Starting phenix.real_space_refine on Mon Aug 10 03:21:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c8h_16476/08_2026/8c8h_16476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c8h_16476/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8c8h_16476/08_2026/8c8h_16476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c8h_16476/08_2026/8c8h_16476.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8c8h_16476/08_2026/8c8h_16476.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c8h_16476/08_2026/8c8h_16476.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c8h_16476/08_2026/8c8h_16476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c8h_16476/08_2026/8c8h_16476.map" } 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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 6.74, per 1000 atoms: 0.16 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: 2.76 Conformation dependent library (CDL) restraints added in 1.6 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: 4.91 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: 9.12 Time building geometry restraints manager: 3.84 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=" 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 bond pdb=" N ARG B 45 " pdb=" CA ARG B 45 " ideal model delta sigma weight residual 1.458 1.445 0.013 1.30e-02 5.92e+03 1.04e+00 bond pdb=" C VAL A 746 " pdb=" O VAL A 746 " ideal model delta sigma weight residual 1.237 1.249 -0.012 1.19e-02 7.06e+03 1.01e+00 bond pdb=" C ARG C 168 " pdb=" O ARG C 168 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.16e-02 7.43e+03 9.62e-01 ... (remaining 42198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 56991 2.78 - 5.56: 335 5.56 - 8.34: 17 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=" 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=" C LYS A 937 " pdb=" N PHE A 938 " pdb=" CA PHE A 938 " ideal model delta sigma weight residual 120.72 115.80 4.92 1.67e+00 3.59e-01 8.66e+00 angle pdb=" C TYR B 467 " pdb=" N LEU B 468 " pdb=" CA LEU B 468 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.54e+00 angle pdb=" C ASP C 105 " pdb=" N LYS C 106 " pdb=" CA LYS C 106 " ideal model delta sigma weight residual 121.54 126.89 -5.35 1.91e+00 2.74e-01 7.83e+00 ... (remaining 57341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 23177 17.86 - 35.71: 1731 35.71 - 53.57: 522 53.57 - 71.43: 243 71.43 - 89.29: 30 Dihedral angle restraints: 25703 sinusoidal: 11151 harmonic: 14552 Sorted by residual: dihedral pdb=" C4' G U 18 " pdb=" C3' G U 18 " pdb=" C2' G U 18 " pdb=" C1' G U 18 " ideal model delta sinusoidal sigma weight residual 36.34 -45.20 81.55 1 3.10e+00 1.04e-01 8.52e+02 dihedral pdb=" C4' G U 17 " pdb=" C3' G U 17 " pdb=" C2' G U 17 " pdb=" C1' G U 17 " ideal model delta sinusoidal sigma weight residual 36.34 -37.68 74.02 1 3.10e+00 1.04e-01 7.24e+02 dihedral pdb=" C4' U U 35 " pdb=" C3' U U 35 " pdb=" C2' U U 35 " pdb=" C1' U U 35 " ideal model delta sinusoidal sigma weight residual 36.34 -37.34 73.69 1 3.10e+00 1.04e-01 7.18e+02 ... (remaining 25700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5731 0.069 - 0.138: 717 0.138 - 0.207: 19 0.207 - 0.276: 76 0.276 - 0.344: 9 Chirality restraints: 6552 Sorted by residual: chirality pdb=" C3' U U 35 " pdb=" C4' U U 35 " pdb=" O3' U U 35 " pdb=" C2' U U 35 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C3' G U 18 " pdb=" C4' G U 18 " pdb=" O3' G U 18 " pdb=" C2' G U 18 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" P U U 19 " pdb=" OP1 U U 19 " pdb=" OP2 U U 19 " pdb=" O5' U U 19 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 41.270 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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= 0.117 Angle : 0.595 16.801 57372 Z= 0.317 Chirality : 0.051 0.344 6552 Planarity : 0.006 0.073 7012 Dihedral : 15.377 89.286 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/Z covalent geometry : bond 0.00235 / 0.12 (42203) covalent geometry : angle 0.58760 / 0.32 (57346) SS BOND : bond 0.00143 / 0.07 ( 4) SS BOND : angle 0.85209 / 0.42 ( 8) hydrogen bonds : bond 0.13526 / 9.22 ( 1645) hydrogen bonds : angle 6.37067 / 4.55 ( 4666) metal coordination : bond 0.01432 / 0.67 ( 16) metal coordination : angle 5.14530 / 2.88 ( 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 : 1.431 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: 0.2366 time to fit residues: 530.9827 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 : 1.206 ------------------------------------------------------------------------------- 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: 10.0000 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... B 40 ASN B 169 ASN B 288 ASN ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 387 ASN ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS B 436 GLN 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 ** B1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 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 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 728 GLN I 735 ASN I 753 ASN I 781 ASN J 51 GLN J 53 ASN ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 24 GLN C 27 ASN C 28 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 73 ASN S 135 ASN S 225 ASN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.113583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088903 restraints weight = 250401.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090653 restraints weight = 111231.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091235 restraints weight = 67540.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.091367 restraints weight = 63183.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.092370 restraints weight = 51499.147| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 42223 Z= 0.344 Angle : 0.930 25.889 57372 Z= 0.455 Chirality : 0.061 1.131 6552 Planarity : 0.006 0.067 7012 Dihedral : 12.627 165.050 6417 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.83 % Allowed : 15.94 % Favored : 80.23 % 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: -1.82 (0.11), residues: 4859 helix: -0.40 (0.11), residues: 1793 sheet: -1.22 (0.20), residues: 658 loop : -1.82 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 12 TYR 0.035 0.003 TYR I 734 PHE 0.027 0.003 PHE A 938 TRP 0.019 0.002 TRP A 365 HIS 0.011 0.002 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00760 / 0.34 (42203) covalent geometry : angle 0.92449 / 0.45 (57346) SS BOND : bond 0.00238 / 0.12 ( 4) SS BOND : angle 2.37396 / 1.22 ( 8) hydrogen bonds : bond 0.05364 / 3.57 ( 1645) hydrogen bonds : angle 5.42679 / 3.82 ( 4666) metal coordination : bond 0.02066 / 1.20 ( 16) metal coordination : angle 5.72940 / 3.06 ( 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 762 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 589 time to evaluate : 1.443 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: 0.9204 (m) cc_final: 0.8726 (t) REVERT: B 307 PHE cc_start: 0.7669 (t80) cc_final: 0.7278 (t80) REVERT: B 311 MET cc_start: 0.8057 (ttm) cc_final: 0.7825 (ttm) REVERT: B 319 MET cc_start: 0.7371 (mmt) cc_final: 0.6712 (mmm) REVERT: B 474 ASP cc_start: 0.7863 (t70) cc_final: 0.7583 (t0) REVERT: B 482 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8693 (m) REVERT: B 513 ILE cc_start: 0.8678 (mt) cc_final: 0.8431 (tp) REVERT: B 647 PHE cc_start: 0.8261 (t80) cc_final: 0.7965 (t80) REVERT: B 662 ASP cc_start: 0.8241 (t0) cc_final: 0.7907 (t0) REVERT: B 680 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.6947 (p0) REVERT: B 704 ASP cc_start: 0.7298 (m-30) cc_final: 0.6302 (m-30) REVERT: B 716 MET cc_start: 0.7714 (mtp) cc_final: 0.7179 (mtp) REVERT: B 771 ASP cc_start: 0.8759 (t0) cc_final: 0.7947 (t0) REVERT: B 785 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: B 862 THR cc_start: 0.8557 (m) cc_final: 0.8329 (t) REVERT: F 74 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8889 (p) REVERT: F 152 ASP cc_start: 0.8094 (m-30) cc_final: 0.7847 (m-30) REVERT: G 83 ASP cc_start: 0.7704 (m-30) cc_final: 0.7036 (m-30) REVERT: G 103 ASP cc_start: 0.8035 (p0) cc_final: 0.7124 (m-30) REVERT: G 104 LEU cc_start: 0.9227 (tp) cc_final: 0.9026 (tp) REVERT: G 141 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8215 (mp) REVERT: I 121 MET cc_start: 0.8230 (mmm) cc_final: 0.8009 (mmt) REVERT: I 168 MET cc_start: 0.8671 (mtp) cc_final: 0.8278 (mmm) REVERT: I 205 