Starting phenix.real_space_refine on Mon Aug 25 11:35:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k5a_36899/08_2025/8k5a_36899.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k5a_36899/08_2025/8k5a_36899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k5a_36899/08_2025/8k5a_36899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k5a_36899/08_2025/8k5a_36899.map" model { file = "/net/cci-nas-00/data/ceres_data/8k5a_36899/08_2025/8k5a_36899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k5a_36899/08_2025/8k5a_36899.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians P 57 5.49 5 S 112 5.16 5 C 17026 2.51 5 N 4875 2.21 5 O 5435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27505 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1788 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "D" Number of atoms: 10494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1352, 10494 Classifications: {'peptide': 1352} Modifications used: {'COO': 1} Link IDs: {'CIS': 7, 'PTRANS': 55, 'TRANS': 1289} Chain breaks: 1 Chain: "E" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 606 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "G" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "H" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "I" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 448 Inner-chain residues flagged as termini: ['pdbres=" DA I 14 "'] Classifications: {'DNA': 22} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Time building chain proxies: 5.56, per 1000 atoms: 0.20 Number of scatterers: 27505 At special positions: 0 Unit cell: (135.3, 158.26, 160.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 57 15.00 O 5435 8.00 N 4875 7.00 C 17026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6204 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 52 sheets defined 39.1% alpha, 16.3% beta 18 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.967A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 163 removed outlier: 3.536A pdb=" N SER A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.398A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.646A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.725A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'B' and resid 229 through 232 removed outlier: 3.907A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.684A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.845A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 391 removed outlier: 4.061A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 482 Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.717A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 608 through 614 removed outlier: 3.772A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.640A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.659A pdb=" N ASP C 674 " --> pdb=" O LEU C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.592A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 806 through 810 removed outlier: 3.529A pdb=" N GLY C 809 " --> pdb=" O PRO C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.594A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 985 through 992 removed outlier: 3.501A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 999 removed outlier: 3.639A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 999 " --> pdb=" O ARG C 996 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 994 through 999' Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 3.996A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1137 through 1151 Processing helix chain 'C' and resid 1166 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1332 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 94 through 101 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.996A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.893A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.519A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.844A pdb=" N MET D 237 " --> pdb=" O LYS D 233 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE D 238 " --> pdb=" O PRO D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 238' Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.639A pdb=" N ARG D 250 " --> pdb=" O PRO D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.934A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.711A pdb=" N LYS D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.941A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 515 removed outlier: 3.585A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 538 removed outlier: 3.528A pdb=" N GLU D 532 " --> pdb=" O THR D 528 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 581 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.951A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.589A pdb=" N ALA D 741 " --> pdb=" O ILE D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.660A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.585A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1136 through 1146 removed outlier: 3.763A pdb=" N ARG D1140 " --> pdb=" O GLY D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.688A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.534A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 4.164A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D1324 " --> pdb=" O ILE D1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1359 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.558A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'G' and resid 31 through 39 Processing helix chain 'G' and resid 41 through 52 removed outlier: 3.549A pdb=" N MET G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 87 Processing helix chain 'G' and resid 107 through 128 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.627A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU A 198 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA A 189 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.967A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.540A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.471A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AA9, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 110 