 restraints weight = 40623.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.096873 restraints weight = 35292.781| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42223 Z= 0.120 Angle : 0.601 13.210 57372 Z= 0.309 Chirality : 0.044 0.209 6552 Planarity : 0.004 0.053 7012 Dihedral : 11.452 152.421 6384 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.34 % Allowed : 17.80 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.12), residues: 4859 helix: 0.60 (0.12), residues: 1762 sheet: -0.74 (0.20), residues: 659 loop : -1.47 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 184 TYR 0.037 0.001 TYR R 41 PHE 0.028 0.001 PHE A 938 TRP 0.015 0.001 TRP A 365 HIS 0.026 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00262 (42203) covalent geometry : angle 0.59569 (57346) SS BOND : bond 0.00565 ( 4) SS BOND : angle 1.32736 ( 8) hydrogen bonds : bond 0.03860 ( 1645) hydrogen bonds : angle 4.88914 ( 4666) metal coordination : bond 0.00651 ( 16) metal coordination : angle 4.64803 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 547 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 SER cc_start: 0.9154 (m) cc_final: 0.8700 (t) REVERT: B 320 ASN cc_start: 0.6292 (t0) cc_final: 0.5930 (p0) REVERT: B 474 ASP cc_start: 0.7827 (t70) cc_final: 0.7345 (t0) REVERT: B 482 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8625 (m) REVERT: B 662 ASP cc_start: 0.7865 (t0) cc_final: 0.7546 (t0) REVERT: B 680 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.6829 (p0) REVERT: B 716 MET cc_start: 0.7502 (mtp) cc_final: 0.7266 (mtp) REVERT: B 771 ASP cc_start: 0.8574 (t0) cc_final: 0.7829 (t0) REVERT: B 785 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: B 862 THR cc_start: 0.8394 (m) cc_final: 0.8121 (t) REVERT: B 928 MET cc_start: 0.8126 (tpp) cc_final: 0.7924 (tpp) REVERT: B 966 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7702 (mmt) REVERT: B 1085 TYR cc_start: 0.8226 (m-80) cc_final: 0.7465 (m-10) REVERT: E 72 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8740 (p) REVERT: F 152 ASP cc_start: 0.7960 (m-30) cc_final: 0.7727 (m-30) REVERT: G 83 ASP cc_start: 0.7688 (m-30) cc_final: 0.7115 (m-30) REVERT: G 103 ASP cc_start: 0.7661 (p0) cc_final: 0.6835 (m-30) REVERT: G 104 LEU cc_start: 0.9158 (tp) cc_final: 0.8941 (tp) REVERT: G 124 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.6065 (p90) REVERT: I 168 MET cc_start: 0.8494 (mtp) cc_final: 0.8085 (mmm) REVERT: I 205 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8017 (tttt) REVERT: I 259 TRP cc_start: 0.8752 (m-10) cc_final: 0.8453 (m-10) REVERT: I 415 MET cc_start: 0.7629 (mmm) cc_final: 0.7253 (ttt) REVERT: I 487 MET cc_start: 0.7408 (mmp) cc_final: 0.6768 (mmm) REVERT: I 599 LEU cc_start: 0.5296 (OUTLIER) cc_final: 0.5090 (pp) REVERT: J 10 CYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7415 (p) REVERT: R 72 ASN cc_start: 0.8424 (p0) cc_final: 0.8009 (p0) REVERT: R 73 ASN cc_start: 0.6755 (m-40) cc_final: 0.6202 (m-40) REVERT: K 392 MET cc_start: 0.7086 (ttm) cc_final: 0.6786 (tpp) REVERT: A 18 ASN cc_start: 0.7538 (m-40) cc_final: 0.6162 (m-40) REVERT: A 105 ASP cc_start: 0.8323 (m-30) cc_final: 0.7665 (p0) REVERT: A 107 ASN cc_start: 0.7013 (t0) cc_final: 0.6475 (t0) REVERT: A 266 THR cc_start: 0.8636 (p) cc_final: 0.8411 (p) REVERT: A 287 ARG cc_start: 0.8624 (ttp-170) cc_final: 0.8349 (ttm-80) REVERT: A 614 ARG cc_start: 0.8689 (mmt-90) cc_final: 0.8461 (mmt180) REVERT: A 675 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 677 MET cc_start: 0.8465 (ttp) cc_final: 0.8236 (ttm) REVERT: A 781 ILE cc_start: 0.8391 (mm) cc_final: 0.8106 (mm) REVERT: A 836 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.8959 (p) REVERT: A 837 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8427 (tt) REVERT: A 1026 TYR cc_start: 0.8055 (m-80) cc_final: 0.7731 (m-80) REVERT: A 1031 GLU cc_start: 0.8314 (mp0) cc_final: 0.8049 (mp0) REVERT: A 1063 GLU cc_start: 0.8678 (pt0) cc_final: 0.8255 (tm-30) REVERT: A 1242 SER cc_start: 0.8789 (m) cc_final: 0.8407 (p) REVERT: Q 16 LYS cc_start: 0.6036 (OUTLIER) cc_final: 0.5822 (ptmt) REVERT: Q 62 LYS cc_start: 0.8773 (tmmt) cc_final: 0.8549 (tmtt) REVERT: Q 74 GLU cc_start: 0.3017 (mm-30) cc_final: 0.2587 (mm-30) REVERT: Q 78 PHE cc_start: 0.5305 (m-10) cc_final: 0.4661 (m-10) REVERT: Q 102 MET cc_start: 0.5734 (mtp) cc_final: 0.5365 (mpp) REVERT: Q 105 ARG cc_start: 0.7667 (ttt-90) cc_final: 0.7273 (ttt180) REVERT: Y 48 MET cc_start: 0.7852 (tpp) cc_final: 0.7552 (tpp) REVERT: Y 63 MET cc_start: 0.8658 (ttp) cc_final: 0.8228 (tmm) REVERT: Y 70 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8181 (tppt) REVERT: Y 220 GLU cc_start: 0.8486 (tt0) cc_final: 0.7903 (mm-30) REVERT: Y 258 MET cc_start: 0.2509 (mtt) cc_final: 0.2187 (mmt) REVERT: Y 531 PHE cc_start: 0.8567 (m-80) cc_final: 0.7951 (m-80) REVERT: C 279 MET cc_start: 0.7972 (mmm) cc_final: 0.7101 (mmt) REVERT: S 39 ASP cc_start: 0.8660 (p0) cc_final: 0.8052 (p0) REVERT: S 42 GLU cc_start: 0.8843 (tt0) cc_final: 0.8560 (tt0) REVERT: S 106 MET cc_start: 0.6515 (mmm) cc_final: 0.6219 (mmt) REVERT: S 243 LEU cc_start: 0.7823 (mp) cc_final: 0.7140 (tp) outliers start: 151 outliers final: 85 residues processed: 652 average time/residue: 0.2403 time to fit residues: 263.0701 Evaluate side-chains 560 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 463 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 966 MET Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1080 ASP Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 124 PHE Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 395 PHE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 599 LEU Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 28 VAL Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 46 