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8108 (tttt) REVERT: I 372 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7884 (mm) REVERT: I 415 MET cc_start: 0.7618 (mmm) cc_final: 0.7234 (ttt) REVERT: I 487 MET cc_start: 0.7236 (mmp) cc_final: 0.6669 (mmm) REVERT: I 593 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: I 646 LYS cc_start: 0.9313 (mtpp) cc_final: 0.8929 (ptpp) REVERT: I 695 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8010 (p0) REVERT: I 715 MET cc_start: 0.8378 (tpt) cc_final: 0.8145 (tpt) REVERT: R 72 ASN cc_start: 0.8853 (p0) cc_final: 0.8563 (p0) REVERT: R 76 TYR cc_start: 0.8788 (m-10) cc_final: 0.8380 (m-10) REVERT: A 107 ASN cc_start: 0.7360 (t0) cc_final: 0.6836 (t0) REVERT: A 266 THR cc_start: 0.8672 (p) cc_final: 0.8444 (p) REVERT: A 287 ARG cc_start: 0.8610 (ttp-170) cc_final: 0.8288 (ttm-80) REVERT: A 536 MET cc_start: 0.9136 (mmm) cc_final: 0.8808 (mmt) REVERT: A 675 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7964 (mm-30) REVERT: A 781 ILE cc_start: 0.8504 (mm) cc_final: 0.8216 (mm) REVERT: A 1026 TYR cc_start: 0.8121 (m-80) cc_final: 0.7840 (m-80) REVERT: A 1103 ILE cc_start: 0.9038 (mp) cc_final: 0.8690 (mt) REVERT: A 1242 SER cc_start: 0.8932 (m) cc_final: 0.8577 (p) REVERT: Q 102 MET cc_start: 0.6201 (mtp) cc_final: 0.5665 (mpp) REVERT: Q 105 ARG cc_start: 0.7491 (ttt-90) cc_final: 0.6847 (ttp-170) REVERT: Y 23 MET cc_start: 0.7419 (ttm) cc_final: 0.7130 (ttm) REVERT: Y 179 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7874 (tmm) REVERT: Y 258 MET cc_start: 0.2698 (mtt) cc_final: 0.2078 (mmt) REVERT: Y 391 GLN cc_start: 0.2525 (OUTLIER) cc_final: 0.2062 (pm20) REVERT: Y 463 MET cc_start: 0.2016 (mmm) cc_final: 0.1745 (mmt) REVERT: Y 531 PHE cc_start: 0.8692 (m-80) cc_final: 0.8080 (m-80) REVERT: C 31 LYS cc_start: 0.8400 (mtmt) cc_final: 0.8016 (mtmm) REVERT: C 98 ASP cc_start: 0.7426 (m-30) cc_final: 0.7131 (t0) REVERT: C 142 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8700 (tp) REVERT: C 170 TYR cc_start: 0.7861 (t80) cc_final: 0.7462 (t80) outliers start: 173 outliers final: 89 residues processed: 724 average time/residue: 0.2283 time to fit residues: 276.7628 Evaluate side-chains 560 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 460 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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 74 THR 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 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 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 601 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 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 24 MET Chi-restraints excluded: chain Y residue 78 ASN Chi-restraints excluded: chain Y residue 179 MET 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 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: 0.5980 chunk 107 optimal weight: 8.9990 chunk 376 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 290 optimal weight: 0.9980 chunk 464 optimal weight: 3.9990 chunk 330 optimal weight: 0.7980 chunk 280 optimal weight: 0.9990 chunk 383 optimal weight: 0.9990 chunk 384 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 288 ASN B 318 HIS ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 380 ASN ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 HIS B 789 ASN ** B1110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 ASN ** 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 385 HIS ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 GLN A 941 GLN A1023 ASN A1149 ASN ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 HIS C 137 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.117577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091488 restraints weight = 255132.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.095225 restraints weight = 109040.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.096320 restraints weight = 54099.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.097178 restraints weight = 33837.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.097305 restraints weight = 30644.561| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 42223 Z= 0.140 Angle : 0.686 15.851 57372 Z= 0.339 Chirality : 0.051 0.501 6552 Planarity : 0.004 0.053 7012 Dihedral : 12.458 169.902 6385 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.14 % Allowed : 16.54 % Favored : 80.32 % 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: -1.20 (0.12), residues: 4859 helix: 0.27 (0.12), residues: 1777 sheet: -0.83 (0.21), residues: 646 loop : -1.60 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 184 TYR 0.035 0.002 TYR I 734 PHE 0.027 0.001 PHE A 938 TRP 0.015 0.002 TRP A 365 HIS 0.008 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (42203) covalent geometry : angle 0.68088 / 0.34 (57346) SS BOND : bond 0.00155 / 0.08 ( 4) SS BOND : angle 1.11340 / 0.56 ( 8) hydrogen bonds : bond 0.04193 / 2.78 ( 1645) hydrogen bonds : angle 5.03847 / 3.54 ( 4666) metal coordination : bond 0.01032 / 0.47 ( 16) metal coordination : angle 4.62117 / 2.58 ( 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 707 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 565 time to evaluate : 1.417 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 237 SER cc_start: 0.9119 (m) cc_final: 0.8675 (t) REVERT: B 319 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7182 (mmt) REVERT: B 386 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8088 (mpp) REVERT: B 474 ASP cc_start: 0.7823 (t70) cc_final: 0.7579 (t0) REVERT: B 482 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8654 (m) REVERT: B 662 ASP cc_start: 0.8061 (t0) cc_final: 0.7414 (t0) REVERT: B 680 ASN cc_start: 0.7289 (OUTLIER) cc_final: 0.6632 (p0) REVERT: B 716 MET cc_start: 0.7571 (mtp) cc_final: 0.7222 (mtp) REVERT: B 771 ASP cc_start: 0.8650 (t0) cc_final: 0.7831 (t0) REVERT: B 785 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: B 862 THR cc_start: 0.8503 (m) cc_final: 0.8263 (t) REVERT: B 1131 MET cc_start: 0.8865 (mmp) cc_final: 0.8635 (mmp) REVERT: E 152 LEU cc_start: 0.8682 (mt) cc_final: 0.8257 (mt) REVERT: F 74 THR cc_start: 0.9026 (m) cc_final: 0.8777 (p) REVERT: F 152 ASP cc_start: 0.7891 (m-30) cc_final: 0.7656 (m-30) REVERT: G 83 ASP cc_start: 0.7572 (m-30) cc_final: 0.6819 (m-30) REVERT: G 103 ASP cc_start: 0.7955 (p0) cc_final: 0.6969 (m-30) REVERT: G 104 LEU cc_start: 0.9188 (tp) cc_final: 0.8964 (tp) REVERT: G 141 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8115 (mp) REVERT: I 168 MET cc_start: 0.8489 (mtp) cc_final: 0.8079 (mmm) REVERT: I 205 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8025 (tttt) REVERT: I 211 TYR cc_start: 0.7146 (m-80) cc_final: 0.6821 (m-80) REVERT: I 259 TRP cc_start: 0.8845 (m-10) cc_final: 0.8507 (m-10) REVERT: I 372 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7746 (mm) REVERT: I 415 MET cc_start: 0.7705 (mmm) cc_final: 0.7203 (ttt) REVERT: I 487 MET cc_start: 0.7251 (mmp) cc_final: 0.6675 (mmm) REVERT: I 599 LEU cc_start: 0.5267 (OUTLIER) cc_final: 0.4941 (pp) REVERT: I 646 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8936 (mtmt) REVERT: J 10 CYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7514 (p) REVERT: R 6 ILE cc_start: 0.8817 (mt) cc_final: 0.8608 (mm) REVERT: R 14 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.5226 (ptm160) REVERT: R 72 ASN cc_start: 0.8595 (p0) cc_final: 0.8261 (p0) REVERT: R 73 ASN cc_start: 0.6841 (m-40) cc_final: 0.6445 (m-40) REVERT: A 105 ASP cc_start: 0.8319 (m-30) cc_final: 0.7653 (p0) REVERT: A 107 ASN cc_start: 0.7120 (t0) cc_final: 0.6608 (t0) REVERT: A 140 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7114 (mm-40) REVERT: A 266 THR cc_start: 0.8604 (p) cc_final: 0.8377 (p) REVERT: A 287 ARG cc_start: 0.8648 (ttp-170) cc_final: 0.8246 (ttm-80) REVERT: A 633 MET cc_start: 0.8402 (mtp) cc_final: 0.8201 (mtp) REVERT: A 675 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 781 ILE cc_start: 0.8429 (mm) cc_final: 0.8178 (mm) REVERT: A 836 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9067 (p) REVERT: A 837 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8484 (tp) REVERT: A 1026 TYR cc_start: 0.8089 (m-80) cc_final: 0.7863 (m-80) REVERT: A 1028 LYS cc_start: 0.9388 (ttpp) cc_final: 0.9115 (ttpp) REVERT: A 1242 SER cc_start: 0.8916 (m) cc_final: 0.8546 (p) REVERT: Q 74 GLU cc_start: 0.2910 (mm-30) cc_final: 0.2693 (mm-30) REVERT: Q 78 PHE cc_start: 0.5252 (m-80) cc_final: 0.4705 (m-10) REVERT: Q 102 MET cc_start: 0.5719 (mtp) cc_final: 0.5328 (mpp) REVERT: Q 105 ARG cc_start: 0.7538 (ttt-90) cc_final: 0.7019 (ttt180) REVERT: Y 19 MET cc_start: 0.8058 (mmp) cc_final: 0.7325 (mmm) REVERT: Y 70 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8217 (tppt) REVERT: Y 192 GLN cc_start: 0.8772 (pt0) cc_final: 0.8424 (pt0) REVERT: Y 220 GLU cc_start: 0.8394 (tt0) cc_final: 0.7849 (mm-30) REVERT: Y 258 MET cc_start: 0.2557 (mtt) cc_final: 0.2202 (mmp) REVERT: Y 531 PHE cc_start: 0.8568 (m-80) cc_final: 0.8033 (m-80) REVERT: C 279 MET cc_start: 0.8133 (mmm) cc_final: 0.7332 (mmt) REVERT: S 39 ASP cc_start: 0.8732 (p0) cc_final: 0.8281 (p0) REVERT: S 139 ILE cc_start: 0.7874 (pt) cc_final: 0.7579 (tp) outliers start: 142 outliers final: 82 residues processed: 675 average time/residue: 0.2217 time to fit residues: 252.2988 Evaluate side-chains 559 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 463 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 MET 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 608 GLU 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 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 72 THR 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 66 ILE Chi-restraints excluded: chain F residue 82 ILE 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 372 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 599 LEU Chi-restraints excluded: chain I residue 647 GLU 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 14 ARG Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 99 THR 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 90 CYS Chi-restraints excluded: chain A residue 140 GLN 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 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 676 LEU 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 916 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1117 THR 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 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 441 VAL 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 211 CYS 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 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: 20.0000 chunk 330 optimal weight: 0.4980 chunk 425 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 374 optimal weight: 6.9990 chunk 456 optimal weight: 10.0000 chunk 345 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 543 ASN ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 373 GLN ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Q 43 HIS Y 78 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.117142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.092224 restraints weight = 264515.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.094884 restraints weight = 115678.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095542 restraints weight = 62113.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.095843 restraints weight = 46772.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.096060 restraints weight = 42757.305| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42223 Z= 0.138 Angle : 0.653 13.654 57372 Z= 0.323 Chirality : 0.049 0.419 6552 Planarity : 0.004 0.049 7012 Dihedral : 12.402 177.256 6381 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.43 % Allowed : 17.56 % Favored : 79.01 % 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: 0.62 (0.12), residues: 1761 sheet: -0.73 (0.20), residues: 659 loop : -1.48 (0.12), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 184 TYR 0.037 0.002 TYR R 41 PHE 0.027 0.001 PHE A 938 TRP 0.014 0.001 TRP A 365 HIS 0.013 0.001 HIS R 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (42203) covalent geometry : angle 0.64896 / 0.32 (57346) SS BOND : bond 0.00113 / 0.06 ( 4) SS BOND : angle 0.83995 / 0.42 ( 8) hydrogen bonds : bond 0.03953 / 2.60 ( 1645) hydrogen bonds : angle 4.89555 / 3.43 ( 4666) metal coordination : bond 0.01377 / 0.57 ( 16) metal coordination : angle 3.92557 / 2.34 ( 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 669 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 514 time to evaluate : 1.650 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 237 SER cc_start: 0.9149 (m) cc_final: 0.8698 (t) REVERT: B 474 ASP cc_start: 0.7778 (t70) cc_final: 0.7269 (t0) REVERT: B 482 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8634 (m) REVERT: B 662 ASP cc_start: 0.7792 (t0) cc_final: 0.7449 (t0) REVERT: B 680 ASN cc_start: 0.7281 (OUTLIER) cc_final: 0.6933 (p0) REVERT: B 716 MET cc_start: 0.7527 (mtp) cc_final: 0.7206 (mtp) REVERT: B 771 ASP cc_start: 0.8636 (t0) cc_final: 0.7862 (t0) REVERT: B 785 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: B 862 THR cc_start: 0.8479 (m) cc_final: 0.8210 (t) REVERT: B 928 MET cc_start: 0.8096 (tpp) cc_final: 0.7858 (tpp) REVERT: B 1085 TYR cc_start: 0.8184 (m-80) cc_final: 0.7461 (m-10) REVERT: E 169 MET cc_start: 0.7751 (ttp) cc_final: 0.7407 (ttp) REVERT: F 74 THR cc_start: 0.9038 (m) cc_final: 0.8785 (p) REVERT: F 152 ASP cc_start: 0.7964 (m-30) cc_final: 0.7717 (m-30) REVERT: G 83 ASP cc_start: 0.7664 (m-30) cc_final: 0.7110 (m-30) REVERT: G 103 ASP cc_start: 0.7769 (p0) cc_final: 0.6772 (m-30) REVERT: G 104 LEU cc_start: 0.9138 (tp) cc_final: 0.8929 (tp) REVERT: I 168 MET cc_start: 0.8494 (mtp) cc_final: 0.8062 (mmm) REVERT: I 205 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8006 (tttt) REVERT: I 259 TRP cc_start: 0.8740 (m-10) cc_final: 0.8394 (m-10) REVERT: I 372 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7626 (mm) REVERT: I 415 MET cc_start: 0.7574 (mmm) cc_final: 0.7171 (ttt) REVERT: I 486 LYS cc_start: 0.8876 (mttt) cc_final: 0.8378 (ptmt) REVERT: I 487 MET cc_start: 0.7394 (mmp) cc_final: 0.7076 (mmm) REVERT: I 595 ARG cc_start: 0.6869 (mmt180) cc_final: 0.6532 (mmt180) REVERT: I 599 LEU cc_start: 0.5301 (OUTLIER) cc_final: 0.5075 (pp) REVERT: I 790 MET cc_start: 0.7615 (mmt) cc_final: 0.7212 (mpp) REVERT: J 10 CYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7381 (p) REVERT: R 72 ASN cc_start: 0.8479 (p0) cc_final: 0.8061 (p0) REVERT: R 73 ASN cc_start: 0.6785 (m-40) cc_final: 0.6300 (m-40) REVERT: K 392 MET cc_start: 0.7072 (ttm) cc_final: 0.6754 (tpp) REVERT: A 105 ASP cc_start: 0.8325 (m-30) cc_final: 0.7657 (p0) REVERT: A 107 ASN cc_start: 0.7022 (t0) cc_final: 0.6476 (t0) REVERT: A 266 THR cc_start: 0.8663 (p) cc_final: 0.8451 (p) REVERT: A 287 ARG cc_start: 0.8642 (ttp-170) cc_final: 0.8351 (ttm-80) REVERT: A 614 ARG cc_start: 0.8721 (mmt-90) cc_final: 0.8497 (mmt180) REVERT: A 675 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7748 (mm-30) REVERT: A 687 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6853 (mtt-85) REVERT: A 771 TYR cc_start: 0.8483 (m-80) cc_final: 0.8148 (m-80) REVERT: A 781 ILE cc_start: 0.8408 (mm) cc_final: 0.8094 (mm) REVERT: A 836 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9034 (p) REVERT: A 1026 TYR cc_start: 0.8065 (m-80) cc_final: 0.7759 (m-80) REVERT: A 1063 GLU cc_start: 0.8661 (pt0) cc_final: 0.8231 (tm-30) REVERT: A 1242 SER cc_start: 0.8862 (m) cc_final: 0.8484 (p) REVERT: Q 102 MET cc_start: 0.5769 (mtp) cc_final: 0.5448 (mpp) REVERT: Y 19 MET cc_start: 0.8078 (mmp) cc_final: 0.7393 (mmm) REVERT: Y 63 MET cc_start: 0.8645 (ttp) cc_final: 0.8247 (tmm) REVERT: Y 70 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8204 (tppt) REVERT: Y 220 GLU cc_start: 0.8528 (tt0) cc_final: 0.7931 (mm-30) REVERT: Y 258 MET cc_start: 0.2452 (mtt) cc_final: 0.2106 (mmp) REVERT: Y 531 PHE cc_start: 0.8552 (m-80) cc_final: 0.7958 (m-80) REVERT: S 39 ASP cc_start: 0.8648 (p0) cc_final: 0.8337 (p0) REVERT: S 42 GLU cc_start: 0.8879 (tt0) cc_final: 0.8608 (tt0) REVERT: S 106 MET cc_start: 0.6536 (mmm) cc_final: 0.6181 (mmt) outliers start: 155 outliers final: 96 residues processed: 629 average time/residue: 0.2363 time to fit residues: 250.6967 Evaluate side-chains 563 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 458 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 189 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 415 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 608 GLU 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 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 1060 CYS Chi-restraints excluded: chain B residue 1061 LEU 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 82 ILE 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 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 