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.386A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.615A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU C 102 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.600A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 160 Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.285A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.868A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.044A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.609A pdb=" N ASP C 654 " --> pdb=" O ALA C 617 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 623 through 624 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.005A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 752 removed outlier: 5.847A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 4.467A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.561A pdb=" N VAL C1225 " --> pdb=" O ILE C1210 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.540A pdb=" N VAL C1052 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.878A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1245 removed outlier: 6.363A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1268 through 1269 removed outlier: 3.527A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AD7, first strand: chain 'D' and resid 103 through 111 removed outlier: 10.346A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD9, first strand: chain 'D' and resid 491 through 492 removed outlier: 4.645A pdb=" N GLU D 497 " --> pdb=" O SER D 492 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 7.326A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE3, first strand: chain 'D' and resid 748 through 749 Processing sheet with id=AE4, first strand: chain 'D' and resid 809 through 811 removed outlier: 5.786A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE6, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AE7, first strand: chain 'D' and resid 842 through 843 removed outlier: 4.268A pdb=" N ARG D 842 " --> pdb=" O LEU D 864 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.526A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D1002 " --> pdb=" O ASN D1019 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 957 through 961 removed outlier: 4.460A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 965 through 968 removed outlier: 3.927A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 6.599A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1035 through 1038 Processing sheet with id=AF4, first strand: chain 'D' and resid 1188 through 1190 removed outlier: 3.606A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1195 through 1196 removed outlier: 3.782A pdb=" N GLN D1195 " --> pdb=" O ASP D1212 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 6.656A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 92 through 94 1134 hydrogen bonds defined for protein. 3219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 6.35 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8268 1.33 - 1.46: 4688 1.46 - 1.58: 14777 1.58 - 1.70: 115 1.70 - 1.82: 194 Bond restraints: 28042 Sorted by residual: bond pdb=" CB ILE D 355 " pdb=" CG2 ILE D 355 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.99e+00 bond pdb=" CG PRO D1191 " pdb=" CD PRO D1191 " ideal model delta sigma weight residual 1.503 1.439 0.064 3.40e-02 8.65e+02 3.57e+00 bond pdb=" CB PRO D1191 " pdb=" CG PRO D1191 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.41e+00 bond pdb=" CA GLU D 913 " pdb=" C GLU D 913 " ideal model delta sigma weight residual 1.532 1.515 0.017 9.60e-03 1.09e+04 3.16e+00 bond pdb=" C GLN C1061 " pdb=" N PRO C1062 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.19e-02 7.06e+03 3.16e+00 ... (remaining 28037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 37771 3.07 - 6.14: 331 6.14 - 9.21: 35 9.21 - 12.28: 2 12.28 - 15.35: 1 Bond angle restraints: 38140 Sorted by residual: angle pdb=" C GLN E 29 " pdb=" N MET E 30 " pdb=" CA MET E 30 " ideal model delta sigma weight residual 121.92 110.30 11.62 1.73e+00 3.34e-01 4.51e+01 angle pdb=" N VAL G 12 " pdb=" CA VAL G 12 " pdb=" C VAL G 12 " ideal model delta sigma weight residual 112.90 106.59 6.31 9.60e-01 1.09e+00 4.32e+01 angle pdb=" N SER C1162 " pdb=" CA SER C1162 " pdb=" C SER C1162 " ideal model delta sigma weight residual 114.56 106.63 7.93 1.27e+00 6.20e-01 3.90e+01 angle pdb=" N ILE D 499 " pdb=" CA ILE D 499 " pdb=" C ILE D 499 " ideal model delta sigma weight residual 112.90 107.44 5.46 9.60e-01 1.09e+00 3.23e+01 angle pdb=" N ARG D 47 " pdb=" CA ARG D 47 " pdb=" C ARG D 47 " ideal model delta sigma weight residual 114.31 107.21 7.10 1.29e+00 6.01e-01 3.03e+01 ... (remaining 38135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.83: 16184 26.83 - 53.65: 682 53.65 - 80.48: 230 80.48 - 107.30: 34 107.30 - 134.13: 2 Dihedral angle restraints: 17132 sinusoidal: 7491 harmonic: 9641 Sorted by residual: dihedral pdb=" CA GLN E 29 " pdb=" C GLN E 29 " pdb=" N MET E 30 " pdb=" CA MET E 30 " ideal model delta harmonic sigma weight residual 180.00 153.75 26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA THR C1292 " pdb=" C THR C1292 " pdb=" N VAL C1293 " pdb=" CA VAL C1293 " ideal model delta harmonic sigma weight residual -180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA PHE E 17 " pdb=" C PHE E 17 " pdb=" N ASP E 18 " pdb=" CA ASP E 18 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 17129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3689 0.062 - 0.123: 608 0.123 - 0.185: 48 0.185 - 0.247: 3 0.247 - 0.309: 1 Chirality restraints: 4349 Sorted by residual: chirality pdb=" CA GLN E 72 " pdb=" N GLN E 72 " pdb=" C GLN E 72 " pdb=" CB GLN E 72 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA GLN E 29 " pdb=" N GLN E 29 " pdb=" C GLN E 29 " pdb=" CB GLN E 29 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA MET D 466 " pdb=" N MET D 466 " pdb=" C MET D 466 " pdb=" CB MET D 466 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 4346 not shown) Planarity restraints: 4796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D1190 " -0.058 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO D1191 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D1191 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D1191 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1276 " -0.020 2.00e-02 2.50e+03 1.73e-02 7.51e+00 pdb=" CG TRP C1276 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP C1276 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C1276 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1276 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1276 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1276 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1276 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C1276 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1285 " -0.020 2.00e-02 2.50e+03 1.63e-02 5.31e+00 pdb=" CG TYR C1285 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C1285 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR C1285 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C1285 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C1285 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C1285 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR C1285 " 0.002 2.00e-02 2.50e+03 ... (remaining 4793 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 746 2.68 - 3.23: 28279 3.23 - 3.79: 46188 3.79 - 4.34: 62130 4.34 - 4.90: 99311 Nonbonded interactions: 236654 Sorted by model distance: nonbonded pdb=" OD2 ASP C 516 " pdb=" OG SER C 522 " model vdw 2.119 3.040 nonbonded pdb=" O ARG B 45 " pdb=" OG SER B 49 " model vdw 2.150 3.040 nonbonded pdb=" O LEU D 188 " pdb=" OG SER D 191 " model vdw 2.178 3.040 nonbonded pdb=" O ASP G 126 " pdb=" NH1 ARG G 129 " model vdw 2.179 3.120 nonbonded pdb=" OE1 GLN G 49 " pdb=" OH TYR G 62 " model vdw 2.198 3.040 ... (remaining 236649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 233) selection = (chain 'B' and resid 7 through 233) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.480 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 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 : 0.004 0.092 28042 Z= 0.195 Angle : 0.770 15.346 38140 Z= 0.447 Chirality : 0.044 0.309 4349 Planarity : 0.005 0.083 4796 Dihedral : 16.784 134.130 10928 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.25 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: -1.17 (0.14), residues: 3341 helix: 0.44 (0.15), residues: 1193 sheet: -0.82 (0.27), residues: 379 loop : -1.66 (0.13), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1216 TYR 0.038 0.002 TYR C1285 PHE 0.031 0.002 PHE E 17 TRP 0.047 0.002 TRP C1276 HIS 0.007 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00397 (28042) covalent geometry : angle 0.77007 (38140) hydrogen bonds : bond 0.15838 ( 1176) hydrogen bonds : angle 7.33450 ( 3307) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 611 time to evaluate : 1.016 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: A 15 ASP cc_start: 0.6826 (p0) cc_final: 0.6569 (p0) REVERT: A 93 GLN cc_start: 0.7705 (pm20) cc_final: 0.6732 (pp30) REVERT: A 199 ASP cc_start: 0.7703 (m-30) cc_final: 0.7287 (m-30) REVERT: A 227 GLN cc_start: 0.7757 (mm110) cc_final: 0.7460 (mm-40) REVERT: B 59 VAL cc_start: 0.8253 (m) cc_final: 0.8049 (m) REVERT: B 95 LYS cc_start: 0.7837 (pptt) cc_final: 0.7625 (pptt) REVERT: B 193 GLU cc_start: 0.6945 (pt0) cc_final: 0.6733 (pt0) REVERT: C 85 CYS cc_start: 0.7670 (m) cc_final: 0.7226 (m) REVERT: C 184 LEU cc_start: 0.5538 (tp) cc_final: 0.4725 (tt) REVERT: C 369 MET cc_start: 0.6979 (ppp) cc_final: 0.6600 (ppp) REVERT: C 390 PHE cc_start: 0.6590 (m-80) cc_final: 0.6120 (m-80) REVERT: C 392 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8140 (tt0) REVERT: C 419 ILE cc_start: 0.7564 (pt) cc_final: 0.7212 (mt) REVERT: C 454 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.7255 (ttp-110) REVERT: C 473 ARG cc_start: 0.7783 (ttp80) cc_final: 0.7536 (ttp80) REVERT: C 488 MET cc_start: 0.5819 (tpt) cc_final: 0.5591 (mtp) REVERT: C 510 GLN cc_start: 0.7553 (pt0) cc_final: 0.7318 (tt0) REVERT: C 512 SER cc_start: 0.8440 (t) cc_final: 0.8126 (t) REVERT: C 605 TYR cc_start: 0.8446 (m-80) cc_final: 0.8162 (m-80) REVERT: C 672 GLU cc_start: 0.5780 (pt0) cc_final: 0.5384 (pm20) REVERT: C 704 MET cc_start: 0.6155 (mmp) cc_final: 0.5613 (mtp) REVERT: C 775 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7383 (tt0) REVERT: C 790 ASP cc_start: 0.7065 (t0) cc_final: 0.6701 (t70) REVERT: C 814 ASP cc_start: 0.6571 (m-30) cc_final: 0.6186 (m-30) REVERT: C 958 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7939 (tptp) REVERT: C 1030 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7124 (tm-30) REVERT: C 1089 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6135 (pm20) REVERT: C 1107 MET cc_start: 0.7071 (mmp) cc_final: 0.6528 (mmp) REVERT: C 1174 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6512 (tm-30) REVERT: C 1232 MET cc_start: 0.7640 (mmm) cc_final: 0.7084 (mmm) REVERT: C 1240 ASP cc_start: 0.8065 (t0) cc_final: 0.7777 (t0) REVERT: C 1269 ARG cc_start: 0.6018 (ttp80) cc_final: 0.5405 (ttm-80) REVERT: C 1319 MET cc_start: 0.2708 (mmp) cc_final: 0.2360 (mmm) REVERT: D 15 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6715 (mm-30) REVERT: D 29 MET cc_start: 0.8480 (ppp) cc_final: 0.8221 (ppp) REVERT: D 137 ARG cc_start: 0.7286 (mmm160) cc_final: 0.6924 (mtt180) REVERT: D 198 CYS cc_start: 0.8842 (m) cc_final: 0.8314 (p) REVERT: D 236 TRP cc_start: 0.8345 (m-10) cc_final: 0.8032 (m-10) REVERT: D 278 ARG cc_start: 0.7351 (mtt180) cc_final: 0.6686 (mtp180) REVERT: D 297 ARG cc_start: 0.6472 (ttm170) cc_final: 0.6135 (tpt-90) REVERT: D 337 ARG cc_start: 0.3522 (tpt170) cc_final: 0.3032 (mmt90) REVERT: D 398 LYS cc_start: 0.8603 (mttm) cc_final: 0.8363 (pttt) REVERT: D 400 MET cc_start: 0.5517 (tpt) cc_final: 0.4988 (tpt) REVERT: D 414 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7258 (mt-10) REVERT: D 465 GLN cc_start: 0.7819 (pt0) cc_final: 0.6875 (pm20) REVERT: D 623 GLN cc_start: 0.5509 (mm-40) cc_final: 0.4992 (mt0) REVERT: D 716 GLN cc_start: 0.6473 (pp30) cc_final: 0.5995 (pp30) REVERT: D 725 MET cc_start: 0.5804 (tpt) cc_final: 0.4869 (tpp) REVERT: D 738 ARG cc_start: 0.5637 (ttt180) cc_final: 0.5084 (tmm160) REVERT: D 780 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7613 (tpp80) REVERT: D 781 LYS cc_start: 0.7423 (tttp) cc_final: 0.7017 (ttmt) REVERT: D 822 MET cc_start: 0.6654 (ttt) cc_final: 0.5961 (ttt) REVERT: D 827 GLU cc_start: 0.8149 (mp0) cc_final: 0.7624 (pm20) REVERT: D 