ASP Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 78 ASN Chi-restraints excluded: chain Y residue 408 ASN Chi-restraints excluded: chain Y residue 445 SER Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 536 LEU Chi-restraints excluded: chain Y residue 547 SER Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 417 optimal weight: 3.9990 chunk 423 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 308 optimal weight: 4.9990 chunk 253 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 486 optimal weight: 10.0000 chunk 231 optimal weight: 0.6980 chunk 362 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN I 626 GLN I 664 ASN I 703 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 373 GLN ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS A 450 HIS ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 ASN ** Y 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.112995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087758 restraints weight = 262210.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091295 restraints weight = 115078.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.091180 restraints weight = 59220.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.091386 restraints weight = 49572.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091557 restraints weight = 42693.385| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 42223 Z= 0.279 Angle : 0.728 13.168 57372 Z= 0.375 Chirality : 0.048 0.227 6552 Planarity : 0.005 0.067 7012 Dihedral : 11.538 154.497 6378 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.25 % Allowed : 18.55 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.12), residues: 4859 helix: 0.55 (0.12), residues: 1776 sheet: -0.90 (0.20), residues: 677 loop : -1.56 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 119 TYR 0.038 0.002 TYR A 771 PHE 0.026 0.002 PHE R 84 TRP 0.019 0.002 TRP Y 79 HIS 0.025 0.002 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00627 (42203) covalent geometry : angle 0.72349 (57346) SS BOND : bond 0.00956 ( 4) SS BOND : angle 2.40686 ( 8) hydrogen bonds : bond 0.04573 ( 1645) hydrogen bonds : angle 5.20922 ( 4666) metal coordination : bond 0.02461 ( 16) metal coordination : angle 4.56434 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 465 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 ASN cc_start: 0.8166 (t0) cc_final: 0.7642 (p0) REVERT: B 237 SER cc_start: 0.9261 (m) cc_final: 0.8734 (t) REVERT: B 319 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6535 (mmm) REVERT: B 320 ASN cc_start: 0.6516 (t0) cc_final: 0.5969 (p0) REVERT: B 474 ASP cc_start: 0.8087 (t70) cc_final: 0.7821 (t0) REVERT: B 662 ASP cc_start: 0.8367 (t0) cc_final: 0.7945 (t0) REVERT: B 716 MET cc_start: 0.7709 (mtp) cc_final: 0.7229 (mtp) REVERT: B 771 ASP cc_start: 0.8692 (t0) cc_final: 0.8047 (t0) REVERT: B 785 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: B 1068 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.7676 (t0) REVERT: B 1070 ILE cc_start: 0.8820 (tp) cc_final: 0.8523 (tp) REVERT: G 83 ASP cc_start: 0.7811 (m-30) cc_final: 0.7224 (m-30) REVERT: I 168 MET cc_start: 0.8522 (mtp) cc_final: 0.8075 (mmm) REVERT: I 205 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8098 (tttt) REVERT: I 487 MET cc_start: 0.7417 (mmp) cc_final: 0.6850 (mmm) REVERT: I 593 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: I 595 ARG cc_start: 0.7203 (mmt180) cc_final: 0.6993 (mmt180) REVERT: R 72 ASN cc_start: 0.8529 (p0) cc_final: 0.8077 (p0) REVERT: R 73 ASN cc_start: 0.6930 (m-40) cc_final: 0.6327 (m-40) REVERT: A 105 ASP cc_start: 0.8550 (m-30) cc_final: 0.7835 (p0) REVERT: A 287 ARG cc_start: 0.8743 (ttp-170) cc_final: 0.8378 (ttm-80) REVERT: A 614 ARG cc_start: 0.8667 (mmt-90) cc_final: 0.8461 (mmt180) REVERT: A 675 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7964 (mm-30) REVERT: A 687 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6906 (mtt-85) REVERT: A 781 ILE cc_start: 0.8616 (mm) cc_final: 0.8320 (mm) REVERT: A 836 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9124 (p) REVERT: A 882 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9070 (pt) REVERT: A 1024 ARG cc_start: 0.9318 (ptp-110) cc_final: 0.8744 (ttm110) REVERT: A 1026 TYR cc_start: 0.8059 (m-10) cc_final: 0.7602 (m-80) REVERT: A 1050 ILE cc_start: 0.8707 (pt) cc_final: 0.8488 (pt) REVERT: A 1063 GLU cc_start: 0.8696 (pt0) cc_final: 0.8128 (tm-30) REVERT: A 1242 SER cc_start: 0.8977 (m) cc_final: 0.8413 (p) REVERT: A 1247 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8535 (mt) REVERT: Q 102 MET cc_start: 0.5918 (mtp) cc_final: 0.5564 (mpp) REVERT: Y 63 MET cc_start: 0.8609 (ttp) cc_final: 0.8189 (tmm) REVERT: Y 108 ASP cc_start: 0.6157 (m-30) cc_final: 0.5769 (m-30) REVERT: Y 179 MET cc_start: 0.8579 (tpt) cc_final: 0.8266 (tpp) REVERT: Y 192 GLN cc_start: 0.8821 (pt0) cc_final: 0.8349 (pt0) REVERT: Y 531 PHE cc_start: 0.8636 (m-80) cc_final: 0.8291 (m-80) REVERT: C 142 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8661 (tp) REVERT: C 180 ASP cc_start: 0.8354 (p0) cc_final: 0.8153 (p0) REVERT: C 279 MET cc_start: 0.8281 (mmm) cc_final: 0.7569 (mmt) REVERT: S 39 ASP cc_start: 0.8691 (p0) cc_final: 0.8244 (p0) REVERT: S 42 GLU cc_start: 0.8838 (tt0) cc_final: 0.8632 (tt0) REVERT: S 106 MET cc_start: 0.6627 (mmm) cc_final: 0.6300 (mmm) REVERT: S 243 LEU cc_start: 0.7961 (mp) cc_final: 0.7317 (tp) outliers start: 192 outliers final: 125 residues processed: 608 average time/residue: 0.2400 time to fit residues: 246.7928 Evaluate side-chains 568 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 434 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1068 ASN Chi-restraints excluded: chain B residue 1080 ASP Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 276 