276 ILE Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 372 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 599 LEU Chi-restraints excluded: chain I residue 647 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 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 K residue 439 ILE 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 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 385 HIS 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 687 ARG 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 836 THR 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 1199 ASN 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 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 244 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 417 optimal weight: 6.9990 chunk 423 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 308 optimal weight: 0.9980 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: 2.9990 chunk 362 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 664 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 HIS ** 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 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 ASN ** Y 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN C 230 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.113531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.088855 restraints weight = 263219.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.090901 restraints weight = 120502.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091904 restraints weight = 68122.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092160 restraints weight = 49573.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.092481 restraints weight = 41778.496| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 42223 Z= 0.265 Angle : 0.750 11.262 57372 Z= 0.376 Chirality : 0.051 0.362 6552 Planarity : 0.005 0.052 7012 Dihedral : 12.499 176.745 6379 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.07 % Allowed : 18.20 % Favored : 77.73 % 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: -1.01 (0.12), residues: 4859 helix: 0.53 (0.12), residues: 1784 sheet: -0.87 (0.20), residues: 682 loop : -1.56 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 270 TYR 0.028 0.002 TYR C 170 PHE 0.024 0.002 PHE A 938 TRP 0.016 0.002 TRP Y 79 HIS 0.018 0.002 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.26 (42203) covalent geometry : angle 0.74669 / 0.38 (57346) SS BOND : bond 0.00205 / 0.11 ( 4) SS BOND : angle 0.95832 / 0.50 ( 8) hydrogen bonds : bond 0.04513 / 2.97 ( 1645) hydrogen bonds : angle 5.17146 / 3.64 ( 4666) metal coordination : bond 0.02128 / 1.09 ( 16) metal coordination : angle 4.06216 / 2.40 ( 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 648 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 464 time to evaluate : 1.637 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: B 159 ASN cc_start: 0.8158 (t0) cc_final: 0.7615 (p0) REVERT: B 237 SER cc_start: 0.9252 (m) cc_final: 0.8766 (t) REVERT: B 474 ASP cc_start: 0.8028 (t70) cc_final: 0.7741 (t0) REVERT: B 662 ASP cc_start: 0.8328 (t0) cc_final: 0.7897 (t0) REVERT: B 680 ASN cc_start: 0.7166 (OUTLIER) cc_final: 0.6880 (p0) REVERT: B 716 MET cc_start: 0.7707 (mtp) cc_final: 0.7239 (mtp) REVERT: B 771 ASP cc_start: 0.8706 (t0) cc_final: 0.8010 (t0) REVERT: B 785 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: B 1068 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.7741 (t0) REVERT: E 116 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.6972 (tp) REVERT: G 83 ASP cc_start: 0.7802 (m-30) cc_final: 0.7192 (m-30) REVERT: I 205 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8092 (tttt) REVERT: I 372 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7511 (mm) REVERT: I 415 MET cc_start: 0.7553 (mmm) cc_final: 0.7135 (ttt) REVERT: I 487 MET cc_start: 0.7498 (mmp) cc_final: 0.6914 (mmm) REVERT: I 595 ARG cc_start: 0.7058 (mmt180) cc_final: 0.6452 (mmp80) REVERT: I 790 MET cc_start: 0.7645 (mmt) cc_final: 0.7255 (mpp) REVERT: R 72 ASN cc_start: 0.8588 (p0) cc_final: 0.8128 (p0) REVERT: R 73 ASN cc_start: 0.6843 (m-40) cc_final: 0.6253 (m-40) REVERT: A 105 ASP cc_start: 0.8495 (m-30) cc_final: 0.7801 (p0) REVERT: A 287 ARG cc_start: 0.8716 (ttp-170) cc_final: 0.8342 (ttm-80) REVERT: A 614 ARG cc_start: 0.8727 (mmt-90) cc_final: 0.8520 (mmt180) REVERT: A 675 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 687 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6994 (mtt-85) REVERT: A 771 TYR cc_start: 0.8668 (m-80) cc_final: 0.8448 (m-80) REVERT: A 781 ILE cc_start: 0.8513 (mm) cc_final: 0.8292 (mm) REVERT: A 882 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9021 (pt) REVERT: A 1026 TYR cc_start: 0.8060 (m-10) cc_final: 0.7609 (m-80) REVERT: A 1028 LYS cc_start: 0.9283 (ttpt) cc_final: 0.9073 (pttt) REVERT: A 1050 ILE cc_start: 0.8672 (pt) cc_final: 0.8453 (pt) REVERT: A 1063 GLU cc_start: 0.8657 (pt0) cc_final: 0.8330 (tm-30) REVERT: A 1242 SER cc_start: 0.8967 (m) cc_final: 0.8402 (p) REVERT: Q 102 MET cc_start: 0.5861 (mtp) cc_final: 0.5528 (mpp) REVERT: Y 48 MET cc_start: 0.7756 (tpp) cc_final: 0.6948 (tpp) REVERT: Y 63 MET cc_start: 0.8652 (ttp) cc_final: 0.8226 (tmm) REVERT: Y 108 ASP cc_start: 0.6114 (m-30) cc_final: 0.5706 (m-30) REVERT: Y 192 GLN cc_start: 0.8813 (pt0) cc_final: 0.8405 (pt0) REVERT: Y 531 PHE cc_start: 0.8641 (m-80) cc_final: 0.8251 (m-80) REVERT: C 180 ASP cc_start: 0.8403 (p0) cc_final: 0.8191 (p0) REVERT: C 279 MET cc_start: 0.8132 (mmt) cc_final: 0.7920 (mmt) REVERT: S 39 ASP cc_start: 0.8679 (p0) cc_final: 0.8218 (p0) REVERT: S 42 GLU cc_start: 0.8868 (tt0) cc_final: 0.8668 (tt0) REVERT: S 105 ASP cc_start: 0.5127 (m-30) cc_final: 0.3905 (t0) REVERT: S 141 ASP cc_start: 0.8188 (t0) cc_final: 0.7917 (t0) REVERT: S 243 LEU cc_start: 0.8077 (mp) cc_final: 0.7249 (tp) outliers start: 184 outliers final: 124 residues processed: 607 average time/residue: 0.2264 time to fit residues: 233.8655 Evaluate side-chains 562 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 431 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain B residue 194 SER 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 582 ILE Chi-restraints excluded: chain B residue 608 GLU 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 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 1013 ILE Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1061 LEU 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 46 THR Chi-restraints excluded: chain E residue 116 LEU 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 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 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 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 372 ILE 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 647 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 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 90 CYS Chi-restraints excluded: chain A residue 163 SER 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 366 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 389 VAL 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 613 VAL Chi-restraints excluded: chain A residue 687 ARG Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 871 VAL 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 929 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 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 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 337 LEU 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 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 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: 0.9990 chunk 251 optimal weight: 9.9990 chunk 284 optimal weight: 0.9980 chunk 487 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 283 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 436 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 ASN ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 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 A 385 HIS ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.114020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.088897 restraints weight = 312021.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.091861 restraints weight = 132969.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.092877 restraints weight = 68703.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092604 restraints weight = 54720.