931 THR cc_start: 0.5113 (p) cc_final: 0.4838 (m) REVERT: D 1151 LYS cc_start: 0.8151 (tmtt) cc_final: 0.7931 (pttt) REVERT: D 1214 PRO cc_start: 0.3702 (Cg_endo) cc_final: 0.2759 (Cg_exo) REVERT: D 1247 LYS cc_start: 0.7035 (pttm) cc_final: 0.6476 (tptp) REVERT: D 1297 LYS cc_start: 0.7422 (tptm) cc_final: 0.6835 (pttm) REVERT: D 1345 ARG cc_start: 0.7490 (ptm160) cc_final: 0.7112 (mmm-85) REVERT: D 1347 LEU cc_start: 0.7018 (mm) cc_final: 0.6798 (mp) REVERT: G 45 MET cc_start: 0.5169 (tmm) cc_final: 0.4849 (tpp) REVERT: G 61 TYR cc_start: 0.8086 (t80) cc_final: 0.7788 (t80) REVERT: G 73 TRP cc_start: 0.8078 (t60) cc_final: 0.7707 (t60) REVERT: G 98 GLU cc_start: 0.5699 (tm-30) cc_final: 0.5122 (tm-30) REVERT: G 107 ASN cc_start: 0.6600 (t0) cc_final: 0.5208 (m110) REVERT: G 110 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8483 (mm-30) outliers start: 0 outliers final: 0 residues processed: 611 average time/residue: 0.1887 time to fit residues: 177.0906 Evaluate side-chains 354 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0020 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN C 83 GLN C 276 GLN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1244 HIS C1268 GLN D 266 ASN D 276 ASN D 320 ASN D 435 GLN ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 ASN D 875 ASN D 907 HIS D1218 HIS ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.214504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.154228 restraints weight = 42441.394| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 4.27 r_work: 0.3741 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28042 Z= 0.216 Angle : 0.729 11.333 38140 Z= 0.380 Chirality : 0.047 0.290 4349 Planarity : 0.006 0.116 4796 Dihedral : 13.532 138.839 4363 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 1.89 % Allowed : 9.56 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: -1.19 (0.14), residues: 3341 helix: 0.36 (0.15), residues: 1242 sheet: -0.80 (0.26), residues: 384 loop : -1.68 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 58 TYR 0.022 0.002 TYR A 68 PHE 0.019 0.002 PHE G 91 TRP 0.026 0.002 TRP C1276 HIS 0.012 0.002 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00499 (28042) covalent geometry : angle 0.72933 (38140) hydrogen bonds : bond 0.05418 ( 1176) hydrogen bonds : angle 5.58700 ( 3307) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 381 time to evaluate : 0.713 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: A 93 GLN cc_start: 0.7616 (pm20) cc_final: 0.6920 (pp30) REVERT: A 136 GLU cc_start: 0.8561 (mp0) cc_final: 0.8268 (mm-30) REVERT: B 95 LYS cc_start: 0.8126 (pptt) cc_final: 0.7867 (pptt) REVERT: C 85 CYS cc_start: 0.7593 (m) cc_final: 0.7376 (m) REVERT: C 121 GLU cc_start: 0.7901 (pt0) cc_final: 0.7439 (pm20) REVERT: C 213 LEU cc_start: 0.8297 (mt) cc_final: 0.8041 (mt) REVERT: C 369 MET cc_start: 0.7015 (ppp) cc_final: 0.6436 (ppp) REVERT: C 390 PHE cc_start: 0.6793 (m-80) cc_final: 0.6332 (m-80) REVERT: C 419 ILE cc_start: 0.7582 (pt) cc_final: 0.7306 (mt) REVERT: C 454 ARG cc_start: 0.8535 (ttp-110) cc_final: 0.8134 (mtm110) REVERT: C 478 ARG cc_start: 0.7478 (mmt-90) cc_final: 0.7216 (tpt-90) REVERT: C 490 GLN cc_start: 0.7814 (pp30) cc_final: 0.7576 (pp30) REVERT: C 592 ARG cc_start: 0.8460 (mtp180) cc_final: 0.7785 (mtp85) REVERT: C 672 GLU cc_start: 0.6656 (pt0) cc_final: 0.6289 (pm20) REVERT: C 704 MET cc_start: 0.7309 (mmp) cc_final: 0.7008 (ttm) REVERT: C 775 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7861 (tt0) REVERT: C 814 ASP cc_start: 0.7762 (m-30) cc_final: 0.7411 (m-30) REVERT: C 949 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7542 (tm-30) REVERT: C 1012 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8710 (mt-10) REVERT: C 1089 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6816 (pm20) REVERT: C 1174 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7253 (tm-30) REVERT: C 1180 MET cc_start: 0.8057 (tpp) cc_final: 0.7698 (ttm) REVERT: C 1232 MET cc_start: 0.8740 (mmm) cc_final: 0.7966 (mmm) REVERT: C 1269 ARG cc_start: 0.7433 (ttp80) cc_final: 0.6607 (ttm-80) REVERT: C 1279 GLU cc_start: 0.7290 (tp30) cc_final: 0.6300 (mt-10) REVERT: C 1315 MET cc_start: 0.4682 (OUTLIER) cc_final: 0.4361 (ttp) REVERT: C 1319 MET cc_start: 0.3464 (mmt) cc_final: 0.3062 (mmm) REVERT: D 29 MET cc_start: 0.8577 (ppp) cc_final: 0.8244 (ppp) REVERT: D 166 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8452 (pp) REVERT: D 236 TRP cc_start: 0.8467 (m-10) cc_final: 0.8198 (m-10) REVERT: D 278 ARG cc_start: 0.7797 (mtt180) cc_final: 0.6943 (mtm-85) REVERT: D 297 ARG cc_start: 0.6485 (ttm170) cc_final: 0.6191 (tpt-90) REVERT: D 337 ARG cc_start: 0.4337 (tpt170) cc_final: 0.3591 (mpt-90) REVERT: D 400 MET cc_start: 0.5406 (tpt) cc_final: 0.5119 (mmm) REVERT: D 623 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6824 (mt0) REVERT: D 716 GLN cc_start: 0.7119 (pp30) cc_final: 0.6241 (pp30) REVERT: D 725 MET cc_start: 0.6726 (tpt) cc_final: 0.6319 (tpp) REVERT: D 738 ARG cc_start: 0.6312 (ttt180) cc_final: 0.5704 (tmm160) REVERT: D 822 MET cc_start: 0.6514 (ttt) cc_final: 0.6312 (ttt) REVERT: D 931 THR cc_start: 0.5260 (p) cc_final: 0.4933 (m) REVERT: D 960 LEU cc_start: 0.7285 (mm) cc_final: 0.6954 (mt) REVERT: D 973 LEU cc_start: 0.5393 (tp) cc_final: 0.4954 (tt) REVERT: D 1151 LYS cc_start: 0.8136 (tmtt) cc_final: 0.7841 (ptmt) REVERT: D 1214 PRO cc_start: 0.5311 (Cg_endo) cc_final: 0.5094 (Cg_exo) REVERT: D 1247 LYS cc_start: 0.7090 (pttm) cc_final: 0.6827 (tptp) REVERT: D 1297 LYS cc_start: 0.7463 (tptm) cc_final: 0.6922 (pttm) REVERT: G 45 MET cc_start: 0.5481 (tmm) cc_final: 0.5214 (ttt) REVERT: G 61 TYR cc_start: 0.8038 (t80) cc_final: 0.7763 (t80) REVERT: G 92 ILE cc_start: 0.4598 (mt) cc_final: 0.4336 (mt) REVERT: G 107 ASN cc_start: 0.6516 (t0) cc_final: 0.5940 (m110) outliers start: 54 outliers final: 30 residues processed: 413 average time/residue: 0.1692 time to fit residues: 109.2824 Evaluate side-chains 346 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 314 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 20 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 313 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 247 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 326 optimal weight: 0.0570 chunk 13 