ILE Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 395 PHE Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 432 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 593 GLU Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 752 SER Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 452 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 687 ARG Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 78 ASN Chi-restraints excluded: chain Y residue 92 ASP Chi-restraints excluded: chain Y residue 137 CYS Chi-restraints excluded: chain Y residue 408 ASN Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 490 ARG Chi-restraints excluded: chain Y residue 536 LEU Chi-restraints excluded: chain Y residue 547 SER Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 117 PHE Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 456 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 251 optimal weight: 10.0000 chunk 284 optimal weight: 0.6980 chunk 487 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 283 optimal weight: 1.9990 chunk 123 optimal weight: 0.2980 chunk 436 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN B 288 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 380 ASN B 543 ASN E 62 GLN ** F 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 703 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS A1235 ASN Y 78 ASN Y 113 ASN Y 391 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.115877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090425 restraints weight = 295764.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.093950 restraints weight = 123907.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.094361 restraints weight = 59826.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.094436 restraints weight = 48345.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.094747 restraints weight = 45410.884| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42223 Z= 0.133 Angle : 0.608 9.899 57372 Z= 0.314 Chirality : 0.045 0.209 6552 Planarity : 0.004 0.054 7012 Dihedral : 11.353 157.017 6374 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.39 % Allowed : 19.53 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.12), residues: 4859 helix: 0.81 (0.13), residues: 1761 sheet: -0.82 (0.20), residues: 670 loop : -1.39 (0.13), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 720 TYR 0.027 0.001 TYR I 450 PHE 0.028 0.001 PHE A 938 TRP 0.015 0.002 TRP A 365 HIS 0.005 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00293 (42203) covalent geometry : angle 0.60421 (57346) SS BOND : bond 0.01163 ( 4) SS BOND : angle 1.54739 ( 8) hydrogen bonds : bond 0.03916 ( 1645) hydrogen bonds : angle 4.92679 ( 4666) metal coordination : bond 0.01330 ( 16) metal coordination : angle 3.90287 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 483 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7003 (pp20) REVERT: B 159 ASN cc_start: 0.8049 (t0) cc_final: 0.7632 (p0) REVERT: B 237 SER cc_start: 0.9216 (m) cc_final: 0.8688 (t) REVERT: B 474 ASP cc_start: 0.7950 (t70) cc_final: 0.7698 (t0) REVERT: B 662 ASP cc_start: 0.8162 (t0) cc_final: 0.7712 (t0) REVERT: B 716 MET cc_start: 0.7554 (mtp) cc_final: 0.7212 (mtp) REVERT: B 771 ASP cc_start: 0.8503 (t0) cc_final: 0.7854 (t0) REVERT: B 785 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: B 862 THR cc_start: 0.8319 (m) cc_final: 0.8065 (t) REVERT: B 1070 ILE cc_start: 0.8802 (tp) cc_final: 0.8524 (tp) REVERT: B 1085 TYR cc_start: 0.8239 (m-80) cc_final: 0.7404 (m-10) REVERT: E 116 LEU cc_start: 0.7535 (mm) cc_final: 0.7019 (tp) REVERT: E 169 MET cc_start: 0.7728 (ttp) cc_final: 0.7420 (ttp) REVERT: G 83 ASP cc_start: 0.7800 (m-30) cc_final: 0.7205 (m-30) REVERT: I 205 LYS cc_start: 0.8607 (mtmt) cc_final: 0.7983 (tttt) REVERT: I 415 MET cc_start: 0.7547 (mmm) cc_final: 0.7024 (ttt) REVERT: I 487 MET cc_start: 0.7486 (mmp) cc_final: 0.6900 (tpt) REVERT: R 72 ASN cc_start: 0.8436 (p0) cc_final: 0.7999 (p0) REVERT: R 73 ASN cc_start: 0.6774 (m-40) cc_final: 0.6130 (m-40) REVERT: A 105 ASP cc_start: 0.8511 (m-30) cc_final: 0.7834 (p0) REVERT: A 287 ARG cc_start: 0.8662 (ttp-170) cc_final: 0.8397 (ttm-80) REVERT: A 614 ARG cc_start: 0.8666 (mmt-90) cc_final: 0.8427 (mmt180) REVERT: A 675 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7830 (mm-30) REVERT: A 687 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6898 (mtt-85) REVERT: A 781 ILE cc_start: 0.8455 (mm) cc_final: 0.8226 (mm) REVERT: A 1026 TYR cc_start: 0.8015 (m-10) cc_final: 0.7643 (m-80) REVERT: A 1031 GLU cc_start: 0.8350 (mp0) cc_final: 0.8090 (mp0) REVERT: A 1063 GLU cc_start: 0.8723 (pt0) cc_final: 0.8372 (tm-30) REVERT: A 1242 SER cc_start: 0.8867 (m) cc_final: 0.8410 (p) REVERT: Q 102 MET cc_start: 0.5865 (mtp) cc_final: 0.5549 (mpp) REVERT: Y 24 MET cc_start: 0.6471 (tpp) cc_final: 0.6113 (tpt) REVERT: Y 63 MET cc_start: 0.8603 (ttp) cc_final: 0.8189 (tmm) REVERT: Y 108 ASP cc_start: 0.6113 (m-30) cc_final: 0.5667 (m-30) REVERT: Y 192 GLN cc_start: 0.8871 (pt0) cc_final: 0.8507 (pt0) REVERT: Y 220 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7876 (mm-30) REVERT: Y 531 PHE cc_start: 0.8568 (m-80) cc_final: 0.8125 (m-80) REVERT: C 180 ASP cc_start: 0.8353 (p0) cc_final: 0.8135 (p0) REVERT: C 279 MET cc_start: 0.8201 (mmm) cc_final: 0.7528 (mmt) REVERT: S 39 ASP cc_start: 0.8658 (p0) cc_final: 0.8220 (p0) REVERT: S 105 ASP cc_start: 0.5207 (m-30) cc_final: 0.4125 (t0) REVERT: S 243 LEU cc_start: 0.7799 (mp) cc_final: 0.6879 (tp) outliers start: 153 outliers final: 106 residues processed: 592 average time/residue: 0.2425 time to fit residues: 242.8176 Evaluate side-chains 556 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 447 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1071 THR Chi-restraints excluded: chain B