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.093146 restraints weight = 49687.661| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 42223 Z= 0.209 Angle : 0.701 11.567 57372 Z= 0.350 Chirality : 0.049 0.374 6552 Planarity : 0.004 0.054 7012 Dihedral : 12.428 172.831 6377 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.81 % Allowed : 19.04 % Favored : 77.15 % 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: -0.91 (0.12), residues: 4859 helix: 0.68 (0.12), residues: 1767 sheet: -0.88 (0.20), residues: 675 loop : -1.51 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 163 TYR 0.025 0.002 TYR C 170 PHE 0.026 0.002 PHE A 938 TRP 0.034 0.002 TRP S 43 HIS 0.008 0.001 HIS R 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (42203) covalent geometry : angle 0.69765 / 0.35 (57346) SS BOND : bond 0.00119 / 0.06 ( 4) SS BOND : angle 0.89615 / 0.45 ( 8) hydrogen bonds : bond 0.04250 / 2.79 ( 1645) hydrogen bonds : angle 5.09568 / 3.58 ( 4666) metal coordination : bond 0.01546 / 0.81 ( 16) metal coordination : angle 3.88491 / 2.38 ( 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 631 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 459 time to evaluate : 1.433 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: 0.8237 (t0) cc_final: 0.7745 (p0) REVERT: B 237 SER cc_start: 0.9163 (m) cc_final: 0.8706 (t) REVERT: B 320 ASN cc_start: 0.6475 (t0) cc_final: 0.6034 (p0) REVERT: B 474 ASP cc_start: 0.7971 (t70) cc_final: 0.7693 (t0) REVERT: B 662 ASP cc_start: 0.8309 (t0) cc_final: 0.7870 (t0) REVERT: B 680 ASN cc_start: 0.7143 (OUTLIER) cc_final: 0.6860 (p0) REVERT: B 716 MET cc_start: 0.7623 (mtp) cc_final: 0.7228 (mtp) REVERT: B 771 ASP cc_start: 0.8505 (t0) cc_final: 0.7940 (t0) REVERT: B 785 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: B 1068 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.7785 (t0) REVERT: G 83 ASP cc_start: 0.7816 (m-30) cc_final: 0.7231 (m-30) REVERT: I 205 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8032 (tttt) REVERT: I 415 MET cc_start: 0.7506 (mmm) cc_final: 0.7060 (ttt) REVERT: I 487 MET cc_start: 0.7531 (mmp) cc_final: 0.6961 (tpt) REVERT: I 626 GLN cc_start: 0.5908 (pm20) cc_final: 0.5503 (tm-30) REVERT: R 72 ASN cc_start: 0.8587 (p0) cc_final: 0.8104 (p0) REVERT: R 73 ASN cc_start: 0.6883 (m-40) cc_final: 0.6241 (m-40) REVERT: A 105 ASP cc_start: 0.8570 (m-30) cc_final: 0.7883 (p0) REVERT: A 287 ARG cc_start: 0.8672 (ttp-170) cc_final: 0.8352 (ttm-80) REVERT: A 613 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8948 (t) REVERT: A 675 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7918 (mm-30) REVERT: A 687 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6955 (mtt-85) REVERT: A 781 ILE cc_start: 0.8452 (mm) cc_final: 0.8214 (mm) REVERT: A 885 MET cc_start: 0.8717 (mmm) cc_final: 0.8467 (mmm) REVERT: A 1026 TYR cc_start: 0.8043 (m-10) cc_final: 0.7600 (m-80) REVERT: A 1050 ILE cc_start: 0.8714 (pt) cc_final: 0.8488 (pt) REVERT: A 1063 GLU cc_start: 0.8679 (pt0) cc_final: 0.8347 (tm-30) REVERT: A 1199 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.7718 (m-40) REVERT: A 1242 SER cc_start: 0.8964 (m) cc_final: 0.8413 (p) REVERT: A 1247 ILE cc_start: 0.9136 (mm) cc_final: 0.8605 (mt) REVERT: Q 102 MET cc_start: 0.5939 (mtp) cc_final: 0.5595 (mpp) REVERT: Y 48 MET cc_start: 0.7834 (tpp) cc_final: 0.7113 (tpp) REVERT: Y 63 MET cc_start: 0.8605 (ttp) cc_final: 0.8208 (tmm) REVERT: Y 108 ASP cc_start: 0.6367 (m-30) cc_final: 0.5954 (m-30) REVERT: Y 192 GLN cc_start: 0.8799 (pt0) cc_final: 0.8415 (pt0) REVERT: C 180 ASP cc_start: 0.8383 (p0) cc_final: 0.8134 (p0) REVERT: S 39 ASP cc_start: 0.8673 (p0) cc_final: 0.8245 (p0) REVERT: S 42 GLU cc_start: 0.8861 (tt0) cc_final: 0.8631 (tt0) REVERT: S 105 ASP cc_start: 0.5190 (m-30) cc_final: 0.3602 (t0) REVERT: S 106 MET cc_start: 0.6061 (mmm) cc_final: 0.5596 (mmm) REVERT: S 243 LEU cc_start: 0.7993 (mp) cc_final: 0.7172 (tp) outliers start: 172 outliers final: 123 residues processed: 589 average time/residue: 0.2338 time to fit residues: 233.1442 Evaluate side-chains 567 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 438 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 241 SER 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 598 GLU Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 689 LEU 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 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 1068 ASN Chi-restraints excluded: chain B residue 1080 ASP Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1158 LEU 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 82 ILE Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 9 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR 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 G residue 154 PHE 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 647 GLU 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 I residue 752 SER Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 2 GLU 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 452 THR 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 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 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 423 MET Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 687 ARG Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 929 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 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 78 ASN Chi-restraints excluded: chain Y residue 92 ASP Chi-restraints excluded: chain Y residue 185 THR 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 142 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain S residue 40 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 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: 5.9990 chunk 240 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 471 optimal weight: 0.9990 chunk 408 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 288 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN B 766 GLN G 64 ASN ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 373 GLN ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS ** A 450 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.116533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.091721 restraints weight = 296021.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.095232 restraints weight = 122019.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.095653 restraints weight = 59241.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.095751 restraints weight = 50684.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.096132 restraints weight = 45912.210| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 42223 Z= 0.128 Angle : 0.643 11.865 57372 Z= 0.321 Chirality : 0.048 0.384 6552 Planarity : 0.004 0.052 7012 Dihedral : 12.274 171.227 6374 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.94 % Allowed : 19.68 % Favored : 77.37 % 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: -0.68 (0.12), residues: 4859 helix: 0.84 (0.13), residues: 1772 sheet: -0.75 (0.20), residues: 667 loop : -1.35 (0.13), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 163 TYR 0.037 0.001 TYR A 771 PHE 0.034 0.001 PHE R 84 TRP 0.030 0.002 TRP S 43 HIS 0.038 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (42203) covalent geometry : angle 0.64007 / 0.32 (57346) SS BOND : bond 0.00104 / 0.05 ( 4) SS BOND : angle 0.66035 / 0.33 ( 8) hydrogen bonds : bond 0.03834 / 2.52 ( 1645) hydrogen bonds : angle 4.87317 / 3.43 ( 4666) metal coordination : bond 0.00812 / 0.42 ( 16) metal coordination : angle 3.50259 / 2.25 ( 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 637 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 504 time to evaluate : 1.608 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: B 8 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6884 (pp20) REVERT: B 151 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7619 (p0) REVERT: B 159 ASN cc_start: 0.8159 (t0) cc_final: 0.7796 (p0) REVERT: B 237 SER cc_start: 0.9213 (m) cc_final: 0.8711 (t) REVERT: B 297 LYS cc_start: 0.8517 (pttt) cc_final: 0.8255 (pttt) REVERT: B 320 ASN cc_start: 0.6347 (t0) cc_final: 0.5882 (p0) REVERT: B 474 ASP cc_start: 0.7954 (t70) cc_final: 0.7644 (t0) REVERT: B 571 VAL cc_start: 0.9503 (t) cc_final: 0.9247 (m) REVERT: B 662 ASP cc_start: 0.8121 (t0) cc_final: 0.7676 (t0) REVERT: B 680 ASN cc_start: 0.7224 (OUTLIER) cc_final: 