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS C 808 ASN C 811 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 ASN ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 GLN G 59 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.212000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.160589 restraints weight = 42682.781| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 4.56 r_work: 0.3697 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28042 Z= 0.218 Angle : 0.689 9.184 38140 Z= 0.360 Chirality : 0.046 0.194 4349 Planarity : 0.005 0.070 4796 Dihedral : 13.546 137.705 4363 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.21 % Favored : 94.67 % Rotamer: Outliers : 3.08 % Allowed : 12.05 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: -1.25 (0.14), residues: 3341 helix: 0.36 (0.15), residues: 1231 sheet: -0.92 (0.26), residues: 382 loop : -1.72 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 780 TYR 0.029 0.002 TYR D 589 PHE 0.019 0.002 PHE C1164 TRP 0.020 0.002 TRP G 36 HIS 0.009 0.002 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00509 (28042) covalent geometry : angle 0.68929 (38140) hydrogen bonds : bond 0.04968 ( 1176) hydrogen bonds : angle 5.39670 ( 3307) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 351 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7799 (pm20) cc_final: 0.7139 (pp30) REVERT: B 35 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7320 (t80) REVERT: B 142 MET cc_start: 0.7774 (mmp) cc_final: 0.7434 (mmp) REVERT: B 206 GLU cc_start: 0.6293 (mt-10) cc_final: 0.5736 (mt-10) REVERT: C 185 ASP cc_start: 0.6848 (m-30) cc_final: 0.6032 (m-30) REVERT: C 369 MET cc_start: 0.7023 (ppp) cc_final: 0.6518 (ppp) REVERT: C 419 ILE cc_start: 0.7589 (pt) cc_final: 0.7341 (mt) REVERT: C 429 MET cc_start: 0.7197 (mtm) cc_final: 0.6994 (mtm) REVERT: C 454 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8200 (ttm110) REVERT: C 478 ARG cc_start: 0.7554 (mmt-90) cc_final: 0.7250 (tpt-90) REVERT: C 515 MET cc_start: 0.8023 (tpt) cc_final: 0.7755 (tpt) REVERT: C 592 ARG cc_start: 0.8604 (mtp180) cc_final: 0.7831 (mtp85) REVERT: C 672 GLU cc_start: 0.6821 (pt0) cc_final: 0.6402 (pm20) REVERT: C 704 MET cc_start: 0.7403 (mmp) cc_final: 0.6985 (mtp) REVERT: C 775 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7846 (tt0) REVERT: C 814 ASP cc_start: 0.7722 (m-30) cc_final: 0.7328 (m-30) REVERT: C 1008 GLN cc_start: 0.4439 (tp-100) cc_final: 0.4208 (tp-100) REVERT: C 1012 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8718 (mt-10) REVERT: C 1089 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6902 (pm20) REVERT: C 1174 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7411 (tm-30) REVERT: C 1180 MET cc_start: 0.8082 (tpp) cc_final: 0.7864 (ttm) REVERT: C 1222 GLU cc_start: 0.6973 (tp30) cc_final: 0.6226 (mt-10) REVERT: C 1233 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8420 (mp) REVERT: C 1269 ARG cc_start: 0.7449 (ttp80) cc_final: 0.6561 (ttm-80) REVERT: C 1279 GLU cc_start: 0.7510 (tp30) cc_final: 0.6549 (mt-10) REVERT: C 1315 MET cc_start: 0.5002 (OUTLIER) cc_final: 0.4765 (ttp) REVERT: C 1319 MET cc_start: 0.3673 (mmt) cc_final: 0.3209 (mmm) REVERT: D 20 ILE cc_start: 0.7354 (tt) cc_final: 0.7115 (tp) REVERT: D 29 MET cc_start: 0.8547 (ppp) cc_final: 0.8046 (ppp) REVERT: D 166 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8430 (pp) REVERT: D 195 GLU cc_start: 0.8454 (mp0) cc_final: 0.8238 (mp0) REVERT: D 198 CYS cc_start: 0.8670 (m) cc_final: 0.8272 (p) REVERT: D 236 TRP cc_start: 0.8446 (m-10) cc_final: 0.8164 (m-10) REVERT: D 278 ARG cc_start: 0.7888 (mtt180) cc_final: 0.6982 (mtp180) REVERT: D 297 ARG cc_start: 0.6430 (ttm170) cc_final: 0.6210 (tpt-90) REVERT: D 330 MET cc_start: 0.5926 (tmm) cc_final: 0.5405 (tmm) REVERT: D 337 ARG cc_start: 0.4490 (tpt170) cc_final: 0.3690 (mpt-90) REVERT: D 400 MET cc_start: 0.5577 (tpt) cc_final: 0.5307 (mmm) REVERT: D 594 GLN cc_start: 0.6792 (OUTLIER) cc_final: 0.5686 (pm20) REVERT: D 623 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6964 (mt0) REVERT: D 738 ARG cc_start: 0.6397 (ttt180) cc_final: 0.5955 (ttp-170) REVERT: D 776 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7330 (p) REVERT: D 881 LYS cc_start: 0.5868 (tttm) cc_final: 0.5518 (tptt) REVERT: D 981 GLU cc_start: 0.6885 (tt0) cc_final: 0.6289 (tp30) REVERT: D 1151 LYS cc_start: 0.8181 (tmtt) cc_final: 0.7915 (pttt) REVERT: D 1214 PRO cc_start: 0.5460 (Cg_endo) cc_final: 0.5108 (Cg_exo) REVERT: D 1244 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8169 (mm-40) REVERT: D 1247 LYS cc_start: 0.7208 (pttm) cc_final: 0.6972 (tptp) REVERT: D 1253 ILE cc_start: 0.7984 (mm) cc_final: 0.7770 (mt) REVERT: E 72 GLN cc_start: 0.4862 (OUTLIER) cc_final: 0.4585 (mp10) REVERT: G 45 MET cc_start: 0.5457 (tmm) cc_final: 0.5255 (ttt) REVERT: G 61 TYR cc_start: 0.7884 (t80) cc_final: 0.7635 (t80) REVERT: G 107 ASN cc_start: 0.6557 (t0) cc_final: 0.5780 (t0) REVERT: G 110 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8388 (mm-30) outliers start: 88 outliers final: 49 residues processed: 407 average time/residue: 0.1998 time to fit residues: 127.7489 Evaluate side-chains 362 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 306 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 109 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 308 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 288 optimal weight: 30.0000 chunk 97 optimal weight: 0.9990 chunk 290 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 131 optimal weight: 0.0010 chunk 209 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 811 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN D 777 HIS D 861 ASN G 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.219034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.167586 restraints weight = 42243.174| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.98 r_work: 0.3795 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28042 Z= 0.128 Angle : 0.608 9.140 38140 Z= 0.316 Chirality : 0.043 0.153 4349 Planarity : 0.004 0.056 4796 Dihedral : 13.440 134.982 4363 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 2.10 % Allowed : 14.29 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: -0.93 (0.14), residues: 3341 helix: 0.66 (0.15), residues: 1236 sheet: -0.75 (0.26), residues: 385 loop : -1.58 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 58 TYR 0.015 0.001 TYR B 177 PHE 0.019 0.002 PHE D 35 TRP 0.021 0.002 TRP G 36 HIS 0.010 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00284 (28042) covalent geometry : angle 0.60808 (38140) hydrogen bonds : bond 0.04496 ( 1176) hydrogen bonds : angle 5.08215 ( 3307) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 349 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7725 (pm20) cc_final: 0.7115 (pp30) REVERT: A 156 SER cc_start: 0.6917 (p) cc_final: 0.6656 (m) REVERT: A 199 ASP cc_start: 0.7025 (m-30) cc_final: 0.6556 (m-30) REVERT: B 35 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7200 (t80) REVERT: B 206 GLU cc_start: 0.5996 (mt-10) cc_final: 0.5676 (mt-10) REVERT: C 121 GLU cc_start: 0.7869 (pt0) cc_final: 0.7406 (pm20) REVERT: C 369 MET cc_start: 0.6998 (ppp) cc_final: 0.6505 (ppp) REVERT: C 419 ILE cc_start: 0.7598 (pt) cc_final: 0.7321 (mt) REVERT: C 454 ARG cc_start: 0.8463 (ttp-110) cc_final: 0.7827 (mtm110) REVERT: C 478 ARG cc_start: 0.7542 (mmt-90) cc_final: 0.7258 (tpt-90) REVERT: C 592 ARG cc_start: 0.8486 (mtp180) cc_final: 0.8047 (mtp85) REVERT: C 672 GLU cc_start: 0.6704 (pt0) cc_final: 0.6461 (pm20) REVERT: C 704 MET cc_start: 0.7309 (mmp) cc_final: 0.7015 (ttm) REVERT: C 775 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7896 (tt0) REVERT: C 814 ASP cc_start: 0.7425 (m-30) cc_final: 0.6886 (m-30) REVERT: C 1174 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7331 (tm-30) REVERT: C 1180 MET cc_start: 0.7997 (tpp) cc_final: 0.7771 (ttm) REVERT: C 1269 ARG cc_start: 0.7442 (ttp80) cc_final: 0.6542 (ttm-80) REVERT: C 1279 GLU cc_start: 0.7129 (tp30) cc_final: 0.6507 (mt-10) REVERT: C 1290 MET cc_start: 0.6790 (mtp) cc_final: 0.6217 (mmt) REVERT: C 1315 MET cc_start: 0.4784 (OUTLIER) cc_final: 0.4491 (ttp) REVERT: C 1319 MET cc_start: 0.3805 (mmt) cc_final: 0.3359 (mmm) REVERT: D 20 ILE cc_start: 0.7218 (tt) cc_final: 0.7012 (tp) REVERT: D 29 MET cc_start: 0.8470 (ppp) cc_final: 0.8083 (ppp) REVERT: D 166 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8396 (pp) REVERT: D 195 GLU cc_start: 0.8493 (mp0) cc_final: 0.8236 (mp0) REVERT: D 198 CYS cc_start: 0.8688 (m) cc_final: 0.8318 (p) REVERT: D 236 TRP cc_start: 0.8410 (m-10) cc_final: 0.8126 (m-10) REVERT: D 278 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7050 (mtp180) REVERT: D 297 ARG cc_start: 0.6398 (ttm170) cc_final: 0.6140 (tpt-90) REVERT: D 330 MET cc_start: 0.5755 (tmm) cc_final: 0.5108 (tmm) REVERT: D 337 ARG cc_start: 0.4272 (tpt170) cc_final: 0.3380 (mpt-90) REVERT: D 345 LYS cc_start: 0.6600 (pttm) cc_final: 0.5495 (tppt) REVERT: D 400 MET cc_start: 0.5606 (tpt) cc_final: 0.5385 (mmm) REVERT: D 576 ARG cc_start: 0.6686 (mtt180) cc_final: 0.6297 (tpp80) REVERT: D 594 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.5638 (pm20) REVERT: D 623 GLN cc_start: 0.7148 (mm-40) cc_final: 0.6873 (mt0) REVERT: D 738 ARG cc_start: 0.6067 (ttt180) cc_final: 0.5540 (ttp80) REVERT: D 960 LEU cc_start: 0.6984 (mm) cc_final: 0.6676 (mt) REVERT: D 981 GLU cc_start: 0.6867 (tt0) cc_final: 0.6248 (tp30) REVERT: D 1151 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7791 (tptp) REVERT: D 1220 ILE cc_start: 0.8752 (mm) cc_final: 0.8527 (mm) REVERT: D 1244 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8073 (mm-40) REVERT: D 1368 ASP cc_start: 0.7562 (t0) cc_final: 0.7171 (t0) REVERT: G 29 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7019 (mm-40) REVERT: G 61 TYR cc_start: 0.7860 (t80) cc_final: 0.7596 (t80) REVERT: G 66 ASP cc_start: 0.7312 (t0) cc_final: 0.6829 (m-30) REVERT: G 107 ASN cc_start: 0.6523 (t0) cc_final: 0.6190 (t0) REVERT: G 110 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8903 (mm-30) outliers start: 60 outliers final: 35 residues processed: 386 average time/residue: 0.1966 time to fit residues: 120.9139 Evaluate side-chains 341 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 302 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 20 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 128 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 150 optimal weight: 0.7980 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 762 ASN C 811 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN D1259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.208191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.145479 restraints weight = 42388.036| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 4.19 r_work: 0.3660 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 28042 Z= 0.320 Angle : 0.778 11.235 38140 Z= 0.403 Chirality : 0.048 0.293 4349 Planarity : 0.006 0.070 4796 Dihedral : 13.708 137.553 4363 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.29 % Favored : 93.56 % Rotamer: Outliers : 4.03 % Allowed : 14.96 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: -1.38 (0.14), residues: 3341 helix: 0.18 (0.15), residues: 1226 sheet: -0.81 (0.27), residues: 356 loop : -1.77 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 67 TYR 0.024 0.002 TYR C1213 PHE 0.024 0.003 PHE C 38 TRP 0.019 0.002 TRP G 36 HIS 0.013 0.002 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00754 (28042) covalent geometry : angle 0.77758 (38140) hydrogen bonds : bond 0.05184 ( 1176) hydrogen bonds : angle 5.48984 ( 3307) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 313 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7819 (pm20) cc_final: 0.7435 (mp-120) REVERT: A 231 PHE cc_start: 0.7899 (m-10) cc_final: 0.7680 (m-10) REVERT: B 35 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7272 (t80) REVERT: C 185 ASP cc_start: 0.6554 (m-30) cc_final: 0.5757 (m-30) REVERT: C 216 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7747 (p) REVERT: C 369 MET cc_start: 0.7106 (ppp) cc_final: 0.6558 (ppp) REVERT: C 446 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: C 478 ARG cc_start: 0.7684 (mmt-90) cc_final: 0.7444 (tpt-90) REVERT: C 592 ARG cc_start: 0.8709 (mtp180) cc_final: 0.7982 (mtp85) REVERT: C 672 GLU cc_start: 0.7022 (pt0) cc_final: 0.6603 (pm20) REVERT: C 704 MET cc_start: 0.7353 (mmp) cc_final: 0.6899 (mmm) REVERT: C 775 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7859 (tt0) REVERT: C 