residue 1080 ASP Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 276 ILE Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 395 PHE Chi-restraints excluded: chain I residue 432 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 752 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 452 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 687 ARG Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 92 ASP Chi-restraints excluded: chain Y residue 185 THR Chi-restraints excluded: chain Y residue 391 GLN Chi-restraints excluded: chain Y residue 408 ASN Chi-restraints excluded: chain Y residue 445 SER Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 536 LEU Chi-restraints excluded: chain Y residue 547 SER Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 392 optimal weight: 6.9990 chunk 253 optimal weight: 20.0000 chunk 431 optimal weight: 7.9990 chunk 240 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 471 optimal weight: 7.9990 chunk 408 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 288 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 391 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.114921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.089492 restraints weight = 289640.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.093045 restraints weight = 123026.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.093488 restraints weight = 58121.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093568 restraints weight = 47715.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093892 restraints weight = 43418.845| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 42223 Z= 0.165 Angle : 0.629 12.859 57372 Z= 0.324 Chirality : 0.045 0.215 6552 Planarity : 0.004 0.068 7012 Dihedral : 11.300 158.258 6371 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.52 % Allowed : 19.61 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.12), residues: 4859 helix: 0.84 (0.13), residues: 1767 sheet: -0.71 (0.20), residues: 667 loop : -1.38 (0.13), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 490 TYR 0.025 0.002 TYR C 170 PHE 0.029 0.002 PHE I 166 TRP 0.014 0.001 TRP A 365 HIS 0.010 0.001 HIS Y 177 Details of bonding type rmsd covalent geometry : bond 0.00378 (42203) covalent geometry : angle 0.62500 (57346) SS BOND : bond 0.00159 ( 4) SS BOND : angle 2.45815 ( 8) hydrogen bonds : bond 0.03966 ( 1645) hydrogen bonds : angle 4.93529 ( 4666) metal coordination : bond 0.01438 ( 16) metal coordination : angle 3.62521 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 469 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 MET cc_start: 0.7122 (ttp) cc_final: 0.6501 (tmm) REVERT: B 151 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7708 (p0) REVERT: B 159 ASN cc_start: 0.8158 (t0) cc_final: 0.7756 (p0) REVERT: B 237 SER cc_start: 0.9208 (m) cc_final: 0.8709 (t) REVERT: B 319 MET cc_start: 0.7332 (mmm) cc_final: 0.6695 (mmm) REVERT: B 320 ASN cc_start: 0.6478 (t0) cc_final: 0.5892 (p0) REVERT: B 474 ASP cc_start: 0.7960 (t70) cc_final: 0.7708 (t0) REVERT: B 662 ASP cc_start: 0.8212 (t0) cc_final: 0.7742 (t0) REVERT: B 716 MET cc_start: 0.7583 (mtp) cc_final: 0.7129 (mtp) REVERT: B 771 ASP cc_start: 0.8539 (t0) cc_final: 0.7880 (t0) REVERT: B 785 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: B 862 THR cc_start: 0.8346 (m) cc_final: 0.8079 (t) REVERT: B 1070 ILE cc_start: 0.8789 (tp) cc_final: 0.8582 (tp) REVERT: E 116 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7341 (tp) REVERT: F 88 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8306 (mm-30) REVERT: G 83 ASP cc_start: 0.7766 (m-30) cc_final: 0.7161 (m-30) REVERT: I 174 TYR cc_start: 0.8120 (t80) cc_final: 0.7911 (t80) REVERT: I 205 LYS cc_start: 0.8596 (mtmt) cc_final: 0.7982 (tttt) REVERT: I 487 MET cc_start: 0.7535 (mmp) cc_final: 0.6946 (tpt) REVERT: I 595 ARG cc_start: 0.7455 (mmt180) cc_final: 0.6797 (mmp80) REVERT: R 72 ASN cc_start: 0.8436 (p0) cc_final: 0.8021 (p0) REVERT: R 73 ASN cc_start: 0.6876 (m-40) cc_final: 0.6242 (m-40) REVERT: K 392 MET cc_start: 0.7232 (ttm) cc_final: 0.6858 (tpp) REVERT: A 105 ASP cc_start: 0.8545 (m-30) cc_final: 0.7855 (p0) REVERT: A 287 ARG cc_start: 0.8679 (ttp-170) cc_final: 0.8418 (ttm-80) REVERT: A 423 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7848 (mtm) REVERT: A 614 ARG cc_start: 0.8678 (mmt-90) cc_final: 0.8452 (mmt180) REVERT: A 675 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7750 (mm-30) REVERT: A 781 ILE cc_start: 0.8492 (mm) cc_final: 0.8263 (mm) REVERT: A 1026 TYR cc_start: 0.8013 (m-10) cc_final: 0.7677 (m-80) REVERT: A 1031 GLU cc_start: 0.8363 (mp0) cc_final: 0.8130 (mp0) REVERT: A 1063 GLU cc_start: 0.8691 (pt0) cc_final: 0.8418 (tm-30) REVERT: A 1199 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.7670 (m-40) REVERT: A 1242 SER cc_start: 0.8913 (m) cc_final: 0.8453 (p) REVERT: Q 102 MET cc_start: 0.5895 (mtp) cc_final: 0.5615 (mpp) REVERT: Y 24 MET cc_start: 0.6436 (tpp) cc_final: 0.6193 (tpp) REVERT: Y 63 MET cc_start: 0.8567 (ttp) cc_final: 0.8219 (tmm) REVERT: Y 108 ASP cc_start: 0.6182 (m-30) cc_final: 0.5784 (m-30) REVERT: Y 179 MET cc_start: 0.8562 (tpp) cc_final: 0.8330 (tpt) REVERT: Y 192 GLN cc_start: 0.8842 (pt0) cc_final: 0.8479 (pt0) REVERT: Y 531 PHE cc_start: 0.8580 (m-80) cc_final: 0.8186 (m-80) REVERT: C 180 ASP cc_start: 0.8352 (p0) cc_final: 0.8127 (p0) REVERT: C 279 MET cc_start: 0.8162 (mmm) cc_final: 0.7513 (mmt) REVERT: S 39 ASP cc_start: 0.8657 (p0) cc_final: 0.8204 (p0) REVERT: S 42 GLU cc_start: 0.8816 (tt0) cc_final: 0.8595 (tt0) REVERT: S 105 ASP cc_start: 0.5600 (m-30) cc_final: 0.4400 (t0) REVERT: S 114 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: S 243 LEU cc_start: 0.7802 (mp) cc_final: 0.7229 (tp) outliers start: 159 outliers final: 122 