0.6922 (p0) REVERT: B 716 MET cc_start: 0.7598 (mtp) cc_final: 0.7233 (mtp) REVERT: B 771 ASP cc_start: 0.8471 (t0) cc_final: 0.7818 (t0) REVERT: B 785 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: B 862 THR cc_start: 0.8348 (m) cc_final: 0.7963 (t) REVERT: B 1068 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7799 (t0) REVERT: B 1085 TYR cc_start: 0.7978 (m-80) cc_final: 0.7464 (m-10) REVERT: G 83 ASP cc_start: 0.7781 (m-30) cc_final: 0.7189 (m-30) REVERT: I 205 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8009 (tttt) REVERT: I 415 MET cc_start: 0.7565 (mmm) cc_final: 0.7058 (ttt) REVERT: I 487 MET cc_start: 0.7504 (mmp) cc_final: 0.6912 (tpt) REVERT: I 511 MET cc_start: 0.8520 (mmm) cc_final: 0.8265 (mmm) REVERT: I 595 ARG cc_start: 0.7322 (mmt180) cc_final: 0.6623 (mmp80) REVERT: R 72 ASN cc_start: 0.8486 (p0) cc_final: 0.8045 (p0) REVERT: R 73 ASN cc_start: 0.6838 (m-40) cc_final: 0.6226 (m-40) REVERT: K 392 MET cc_start: 0.7265 (ttm) cc_final: 0.6904 (tpp) REVERT: A 105 ASP cc_start: 0.8489 (m-30) cc_final: 0.7831 (p0) REVERT: A 287 ARG cc_start: 0.8654 (ttp-170) cc_final: 0.8272 (ttm-80) REVERT: A 420 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 613 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8972 (t) REVERT: A 614 ARG cc_start: 0.8624 (mmt-90) cc_final: 0.8395 (mmt180) REVERT: A 781 ILE cc_start: 0.8388 (mm) cc_final: 0.8157 (mm) REVERT: A 837 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8373 (tp) REVERT: A 1026 TYR cc_start: 0.8052 (m-10) cc_final: 0.7675 (m-80) REVERT: A 1031 GLU cc_start: 0.8368 (mp0) cc_final: 0.8122 (mp0) REVERT: A 1063 GLU cc_start: 0.8704 (pt0) cc_final: 0.8390 (tm-30) REVERT: A 1199 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8137 (m-40) REVERT: A 1242 SER cc_start: 0.8893 (m) cc_final: 0.8450 (p) REVERT: Q 95 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8078 (mm-30) REVERT: Q 102 MET cc_start: 0.5942 (mtp) cc_final: 0.5624 (mpp) REVERT: Y 24 MET cc_start: 0.6371 (tpp) cc_final: 0.6158 (tpt) REVERT: Y 48 MET cc_start: 0.7854 (tpp) cc_final: 0.7231 (tpp) REVERT: Y 63 MET cc_start: 0.8646 (ttp) cc_final: 0.8214 (tmm) REVERT: Y 113 ASN cc_start: 0.8531 (p0) cc_final: 0.8262 (p0) REVERT: Y 192 GLN cc_start: 0.8816 (pt0) cc_final: 0.8461 (pt0) REVERT: Y 220 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7905 (mm-30) REVERT: Y 531 PHE cc_start: 0.8551 (m-80) cc_final: 0.8152 (m-80) REVERT: C 180 ASP cc_start: 0.8330 (p0) cc_final: 0.8091 (p0) REVERT: C 279 MET cc_start: 0.8202 (mmt) cc_final: 0.7934 (mmt) REVERT: S 39 ASP cc_start: 0.8620 (p0) cc_final: 0.8198 (p0) REVERT: S 42 GLU cc_start: 0.8847 (tt0) cc_final: 0.8490 (tt0) REVERT: S 105 ASP cc_start: 0.5331 (m-30) cc_final: 0.3886 (t0) REVERT: S 106 MET cc_start: 0.6242 (mmm) cc_final: 0.5699 (mmm) REVERT: S 141 ASP cc_start: 0.8054 (t0) cc_final: 0.7493 (m-30) REVERT: S 243 LEU cc_start: 0.7875 (mp) cc_final: 0.6919 (tp) outliers start: 133 outliers final: 98 residues processed: 600 average time/residue: 0.2312 time to fit residues: 234.8024 Evaluate side-chains 557 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 451 time to evaluate : 1.682 ------------------------------------------------------------------------------- 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 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 302 LEU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 689 LEU 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 863 ASP Chi-restraints excluded: chain B residue 1015 TYR 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 126 SER Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 9 TYR 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 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 328 HIS 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 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 33 VAL Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 2 GLU 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 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 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 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 423 MET 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 613 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 837 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 78 ASN 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 187 PHE 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 145 ASN 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: 1.9990 chunk 56 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 470 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 236 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS Y 78 ASN ** Y 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 391 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.116632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.091986 restraints weight = 309352.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095106 restraints weight = 131234.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.095820 restraints weight = 68065.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.095663 restraints weight = 58354.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096182 restraints weight = 50088.188| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- 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 = 0.23 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 = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 42223 Z= 0.135 Angle : 0.655 13.859 57372 Z= 0.326 Chirality : 0.048 0.385 6552 Planarity : 0.004 0.100 7012 Dihedral : 12.224 171.766 6373 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.92 % Allowed : 20.30 % Favored : 76.78 % 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: -0.57 (0.12), residues: 4859 helix: 0.93 (0.13), residues: 1761 sheet: -0.65 (0.20), residues: 664 loop : -1.29 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Q 105 TYR 0.042 0.002 TYR A 771 PHE 0.030 0.001 PHE B 190 TRP 0.023 0.002 TRP I 259 HIS 0.014 0.001 HIS R 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (42203) covalent geometry : angle 0.65245 / 0.33 (57346) SS BOND : bond 0.00265 / 0.13 ( 4) SS BOND : angle 0.69711 / 0.35 ( 8) hydrogen bonds : bond 0.03792 / 2.48 ( 1645) hydrogen bonds : angle 4.84376 / 3.40 ( 4666) metal coordination : bond 0.00891 / 0.47 ( 16) metal coordination : angle 3.49498 / 2.26 ( 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 618 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 486 time to evaluate : 1.367 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: B 8 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6896 (pp20) REVERT: B 159 ASN cc_start: 0.8162 (t0) cc_final: 0.7904 (p0) REVERT: B 237 SER cc_start: 0.9137 (m) cc_final: 0.8577 (t) REVERT: B 320 ASN cc_start: 0.6241 (t0) cc_final: 0.5849 (p0) REVERT: B 474 ASP cc_start: 0.7856 (t70) cc_final: 0.7602 (t0) REVERT: B 571 VAL cc_start: 0.9485 (t) cc_final: 0.9145 (p) REVERT: B 662 ASP cc_start: 0.8023 (t0) cc_final: 0.7609 (t0) REVERT: B 680 ASN cc_start: 0.7269 (OUTLIER) cc_final: 0.7065 (p0) REVERT: B 716 MET cc_start: 0.7518 (mtp) cc_final: 0.7169 (mtp) REVERT: B 771 ASP cc_start: 0.8510 (t0) cc_final: 0.7827 (t0) REVERT: B 785 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: B 862 THR cc_start: 0.8382 (m) cc_final: 0.8163 (t) REVERT: B 1085 TYR cc_start: 0.7964 (m-80) cc_final: 0.7463 (m-10) REVERT: G 61 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9045 (tt) REVERT: G 83 ASP cc_start: 0.7720 (m-30) cc_final: 0.7166 (m-30) REVERT: I 205 LYS cc_start: 0.8570 (mtmt) cc_final: 0.7985 (tttt) REVERT: I 415 MET cc_start: 0.7460 (mmm) cc_final: 0.6972 (ttt) REVERT: I 487 MET cc_start: 0.7529 (mmp) cc_final: 0.6920 (tpt) REVERT: I 595 ARG cc_start: 0.7253 (mmt180) cc_final: 0.6544 (mmp80) REVERT: R 48 GLU cc_start: 0.6945 (pm20) cc_final: 0.5961 (pm20) REVERT: R 64 ASP cc_start: 0.6857 (t0) cc_final: 0.6655 (t0) REVERT: R 72 ASN cc_start: 0.8444 (p0) cc_final: 0.8028 (p0) REVERT: R 73 ASN cc_start: 0.6855 (m-40) cc_final: 0.6250 (m-40) REVERT: K 392 MET cc_start: 0.7237 (ttm) cc_final: 0.6710 (tpp) REVERT: A 54 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8239 (mmmt) REVERT: A 105 ASP cc_start: 0.8508 (m-30) cc_final: 0.7850 (p0) REVERT: A 526 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7698 (p0) REVERT: A 781 ILE cc_start: 0.8350 (mm) cc_final: 0.8121 (mm) REVERT: A 837 