800 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7825 (mmt) REVERT: C 814 ASP cc_start: 0.7713 (m-30) cc_final: 0.7251 (m-30) REVERT: C 1174 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7575 (tm-30) REVERT: C 1180 MET cc_start: 0.8175 (tpp) cc_final: 0.7945 (ttm) REVERT: C 1222 GLU cc_start: 0.7166 (tp30) cc_final: 0.6313 (mt-10) REVERT: C 1269 ARG cc_start: 0.7570 (ttp80) cc_final: 0.6637 (ttm-80) REVERT: C 1279 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6532 (mt-10) REVERT: C 1290 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6725 (mmt) REVERT: C 1315 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4821 (ttp) REVERT: C 1319 MET cc_start: 0.3898 (mmt) cc_final: 0.3544 (mmm) REVERT: D 29 MET cc_start: 0.8502 (ppp) cc_final: 0.8095 (ppp) REVERT: D 166 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8393 (pp) REVERT: D 180 MET cc_start: 0.6144 (mmm) cc_final: 0.5201 (tpt) REVERT: D 195 GLU cc_start: 0.8488 (mp0) cc_final: 0.8163 (mp0) REVERT: D 198 CYS cc_start: 0.8728 (m) cc_final: 0.8297 (p) REVERT: D 236 TRP cc_start: 0.8441 (m-10) cc_final: 0.8091 (m-10) REVERT: D 278 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7142 (mtp-110) REVERT: D 297 ARG cc_start: 0.6406 (ttm170) cc_final: 0.6177 (tpt-90) REVERT: D 330 MET cc_start: 0.5897 (tmm) cc_final: 0.5314 (tmm) REVERT: D 337 ARG cc_start: 0.4577 (tpt170) cc_final: 0.3689 (mpt-90) REVERT: D 594 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6124 (pm20) REVERT: D 738 ARG cc_start: 0.6606 (ttt180) cc_final: 0.6030 (ttp-170) REVERT: D 751 ASP cc_start: 0.7106 (p0) cc_final: 0.6801 (p0) REVERT: D 874 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8347 (pt0) REVERT: D 881 LYS cc_start: 0.6015 (tttm) cc_final: 0.5712 (tptt) REVERT: D 981 GLU cc_start: 0.6898 (tt0) cc_final: 0.6246 (tp30) REVERT: D 1151 LYS cc_start: 0.8137 (tmtt) cc_final: 0.7871 (pttt) REVERT: D 1286 LYS cc_start: 0.7369 (mmtm) cc_final: 0.6905 (mtmt) REVERT: D 1368 ASP cc_start: 0.7712 (t0) cc_final: 0.7406 (t70) REVERT: E 30 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.5174 (pmm) REVERT: E 72 GLN cc_start: 0.4968 (OUTLIER) cc_final: 0.4697 (mp10) REVERT: G 29 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7031 (mm-40) REVERT: G 98 GLU cc_start: 0.4747 (tm-30) cc_final: 0.4306 (mp0) REVERT: G 107 ASN cc_start: 0.6437 (t0) cc_final: 0.6107 (t0) REVERT: G 110 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8906 (mm-30) REVERT: G 129 ARG cc_start: 0.4700 (OUTLIER) cc_final: 0.4400 (ppt170) outliers start: 115 outliers final: 72 residues processed: 395 average time/residue: 0.1899 time to fit residues: 120.1438 Evaluate side-chains 371 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 286 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1152 GLU Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 129 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 107 optimal weight: 0.0050 chunk 57 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 333 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 324 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN C 673 HIS ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN G 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.213792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.163661 restraints weight = 42525.622| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 4.36 r_work: 0.3746 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28042 Z= 0.132 Angle : 0.622 9.240 38140 Z= 0.323 Chirality : 0.043 0.183 4349 Planarity : 0.004 0.058 4796 Dihedral : 13.525 134.524 4363 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.61 % Favored : 95.27 % Rotamer: Outliers : 3.01 % Allowed : 16.01 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: -1.02 (0.14), residues: 3341 helix: 0.53 (0.15), residues: 1235 sheet: -0.71 (0.27), residues: 357 loop : -1.59 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1140 TYR 0.020 0.001 TYR C 73 PHE 0.017 0.001 PHE D 176 TRP 0.038 0.002 TRP G 73 HIS 0.013 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00296 (28042) covalent geometry : angle 0.62179 (38140) hydrogen bonds : bond 0.04462 ( 1176) hydrogen bonds : angle 5.14214 ( 3307) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 327 time to evaluate : 1.134 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: A 93 GLN cc_start: 0.7771 (pm20) cc_final: 0.7358 (mp-120) REVERT: A 199 ASP cc_start: 0.7061 (m-30) cc_final: 0.6632 (m-30) REVERT: B 29 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7146 (tm-30) REVERT: B 35 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.7101 (t80) REVERT: B 206 GLU cc_start: 0.5998 (mt-10) cc_final: 0.5615 (mt-10) REVERT: C 185 ASP cc_start: 0.6527 (m-30) cc_final: 0.5617 (m-30) REVERT: C 369 MET cc_start: 0.7100 (ppp) cc_final: 0.6526 (ppp) REVERT: C 392 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8117 (tt0) REVERT: C 454 ARG cc_start: 0.8474 (ttp80) cc_final: 0.7796 (mtm110) REVERT: C 459 MET cc_start: 0.6896 (mtp) cc_final: 0.6633 (mtp) REVERT: C 478 ARG cc_start: 0.7536 (mmt-90) cc_final: 0.7324 (tpt-90) REVERT: C 515 MET cc_start: 0.7839 (tpt) cc_final: 0.7513 (tpt) REVERT: C 524 ILE cc_start: 0.8757 (tt) cc_final: 0.8539 (tt) REVERT: C 592 ARG cc_start: 0.8651 (mtp180) cc_final: 0.8432 (mtp85) REVERT: C 704 MET cc_start: 0.7334 (mmp) cc_final: 0.6808 (mmm) REVERT: C 775 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7840 (tt0) REVERT: C 814 ASP cc_start: 0.7374 (m-30) cc_final: 0.6828 (m-30) REVERT: C 965 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7125 (mm-40) REVERT: C 1072 ASN cc_start: 0.8064 (t0) cc_final: 0.7795 (t0) REVERT: C 1174 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7443 (tm-30) REVERT: C 1180 MET cc_start: 0.7933 (tpp) cc_final: 0.7674 (ttm) REVERT: C 1269 ARG cc_start: 0.7571 (ttp80) cc_final: 0.6623 (ttm-80) REVERT: C 1279 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6592 (mt-10) REVERT: C 1289 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: C 1290 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6397 (mmt) REVERT: C 1315 MET cc_start: 0.4709 (OUTLIER) cc_final: 0.4382 (ttp) REVERT: C 1319 MET cc_start: 0.3897 (mmt) cc_final: 0.3548 (mmm) REVERT: D 29 MET cc_start: 0.8465 (ppp) cc_final: 0.8160 (ppp) REVERT: D 166 