residues processed: 584 average time/residue: 0.2384 time to fit residues: 235.7942 Evaluate side-chains 573 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 445 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1071 THR Chi-restraints excluded: chain B residue 1080 ASP Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 276 ILE Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 395 PHE Chi-restraints excluded: chain I residue 432 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 715 MET Chi-restraints excluded: chain I residue 752 SER Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain R residue 43 HIS Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 441 CYS Chi-restraints excluded: chain K residue 452 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1199 ASN Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 92 ASP Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Y residue 185 THR Chi-restraints excluded: chain Y residue 408 ASN Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 536 LEU Chi-restraints excluded: chain Y residue 547 SER Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 114 GLU Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 296 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 470 optimal weight: 7.9990 chunk 86 optimal weight: 0.0270 chunk 236 optimal weight: 9.9990 chunk 265 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 HIS Y 391 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.116635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.091936 restraints weight = 300058.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095030 restraints weight = 125739.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.095800 restraints weight = 63245.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.095608 restraints weight = 52365.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.096166 restraints weight = 46595.517| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42223 Z= 0.121 Angle : 0.607 11.081 57372 Z= 0.311 Chirality : 0.044 0.313 6552 Planarity : 0.004 0.069 7012 Dihedral : 11.191 160.090 6371 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.08 % Allowed : 20.06 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.12), residues: 4859 helix: 0.89 (0.13), residues: 1771 sheet: -0.67 (0.20), residues: 667 loop : -1.27 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 86 TYR 0.036 0.001 TYR C 274 PHE 0.028 0.001 PHE A 938 TRP 0.015 0.001 TRP A 365 HIS 0.005 0.001 HIS I 328 Details of bonding type rmsd covalent geometry : bond 0.00270 (42203) covalent geometry : angle 0.60331 (57346) SS BOND : bond 0.00298 ( 4) SS BOND : angle 2.19835 ( 8) hydrogen bonds : bond 0.03717 ( 1645) hydrogen bonds : angle 4.81004 ( 4666) metal coordination : bond 0.01014 ( 16) metal coordination : angle 3.53005 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 506 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 MET cc_start: 0.6887 (ttp) cc_final: 0.6240 (tmm) REVERT: B 159 ASN cc_start: 0.8129 (t0) cc_final: 0.7872 (p0) REVERT: B 237 SER cc_start: 0.9174 (m) cc_final: 0.8617 (t) REVERT: B 297 LYS cc_start: 0.8507 (pttt) cc_final: 0.8225 (pttt) REVERT: B 319 MET cc_start: 0.7291 (mmm) cc_final: 0.6516 (mmm) REVERT: B 320 ASN cc_start: 0.6238 (t0) cc_final: 0.5772 (p0) REVERT: B 474 ASP cc_start: 0.7832 (t70) cc_final: 0.7555 (t0) REVERT: B 571 VAL cc_start: 0.9491 (t) cc_final: 0.9159 (p) REVERT: B 662 ASP cc_start: 0.8004 (t0) cc_final: 0.7576 (t0) REVERT: B 691 CYS cc_start: 0.8439 (m) cc_final: 0.8180 (m) REVERT: B 716 MET cc_start: 0.7498 (mtp) cc_final: 0.7141 (mtp) REVERT: B 771 ASP cc_start: 0.8528 (t0) cc_final: 0.7810 (t0) REVERT: B 785 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: B 862 THR cc_start: 0.8272 (m) cc_final: 0.7854 (t) REVERT: B 1085 TYR cc_start: 0.7918 (m-80) cc_final: 0.7310 (m-10) REVERT: E 116 LEU cc_start: 0.7890 (mm) cc_final: 0.7453 (tp) REVERT: E 169 MET cc_start: 0.7472 (ttp) cc_final: 0.7143 (ttp) REVERT: G 61 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9020 (tt) REVERT: G 83 ASP cc_start: 0.7696 (m-30) cc_final: 0.7142 (m-30) REVERT: I 174 TYR cc_start: 0.8015 (t80) cc_final: 0.7813 (t80) REVERT: I 205 LYS cc_start: 0.8545 (mtmt) cc_final: 0.7972 (tttt) REVERT: I 415 MET cc_start: 0.7380 (mmm) cc_final: 0.7148 (ttp) REVERT: I 487 MET cc_start: 0.7530 (mmp) cc_final: 0.6921 (tpt) REVERT: I 595 ARG cc_start: 0.7475 (mmt180) cc_final: 0.7164 (mmp-170) REVERT: I 620 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8590 (p) REVERT: I 790 MET cc_start: 0.7716 (mmt) cc_final: 0.7251 (mpp) REVERT: R 72 ASN cc_start: 0.8396 (p0) cc_final: 0.8010 (p0) REVERT: R 73 ASN cc_start: 0.6823 (m-40) cc_final: 0.6207 (m-40) REVERT: K 392 MET cc_start: 0.7250 (ttm) cc_final: 0.6895 (tpp) REVERT: K 419 MET cc_start: 0.0074 (OUTLIER) cc_final: -0.0150 (ptp) REVERT: A 105 ASP cc_start: 0.8518 (m-30) cc_final: 0.7833 (p0) REVERT: A 287 ARG cc_start: 0.8638 (ttp-170) cc_final: 0.8434 (ttm-80) REVERT: A 608 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9058 (pttp) REVERT: A 614 ARG cc_start: 0.8663 (mmt-90) cc_final: 0.8075 (mmp80) REVERT: A 781 ILE cc_start: 0.8382 (mm) cc_final: 0.8119 (mm) REVERT: A 1026 TYR cc_start: 0.7963 (m-10) cc_final: 0.7637 (m-80) REVERT: A 1031 GLU cc_start: 0.8273 (mp0) cc_final: 0.8023 (mp0) REVERT: A 1063 GLU cc_start: 0.8733 (pt0) cc_final: 0.8436 (tm-30) REVERT: A 1242 SER cc_start: 0.8798 (m) cc_final: 0.8354 (p) REVERT: Q 102 MET cc_start: 0.5723 (mtp) cc_final: 0.5469 (mpp) REVERT: Y 48 MET cc_start: 0.7588 (tpp) cc_final: 0.6980 (tpp) REVERT: Y 63 MET cc_start: 0.8565 (ttp) cc_final: 0.8168 (tmm) REVERT: Y 76 TYR cc_start: 0.7263 (t80) cc_final: 0.6925 (t80) REVERT: Y 108 ASP cc_start: 0.6053 (m-30) cc_final: 0.5629 (m-30) REVERT: Y 177 HIS cc_start: 0.6528 (m-70) cc_final: 0.5608 (m-70) REVERT: Y 192 GLN cc_start: 0.8799 (pt0) cc_final: 0.8493 (pt0) REVERT: Y 531 PHE cc_start: 0.8511 (m-80) cc_final: 0.8111 (m-80) REVERT: C 150 ILE cc_start: 0.8887 (mm) cc_final: 0.8399 (mm) REVERT: C 180 ASP cc_start: 0.8295 (p0) cc_final: 0.8070 (p0) REVERT: C 193 MET cc_start: 0.8099 (mmm) cc_final: 0.7869 (mmp) REVERT: C 250 MET cc_start: 0.7859 (mmm) cc_final: 0.7301 (tpt) REVERT: C 279 MET cc_start: 0.8121 (mmm) cc_final: 0.7442 (mmt) REVERT: S 39 ASP cc_start: 0.8638 (p0) cc_final: 0.8177 (p0) REVERT: S 42 GLU cc_start: 0.8846 (tt0) cc_final: 0.8483 (tt0) REVERT: S 105 ASP cc_start: 0.5348 (m-30) cc_final: 0.4125 (t0) REVERT: S 141 ASP cc_start: 0.7798 (t0) cc_final: 0.7572 (m-30) REVERT: S 147 TYR cc_start: 0.8054 (m-80) cc_final: 0.7425 (m-80) REVERT: S 243 LEU cc_start: 0.7702 (mp) cc_final: 0.7080 (tp) outliers start: 139 outliers final: 100 residues processed: 602 average time/residue: 0.2446 time to fit residues: 249.0853 Evaluate side-chains 565 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 460 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1080 ASP Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 276 ILE Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 395 PHE Chi-restraints excluded: chain I residue 432 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 715 MET Chi-restraints excluded: chain I residue 752 SER Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 43 HIS Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 419 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 441 CYS Chi-restraints excluded: chain K residue 452 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 46 ASP Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Y residue 408 ASN Chi-restraints excluded: chain Y residue 445 SER Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 536 LEU Chi-restraints excluded: chain Y residue 547 SER Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 137 optimal weight: 5.9990 chunk 343 optimal weight: 0.9990 chunk 436 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 chunk 450 optimal weight: 2.9990 chunk 488 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 205 optimal weight: 0.0030 chunk 101 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 420 optimal weight: 0.0670 overall best weight: 0.4528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 ASN ** F 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN Q 43 HIS Y 71 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.117833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.093615 restraints weight = 269714.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.096233 restraints weight = 112113.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.097041 restraints weight = 59914.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.097203 restraints weight = 44431.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.097570 restraints weight = 40689.126| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 42223 Z= 0.115 Angle : 0.608 12.240 57372 Z= 0.312 Chirality : 0.044 0.222 6552 Planarity : 0.004 0.103 7012 Dihedral : 11.117 161.748 6369 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.63 % Allowed : 20.90 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.12), residues: 4859 helix: 0.86 (0.13), residues: 1783 sheet: -0.54 (0.21), residues: 646 loop : -1.27 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG Q 105 TYR 0.036 0.001 TYR C 170 PHE 0.031 0.001 PHE B 190 TRP 0.043 0.002 TRP S 43 HIS 0.006 0.001 HIS R 112 Details of bonding type rmsd covalent geometry : bond 0.00257 (42203) covalent geometry : angle 0.60389 (57346) SS BOND : bond 0.00196 ( 4) SS BOND : angle 2.05980 ( 8) hydrogen bonds : bond 0.03614 ( 1645) hydrogen bonds : angle 4.77233 ( 4666) metal coordination : bond 0.00949 ( 16) metal coordination : angle 3.56822 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 505 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 SER cc_start: 0.8690 (t) cc_final: 0.8475 (p) REVERT: B 107 MET cc_start: 0.6953 (ttp) cc_final: 0.6170 (tmm) REVERT: B 159 ASN cc_start: 0.8229 (t0) cc_final: 0.7865 (p0) REVERT: B 319 MET cc_start: 0.7279 (mmm) cc_final: 0.6977 (mmm) REVERT: B 474 ASP cc_start: 0.7924 (t70) cc_final: 0.7623 (t0) REVERT: B 571 VAL cc_start: 0.9527 (t) cc_final: 0.9152 (p) REVERT: B 662 ASP cc_start: 0.7940 (t0) cc_final: 0.7468 (t0) REVERT: B 691 CYS cc_start: 0.8524 (m) cc_final: 0.8209 (m) REVERT: B 716 MET cc_start: 0.7513 (mtp) cc_final: 0.7171 (mtp) REVERT: B 771 ASP cc_start: 0.8519 (t0) cc_final: 0.7764 (t0) REVERT: B 785 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: B 862 THR cc_start: 0.8370 (m) cc_final: 0.8077 (t) REVERT: B 1085 TYR cc_start: 0.7758 (m-80) cc_final: 0.7045 (m-10) REVERT: F 88 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8224 (mt-10) REVERT: G 61 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9000 (tt) REVERT: G 83 ASP cc_start: 0.7751 (m-30) cc_final: 0.7171 (m-30) REVERT: I 174 TYR cc_start: 0.8100 (t80) cc_final: 0.7879 (t80) REVERT: I 205 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8026 (tttt) REVERT: I 415 MET cc_start: 0.7520 (mmm) cc_final: 0.7281 (ttp) REVERT: I 487 MET cc_start: 0.7512 (mmp) cc_final: 0.6886 (tpt) REVERT: I 595 ARG cc_start: 0.7449 (mmt180) cc_final: 0.6936 (mmm160) REVERT: I 620 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8520 (p) REVERT: R 64 ASP cc_start: 0.6938 (t0) cc_final: 0.6574 (t0) REVERT: R 72 ASN cc_start: 0.8490 (p0) cc_final: 0.8147 (p0) REVERT: R 73 ASN cc_start: 0.6852 (m-40) cc_final: 0.6288 (m-40) REVERT: K 392 MET cc_start: 0.7190 (ttm) cc_final: 0.6676 (tpp) REVERT: A 54 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8271 (mmmt) REVERT: A 