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8438 (tt) REVERT: A 1031 GLU cc_start: 0.8316 (mp0) cc_final: 0.8074 (mp0) REVERT: A 1063 GLU cc_start: 0.8680 (pt0) cc_final: 0.8439 (tm-30) REVERT: A 1242 SER cc_start: 0.8862 (m) cc_final: 0.8413 (p) REVERT: Q 78 PHE cc_start: 0.5442 (m-10) cc_final: 0.4631 (m-10) REVERT: Q 95 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8118 (mm-30) REVERT: Q 102 MET cc_start: 0.5930 (mtp) cc_final: 0.5580 (mpp) REVERT: Y 48 MET cc_start: 0.7823 (tpp) cc_final: 0.7228 (tpp) REVERT: Y 63 MET cc_start: 0.8628 (ttp) cc_final: 0.8191 (tmm) REVERT: Y 108 ASP cc_start: 0.6784 (m-30) cc_final: 0.6325 (m-30) REVERT: Y 113 ASN cc_start: 0.8502 (p0) cc_final: 0.8257 (p0) REVERT: Y 179 MET cc_start: 0.8591 (tpt) cc_final: 0.8335 (tpt) REVERT: Y 192 GLN cc_start: 0.8796 (pt0) cc_final: 0.8466 (pt0) REVERT: Y 531 PHE cc_start: 0.8540 (m-80) cc_final: 0.8142 (m-80) REVERT: C 180 ASP cc_start: 0.8325 (p0) cc_final: 0.8066 (p0) REVERT: C 250 MET cc_start: 0.7854 (mmm) cc_final: 0.7328 (tpt) REVERT: C 279 MET cc_start: 0.8172 (mmt) cc_final: 0.7866 (mmt) REVERT: S 39 ASP cc_start: 0.8734 (p0) cc_final: 0.8454 (p0) REVERT: S 42 GLU cc_start: 0.8867 (tt0) cc_final: 0.8465 (tt0) REVERT: S 105 ASP cc_start: 0.5379 (m-30) cc_final: 0.3963 (t0) REVERT: S 106 MET cc_start: 0.6393 (mmm) cc_final: 0.5887 (mmm) REVERT: S 243 LEU cc_start: 0.7860 (mp) cc_final: 0.6775 (tp) outliers start: 132 outliers final: 102 residues processed: 581 average time/residue: 0.2109 time to fit residues: 209.0540 Evaluate side-chains 561 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 453 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU 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 241 SER 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 680 ASN Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 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 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 97 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 9 TYR 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 G residue 154 PHE 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 328 HIS 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 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 33 VAL Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 51 LEU 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 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 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 400 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 423 MET 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 675 GLU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 837 LEU 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 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 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 142 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 187 PHE 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 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 137 optimal weight: 1.9990 chunk 343 optimal weight: 0.3980 chunk 436 optimal weight: 10.0000 chunk 290 optimal weight: 0.7980 chunk 450 optimal weight: 1.9990 chunk 488 optimal weight: 0.0370 chunk 59 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 420 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 703 ASN ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.117663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.092775 restraints weight = 271732.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.096361 restraints weight = 119256.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.096577 restraints weight = 60054.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.097115 restraints weight = 43347.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.097402 restraints weight = 38542.494| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 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 = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 42223 Z= 0.123 Angle : 0.658 15.166 57372 Z= 0.327 Chirality : 0.048 0.384 6552 Planarity : 0.004 0.053 7012 Dihedral : 12.176 173.311 6371 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.50 % Allowed : 20.90 % Favored : 76.60 % 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: -0.52 (0.12), residues: 4859 helix: 0.93 (0.13), residues: 1767 sheet: -0.62 (0.20), residues: 669 loop : -1.23 (0.13), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 86 TYR 0.032 0.001 TYR A 771 PHE 0.028 0.001 PHE A 938 TRP 0.066 0.002 TRP S 43 HIS 0.014 0.001 HIS R 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (42203) covalent geometry : angle 0.65547 / 0.33 (57346) SS BOND : bond 0.00137 / 0.07 ( 4) SS BOND : angle 0.77464 / 0.38 ( 8) hydrogen bonds : bond 0.03702 / 2.43 ( 1645) hydrogen bonds : angle 4.82277 / 3.38 ( 4666) metal coordination : bond 0.01073 / 0.61 ( 16) metal coordination : angle 3.39951 / 2.22 ( 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 615 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 502 time to evaluate : 1.531 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 71 SER cc_start: 0.8652 (t) cc_final: 0.8230 (p) REVERT: B 159 ASN cc_start: 0.8196 (t0) cc_final: 0.7934 (p0) REVERT: B 237 SER cc_start: 0.9164 (m) cc_final: 0.8611 (t) REVERT: B 320 ASN cc_start: 0.6305 (t0) cc_final: 0.5886 (p0) REVERT: B 474 ASP cc_start: 0.7865 (t70) cc_final: 0.7532 (t0) REVERT: B 571 VAL cc_start: 0.9512 (t) cc_final: 0.9141 (p) REVERT: B 662 ASP cc_start: 0.7941 (t0) cc_final: 0.7520 (t0) REVERT: B 680 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.7046 (p0) REVERT: B 691 CYS cc_start: 0.8420 (m) cc_final: 0.8108 (m) REVERT: B 716 MET cc_start: 0.7528 (mtp) cc_final: 0.7156 (mtp) REVERT: B 771 ASP cc_start: 0.8460 (t0) cc_final: 0.7737 (t0) REVERT: B 785 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: B 861 LEU cc_start: 0.8011 (mt) cc_final: 0.7669 (mt) REVERT: B 862 THR cc_start: 0.8369 (m) cc_final: 0.8121 (p) REVERT: B 1068 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7677 (t0) REVERT: E 72 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8792 (p) REVERT: E 165 PHE cc_start: 0.7526 (m-80) cc_final: 0.7254 (m-80) REVERT: G 61 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9035 (tt) REVERT: G 83 ASP cc_start: 0.7681 (m-30) cc_final: 0.7087 (m-30) REVERT: G 126 ARG cc_start: 0.8013 (tpt90) cc_final: 0.7636 (ttp80) REVERT: I 205 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8017 (tttt) REVERT: I 487 MET cc_start: 0.7499 (mmp) cc_final: 0.6871 (tpt) REVERT: I 595 ARG cc_start: 0.7057 (mmt180) cc_final: 0.6406 (mmp80) REVERT: R 72 ASN cc_start: 0.8491 (p0) cc_final: 0.8099 (p0) REVERT: R 73 ASN cc_start: 0.6836 (m-40) cc_final: 0.6284 (m-40) REVERT: K 392 MET cc_start: 0.6972 (ttm) cc_final: 0.6576 (tpp) REVERT: A 54 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8267 (mmmt) REVERT: A 105 ASP cc_start: 0.8594 (m-30) cc_final: 0.7933 (p0) REVERT: A 781 ILE cc_start: 0.8422 (mm) cc_final: 0.8218 (mm) REVERT: A 837 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8408 (tt) REVERT: A 926 ILE cc_start: 0.8539 (tp) cc_final: 0.7936 (mm) REVERT: A 1026 TYR cc_start: 0.8089 (m-80) cc_final: 0.7806 (m-80) REVERT: A 1031 GLU cc_start: 0.8281 (mp0) cc_final: 0.8049 (mp0) REVERT: A 1242 SER cc_start: 0.8860 (m) cc_final: 0.8421 (p) REVERT: Q 74 GLU cc_start: 0.3241 (mm-30) cc_final: 0.2888 (mm-30) REVERT: Q 78 PHE cc_start: 0.5423 (m-10) cc_final: 0.4695 (m-10) REVERT: Q 102 MET cc_start: 0.5727 (mtp) cc_final: 0.5406 (mpp) REVERT: Y 48 MET cc_start: 0.7801 (tpp) cc_final: 0.7206 (tpp) REVERT: Y 63 MET cc_start: 0.8663 (ttp) cc_final: 0.8190 (tmm) REVERT: Y 108 ASP cc_start: 0.6830 (m-30) cc_final: 0.6369 (m-30) REVERT: Y 113 ASN cc_start: 0.8577 (p0) cc_final: 0.8309 (p0) REVERT: Y 177 HIS cc_start: 0.6440 (m-70) cc_final: 0.5478 (m-70) REVERT: Y 531 PHE cc_start: 0.8542 (m-80) cc_final: 0.7966 (m-80) REVERT: C 180 ASP cc_start: 0.8338 (p0) cc_final: 0.8100 (p0) REVERT: C 250 MET cc_start: 0.7859 (mmm) cc_final: 0.7401 (tpt) REVERT: S 106 MET cc_start: 0.6340 (mmm) cc_final: 0.6052 (mmm) REVERT: S 243 LEU cc_start: 0.7761 (mp) cc_final: 0.7272 (tp) outliers start: 113 outliers final: 91 residues processed: 582 average time/residue: 0.2118 time to fit residues: 210.2728 Evaluate side-chains 564 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 467 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 241 SER 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 