105 ASP cc_start: 0.8477 (m-30) cc_final: 0.7803 (p0) REVERT: A 287 ARG cc_start: 0.8719 (ttp-170) cc_final: 0.8423 (ttm-80) REVERT: A 614 ARG cc_start: 0.8706 (mmt-90) cc_final: 0.8057 (mmp80) REVERT: A 633 MET cc_start: 0.8304 (mmm) cc_final: 0.8079 (mpp) REVERT: A 769 ASP cc_start: 0.8945 (p0) cc_final: 0.8691 (p0) REVERT: A 781 ILE cc_start: 0.8414 (mm) cc_final: 0.8198 (mm) REVERT: A 837 LEU cc_start: 0.8811 (mm) cc_final: 0.8540 (tt) REVERT: A 926 ILE cc_start: 0.8576 (tp) cc_final: 0.7944 (mm) REVERT: A 1026 TYR cc_start: 0.8008 (m-10) cc_final: 0.7657 (m-80) REVERT: A 1031 GLU cc_start: 0.8267 (mp0) cc_final: 0.7987 (mp0) REVERT: A 1063 GLU cc_start: 0.8669 (pt0) cc_final: 0.8416 (tm-30) REVERT: A 1242 SER cc_start: 0.8761 (m) cc_final: 0.8303 (p) REVERT: Q 74 GLU cc_start: 0.2729 (mm-30) cc_final: 0.2502 (mm-30) REVERT: Q 78 PHE cc_start: 0.5307 (m-10) cc_final: 0.4594 (m-10) REVERT: Q 102 MET cc_start: 0.5868 (mtp) cc_final: 0.5552 (mpp) REVERT: Y 48 MET cc_start: 0.7773 (tpp) cc_final: 0.7134 (tpp) REVERT: Y 63 MET cc_start: 0.8607 (ttp) cc_final: 0.8173 (tmm) REVERT: Y 70 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8271 (tppt) REVERT: Y 79 TRP cc_start: 0.6934 (m100) cc_final: 0.6685 (m100) REVERT: Y 177 HIS cc_start: 0.6330 (m-70) cc_final: 0.5439 (m-70) REVERT: Y 531 PHE cc_start: 0.8517 (m-80) cc_final: 0.7982 (m-80) REVERT: C 180 ASP cc_start: 0.8369 (p0) cc_final: 0.8144 (p0) REVERT: C 250 MET cc_start: 0.7892 (mmm) cc_final: 0.7458 (tpt) REVERT: C 279 MET cc_start: 0.8147 (mmm) cc_final: 0.7466 (mmt) REVERT: S 39 ASP cc_start: 0.8806 (p0) cc_final: 0.8565 (p0) REVERT: S 42 GLU cc_start: 0.8910 (tt0) cc_final: 0.8644 (tt0) REVERT: S 105 ASP cc_start: 0.5249 (m-30) cc_final: 0.3925 (t0) REVERT: S 106 MET cc_start: 0.6904 (ptt) cc_final: 0.6227 (mmm) REVERT: S 118 LEU cc_start: 0.8064 (mp) cc_final: 0.7470 (mp) REVERT: S 243 LEU cc_start: 0.7753 (mp) cc_final: 0.7003 (tp) outliers start: 119 outliers final: 98 residues processed: 588 average time/residue: 0.2396 time to fit residues: 239.4572 Evaluate side-chains 569 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 467 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 276 ILE Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 386 ILE Chi-restraints excluded: chain I residue 395 PHE Chi-restraints excluded: chain I residue 432 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 715 MET Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 43 HIS Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 441 CYS Chi-restraints excluded: chain K residue 452 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 46 ASP Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 71 HIS Chi-restraints excluded: chain Y residue 408 ASN Chi-restraints excluded: chain Y residue 445 SER Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 536 LEU Chi-restraints excluded: chain Y residue 547 SER Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 243 optimal weight: 5.9990 chunk 228 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 440 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 356 optimal weight: 7.9990 chunk 328 optimal weight: 0.8980 chunk 301 optimal weight: 0.9980 chunk 352 optimal weight: 7.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN B 282 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 792 ASN I 795 ASN ** R 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN ** K 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.116487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.091696 restraints weight = 293400.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094888 restraints weight = 122591.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095515 restraints weight = 62533.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.095458 restraints weight = 52266.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.095966 restraints weight = 46467.644| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 42223 Z= 0.150 Angle : 0.639 11.708 57372 Z= 0.328 Chirality : 0.045 0.257 6552 Planarity : 0.004 0.093 7012 Dihedral : 11.134 162.252 6369 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.66 % Allowed : 21.39 % Favored : 75.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.12), residues: 4859 helix: 0.91 (0.13), residues: 1777 sheet: -0.65 (0.20), residues: 662 loop : -1.30 (0.13), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 105 TYR 0.034 0.002 TYR G 76 PHE 0.032 0.001 PHE B 190 TRP 0.087 0.002 TRP S 43 HIS 0.011 0.001 HIS Y 71 Details of bonding type rmsd covalent geometry : bond 0.00344 (42203) covalent geometry : angle 0.63597 (57346) SS BOND : bond 0.00251 ( 4) SS BOND : angle 1.78432 ( 8) hydrogen bonds : bond 0.03781 ( 1645) hydrogen bonds : angle 4.84812 ( 4666) metal coordination : bond 0.01013 ( 16) metal coordination : angle 3.40774 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 466 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 MET cc_start: 0.6852 (ttp) cc_final: 0.6148 (tmm) REVERT: B 159 ASN cc_start: 0.8193 (t0) cc_final: 0.7914 (p0) REVERT: B 319 MET cc_start: 0.7331 (mmm) cc_final: 0.6888 (mmm) REVERT: B 474 ASP cc_start: 0.7875 (t70) cc_final: 0.7633 (t0) REVERT: B 571 VAL cc_start: 0.9502 (t) cc_final: 0.9152 (p) REVERT: B 662 ASP cc_start: 0.8052 (t0) cc_final: 0.7565 (t0) REVERT: B 716 MET cc_start: 0.7670 (mtp) cc_final: 0.7205 (mtp) REVERT: B 771 ASP cc_start: 0.8524 (t0) cc_final: 0.7780 (t0) REVERT: B 785 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: B 862 THR cc_start: 0.8341 (m) cc_final: 0.8122 (p) REVERT: B 1085 TYR cc_start: 0.7890 (m-80) cc_final: 0.7248 (m-10) REVERT: G 61 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9028 (tt) REVERT: G 83 ASP cc_start: 0.7750 (m-30) cc_final: 0.7208 (m-30) REVERT: I 174 TYR cc_start: 0.8067 (t80) cc_final: 0.7855 (t80) REVERT: I 205 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8048 (tttt) REVERT: I 415 MET cc_start: 0.7404 (mmm) cc_final: 0.7174 (ttp) REVERT: I 487 MET cc_start: 0.7545 (mmp) cc_final: 0.6918 (tpt) REVERT: I 595 ARG cc_start: 0.7448 (mmt180) cc_final: 0.6904 (mmp80) REVERT: I 620 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8502 (p) REVERT: K 392 MET cc_start: 0.7235 (ttm) cc_final: 0.6703 (tpp) REVERT: A 105 ASP cc_start: 0.8506 (m-30) cc_final: 0.7804 (p0) REVERT: A 287 ARG cc_start: 0.8607 (ttp-170) cc_final: 0.8370 (ttm-80) REVERT: A 580 ASP cc_start: 0.6097 (OUTLIER) cc_final: 0.5490 (m-30) REVERT: A 614 ARG cc_start: 0.8592 (mmt-90) cc_final: 0.7979 (mmp80) REVERT: A 781 ILE cc_start: 0.8475 (mm) cc_final: 0.8255 (mm) REVERT: A 926 ILE cc_start: 0.8587 (tp) cc_final: 0.7963 (mm) REVERT: A 1026 TYR cc_start: 0.8015 (m-10) cc_final: 0.7679 (m-80) REVERT: A 1031 GLU cc_start: 0.8304 (mp0) cc_final: 0.8029 (mp0) REVERT: A 1063 GLU cc_start: 0.8627 (pt0) cc_final: 0.8422 (tm-30) REVERT: A 1242 SER cc_start: 0.8791 (m) cc_final: 0.8300 (p) REVERT: Q 78 PHE cc_start: 0.5365 (m-10) cc_final: 0.4538 (m-10) REVERT: Q 95 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7548 (tm-30) REVERT: Q 102 MET cc_start: 0.5892 (mtp) cc_final: 0.5608 (mpp) REVERT: Y 48 MET cc_start: 0.7711 (tpp) cc_final: 0.7107 (tpp) REVERT: Y 63 MET cc_start: 0.8532 (ttp) cc_final: 0.8120 (tmm) REVERT: Y 79 TRP cc_start: 0.6969 (m100) cc_final: 0.6737 (m100) REVERT: Y 177 HIS cc_start: 0.6441 (m-70) cc_final: 0.5589 (m-70) REVERT: Y 531 PHE cc_start: 0.8509 (m-80) cc_final: 0.8143 (m-80) REVERT: C 180 ASP cc_start: 0.8264 (p0) cc_final: 0.8043 (p0) REVERT: C 257 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6841 (ttp) REVERT: C 279 MET cc_start: 0.8130 (mmm) cc_final: 0.7615 (mmt) REVERT: S 39 ASP cc_start: 0.8817 (p0) cc_final: 0.8477 (p0) REVERT: S 42 GLU cc_start: 0.8846 (tt0) cc_final: 0.8646 (tt0) REVERT: S 106 MET cc_start: 0.6936 (ptt) cc_final: 0.6385 (mmm) REVERT: S 118 LEU cc_start: 0.8067 (mp) cc_final: 0.7330 (mp) REVERT: S 141 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: S 243 LEU cc_start: 0.7867 (mp) cc_final: 0.7058 (tp) outliers start: 120 outliers final: 104 residues processed: 552 average time/residue: 0.2279 time to fit residues: 215.1201 Evaluate side-chains 555 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 445 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1071 THR Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 276 ILE Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 386 ILE Chi-restraints excluded: chain I residue 395 PHE Chi-restraints excluded: chain I residue 432 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 THR Chi-restraints excluded: chain I residue 666 THR Chi-restraints excluded: chain I residue 715 MET Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 43 HIS Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain K residue 415 MET Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 441 CYS Chi-restraints excluded: chain K residue 452 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1261 LEU Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 35 GLN Chi-restraints excluded: chain Y residue 408 ASN Chi-restraints excluded: chain Y residue 445 SER Chi-restraints excluded: chain Y residue 486 THR Chi-restraints excluded: chain Y residue 536 LEU Chi-restraints excluded: chain Y residue 547 SER Chi-restraints excluded: chain Y residue 565 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain S residue 45 MET Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 141 ASP Chi-restraints excluded: chain S residue 244 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 489 optimal weight: 0.0010 chunk 111 optimal weight: 0.3980 chunk 372 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 390 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 354 optimal weight: 7.9990 chunk 422 optimal weight: 2.9990 chunk 2 optimal weight: 0.0040 chunk 425 optimal weight: 20.0000 chunk 289 optimal weight: 0.2980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 HIS E 62 GLN ** F 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 71 HIS ** Y 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.118550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093528 restraints weight = 266421.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097153 restraints weight = 113676.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.097635 restraints weight = 54131.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.098002 restraints weight = 43108.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.098037 restraints weight = 38218.566| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 42223 Z= 0.117 Angle : 0.635 12.126 57372 Z= 0.324 Chirality : 0.045 0.252 6552 Planarity : 0.004 0.082 7012 Dihedral : 11.090 163.136 6369 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.26 % Allowed : 22.14 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.12), residues: 4859 helix: 0.92 (0.13), residues: 1773 sheet: -0.61 (0.21), residues: 644 loop : -1.26 (0.13), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG Q 105 TYR 0.031 0.001 TYR C 170 PHE 0.052 0.001 PHE Y 123 TRP 0.051 0.002 TRP S 43 HIS 0.007 0.001 HIS R 112 Details of bonding type rmsd covalent geometry : bond 0.00262 (42203) covalent geometry : angle 0.63206 (57346) SS BOND : bond 0.00287 ( 4) SS BOND : angle 1.68143 ( 8) hydrogen bonds : bond 0.03571 ( 1645) hydrogen bonds : angle 4.79112 ( 4666) metal coordination : bond 0.00952 ( 16) metal coordination : angle 3.44922 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8747.32 seconds wall clock time: 152 minutes 20.25 seconds (9140.25 seconds total)