680 ASN Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 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 863 ASP 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 1124 SER Chi-restraints excluded: chain E residue 72 THR 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 F residue 82 ILE Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 9 TYR 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 G residue 154 PHE 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 328 HIS 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 715 MET Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 2 GLU 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 439 ILE 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 400 ASP 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 674 THR Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 837 LEU 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 1 MET 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 187 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 243 optimal weight: 10.0000 chunk 228 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 440 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 356 optimal weight: 6.9990 chunk 328 optimal weight: 0.8980 chunk 301 optimal weight: 2.9990 chunk 352 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 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** ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 71 HIS ** Y 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.114597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089999 restraints weight = 301689.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.093222 restraints weight = 125559.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.093455 restraints weight = 65537.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.093587 restraints weight = 53974.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.093910 restraints weight = 49073.303| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 42223 Z= 0.213 Angle : 0.727 11.952 57372 Z= 0.363 Chirality : 0.050 0.389 6552 Planarity : 0.004 0.061 7012 Dihedral : 12.263 176.268 6371 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.46 % Allowed : 21.34 % Favored : 76.20 % 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: -0.66 (0.12), residues: 4859 helix: 0.88 (0.13), residues: 1764 sheet: -0.86 (0.20), residues: 673 loop : -1.30 (0.13), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 52 TYR 0.038 0.002 TYR A 771 PHE 0.028 0.002 PHE B 190 TRP 0.022 0.002 TRP S 43 HIS 0.008 0.001 HIS R 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (42203) covalent geometry : angle 0.72382 / 0.36 (57346) SS BOND : bond 0.00173 / 0.09 ( 4) SS BOND : angle 0.82984 / 0.42 ( 8) hydrogen bonds : bond 0.04153 / 2.74 ( 1645) hydrogen bonds : angle 5.03158 / 3.54 ( 4666) metal coordination : bond 0.01398 / 0.75 ( 16) metal coordination : angle 3.61725 / 2.29 ( 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 571 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 460 time to evaluate : 1.125 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: B 71 SER cc_start: 0.8724 (t) cc_final: 0.8335 (p) REVERT: B 237 SER cc_start: 0.9146 (m) cc_final: 0.8643 (t) REVERT: B 320 ASN cc_start: 0.6327 (t0) cc_final: 0.5930 (p0) REVERT: B 474 ASP cc_start: 0.7931 (t70) cc_final: 0.7671 (t0) REVERT: B 571 VAL cc_start: 0.9515 (t) cc_final: 0.9160 (p) REVERT: B 662 ASP cc_start: 0.8256 (t0) cc_final: 0.7816 (t0) REVERT: B 716 MET cc_start: 0.7712 (mtp) cc_final: 0.7221 (mtp) REVERT: B 771 ASP cc_start: 0.8553 (t0) cc_final: 0.7901 (t0) REVERT: B 785 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: B 862 THR cc_start: 0.8460 (m) cc_final: 0.8181 (p) REVERT: G 83 ASP cc_start: 0.7738 (m-30) cc_final: 0.7193 (m-30) REVERT: I 168 MET cc_start: 0.8501 (mtp) cc_final: 0.8301 (mmm) REVERT: I 205 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8080 (tttt) REVERT: I 211 TYR cc_start: 0.7000 (m-80) cc_final: 0.6799 (m-80) REVERT: I 487 MET cc_start: 0.7585 (mmp) cc_final: 0.6974 (tpt) REVERT: I 595 ARG cc_start: 0.7307 (mmt180) cc_final: 0.6685 (mmp80) REVERT: R 64 ASP cc_start: 0.7103 (t0) cc_final: 0.6745 (t0) REVERT: K 392 MET cc_start: 0.7068 (ttm) cc_final: 0.6543 (tpp) REVERT: A 105 ASP cc_start: 0.8557 (m-30) cc_final: 0.7844 (p0) REVERT: A 781 ILE cc_start: 0.8449 (mm) cc_final: 0.8209 (mm) REVERT: A 1026 TYR cc_start: 0.8058 (m-80) cc_final: 0.7751 (m-80) REVERT: A 1242 SER cc_start: 0.8927 (m) cc_final: 0.8522 (p) REVERT: A 1247 ILE cc_start: 0.9113 (mm) cc_final: 0.8616 (mt) REVERT: Q 102 MET cc_start: 0.5918 (mtp) cc_final: 0.5643 (mpp) REVERT: Y 48 MET cc_start: 0.7903 (tpp) cc_final: 0.7285 (tpp) REVERT: Y 63 MET cc_start: 0.8594 (ttp) cc_final: 0.8128 (tmm) REVERT: Y 531 PHE cc_start: 0.8595 (m-80) cc_final: 0.8273 (m-80) REVERT: C 180 ASP cc_start: 0.8300 (p0) cc_final: 0.8059 (p0) REVERT: S 106 MET cc_start: 0.6505 (mmm) cc_final: 0.6105 (mmm) REVERT: S 243 LEU cc_start: 0.7913 (mp) cc_final: 0.7296 (tp) outliers start: 111 outliers final: 96 residues processed: 543 average time/residue: 0.2121 time to fit residues: 196.5599 Evaluate side-chains 542 residues out of total 4517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 445 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 241 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 435 MET 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 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 1028 VAL Chi-restraints excluded: chain B residue 1068 ASN Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain E residue 72 THR 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 F residue 82 ILE Chi-restraints excluded: chain F residue 139 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 328 HIS 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 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 R residue 1 MET Chi-restraints excluded: chain R residue 2 GLU 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 439 ILE 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 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 674 THR Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 767 VAL 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 1 MET 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 70 LYS Chi-restraints excluded: chain Y residue 71 HIS 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 187 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 489 optimal weight: 4.9990 chunk 111 optimal weight: 0.0170 chunk 372 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 390 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 422 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 425 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** I 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN ** K 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.115681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.091151 restraints weight = 273569.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.093841 restraints weight = 120005.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.094380 restraints weight = 65006.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.094696 restraints weight = 49500.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095091 restraints weight = 42624.632| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 42223 Z= 0.159 Angle : 0.701 15.049 57372 Z= 0.348 Chirality : 0.049 0.389 6552 Planarity : 0.004 0.065 7012 Dihedral : 12.262 178.625 6369 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.39 % Allowed : 21.65 % 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: -0.67 (0.12), residues: 4859 helix: 0.84 (0.13), residues: 1776 sheet: -0.81 (0.20), residues: 659 loop : -1.33 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 52 TYR 0.025 0.002 TYR Y 67 PHE 0.034 0.002 PHE G 154 TRP 0.052 0.002 TRP S 43 HIS 0.008 0.001 HIS Y 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (42203) covalent geometry : angle 0.69818 / 0.35 (57346) SS BOND : bond 0.00197 / 0.10 ( 4) SS BOND : angle 0.78203 / 0.40 ( 8) hydrogen bonds : bond 0.03938 / 2.60 ( 1645) hydrogen bonds : angle 4.98957 / 3.50 ( 4666) metal coordination : bond 0.00982 / 0.49 ( 16) metal coordination : angle 3.46248 / 2.20 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7892.80 seconds wall clock time: 137 minutes 23.58 seconds (8243.58 seconds total)