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8412 (pp) REVERT: D 180 MET cc_start: 0.6047 (mmm) cc_final: 0.5814 (mmm) REVERT: D 195 GLU cc_start: 0.8508 (mp0) cc_final: 0.8231 (mp0) REVERT: D 198 CYS cc_start: 0.8722 (m) cc_final: 0.8311 (p) REVERT: D 236 TRP cc_start: 0.8465 (m-10) cc_final: 0.8120 (m-10) REVERT: D 278 ARG cc_start: 0.7986 (mtt180) cc_final: 0.7109 (mtp180) REVERT: D 297 ARG cc_start: 0.6415 (ttm170) cc_final: 0.6113 (tpt-90) REVERT: D 330 MET cc_start: 0.5775 (tmm) cc_final: 0.5056 (tmm) REVERT: D 337 ARG cc_start: 0.4445 (tpt170) cc_final: 0.3584 (mmt90) REVERT: D 347 VAL cc_start: 0.8116 (p) cc_final: 0.7908 (t) REVERT: D 443 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: D 576 ARG cc_start: 0.6766 (mtt180) cc_final: 0.6231 (tpp80) REVERT: D 594 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.5897 (pm20) REVERT: D 719 PHE cc_start: 0.5396 (m-10) cc_final: 0.5145 (m-80) REVERT: D 724 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.6771 (mtm) REVERT: D 738 ARG cc_start: 0.6345 (ttt180) cc_final: 0.5682 (ttp-170) REVERT: D 751 ASP cc_start: 0.7102 (p0) cc_final: 0.6799 (p0) REVERT: D 881 LYS cc_start: 0.5964 (tttm) cc_final: 0.5679 (tptt) REVERT: D 981 GLU cc_start: 0.6833 (tt0) cc_final: 0.6292 (tp30) REVERT: D 1151 LYS cc_start: 0.8133 (tmtt) cc_final: 0.7813 (pttt) REVERT: D 1286 LYS cc_start: 0.7265 (mmtm) cc_final: 0.6761 (mtpt) REVERT: D 1368 ASP cc_start: 0.7663 (t0) cc_final: 0.7287 (t0) REVERT: E 72 GLN cc_start: 0.4930 (OUTLIER) cc_final: 0.4658 (mp10) REVERT: G 29 GLN cc_start: 0.7891 (mm-40) cc_final: 0.6891 (mm-40) REVERT: G 66 ASP cc_start: 0.7120 (t0) cc_final: 0.6577 (m-30) REVERT: G 129 ARG cc_start: 0.4702 (OUTLIER) cc_final: 0.3571 (ptt180) outliers start: 86 outliers final: 56 residues processed: 385 average time/residue: 0.1986 time to fit residues: 120.8917 Evaluate side-chains 361 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 294 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1152 GLU Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 129 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 278 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 316 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 111 optimal weight: 0.5980 chunk 270 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 811 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.213773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.162813 restraints weight = 42567.946| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 4.16 r_work: 0.3755 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28042 Z= 0.141 Angle : 0.615 10.307 38140 Z= 0.319 Chirality : 0.043 0.191 4349 Planarity : 0.004 0.067 4796 Dihedral : 13.464 134.657 4363 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.12 % Favored : 94.73 % Rotamer: Outliers : 3.33 % Allowed : 15.94 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: -0.92 (0.14), residues: 3341 helix: 0.60 (0.15), residues: 1230 sheet: -0.84 (0.27), residues: 379 loop : -1.47 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 470 TYR 0.030 0.001 TYR C1281 PHE 0.017 0.001 PHE D 176 TRP 0.057 0.003 TRP G 73 HIS 0.008 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00321 (28042) covalent geometry : angle 0.61467 (38140) hydrogen bonds : bond 0.04379 ( 1176) hydrogen bonds : angle 5.06022 ( 3307) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 325 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7847 (pm20) cc_final: 0.7409 (mp-120) REVERT: A 199 ASP cc_start: 0.7011 (m-30) cc_final: 0.6647 (m-30) REVERT: B 29 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6944 (tm-30) REVERT: B 30 PRO cc_start: 0.8554 (Cg_endo) cc_final: 0.7993 (Cg_exo) REVERT: B 35 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.7023 (t80) REVERT: B 206 GLU cc_start: 0.6096 (mt-10) cc_final: 0.5682 (mt-10) REVERT: C 73 TYR cc_start: 0.7508 (p90) cc_final: 0.7234 (p90) REVERT: C 185 ASP cc_start: 0.6516 (m-30) cc_final: 0.5508 (m-30) REVERT: C 216 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7618 (p) REVERT: C 239 MET cc_start: 0.2222 (tpt) cc_final: 0.1228 (tmm) REVERT: C 369 MET cc_start: 0.7049 (ppp) cc_final: 0.6470 (ppp) REVERT: C 392 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8015 (tt0) REVERT: C 443 ASP cc_start: 0.8215 (m-30) cc_final: 0.7984 (m-30) REVERT: C 478 ARG cc_start: 0.7612 (mmt-90) cc_final: 0.7309 (tpt-90) REVERT: C 524 ILE cc_start: 0.8754 (tt) cc_final: 0.8515 (tt) REVERT: C 592 ARG cc_start: 0.8676 (mtp180) cc_final: 0.8464 (mtp85) REVERT: C 704 MET cc_start: 0.7385 (mmp) cc_final: 0.6905 (mmm) REVERT: C 775 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7823 (tt0) REVERT: C 814 ASP cc_start: 0.7451 (m-30) cc_final: 0.6928 (m-30) REVERT: C 965 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7142 (mm-40) REVERT: C 1030 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7823 (pp20) REVERT: C 1034 ARG cc_start: 0.7894 (mmp80) cc_final: 0.7674 (mmp80) REVERT: C 1072 ASN cc_start: 0.8060 (t0) cc_final: 0.7822 (t0) REVERT: C 1174 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7488 (tm-30) REVERT: C 1269 ARG cc_start: 0.7608 (ttp80) cc_final: 0.6650 (ttm-80) REVERT: C 1279 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6630 (mt-10) REVERT: C 1289 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: C 1290 MET cc_start: 0.7043 (mtp) cc_final: 0.6412 (mmt) REVERT: C 1315 MET cc_start: 0.4722 (OUTLIER) cc_final: 0.4384 (ttp) REVERT: C 1319 MET cc_start: 0.3957 (OUTLIER) cc_final: 0.3599 (mmm) REVERT: D 29 MET cc_start: 0.8439 (ppp) cc_final: 0.8162 (ppp) REVERT: D 166 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8413 (pp) REVERT: D 180 MET cc_start: 0.6040 (mmm) cc_final: 0.5712 (mmm) REVERT: D 195 GLU cc_start: 0.8503 (mp0) cc_final: 0.8144 (mp0) REVERT: D 198 CYS cc_start: 0.8719 (m) cc_final: 0.8292 (p) REVERT: D 236 TRP cc_start: 0.8431 (m-10) cc_final: 0.8104 (m-10) REVERT: D 278 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7153 (mtp180) REVERT: D 297 ARG cc_start: 0.6422 (ttm170) cc_final: 0.6117 (tpt-90) REVERT: D 330 MET cc_start: 0.5781 (tmm) cc_final: 0.5056 (tmm) REVERT: D 337 ARG cc_start: 0.4453 (tpt170) cc_final: 0.3503 (mmt90) REVERT: D 340 GLN cc_start: 0.5371 (mm-40) cc_final: 0.5102 (mm-40) REVERT: D 443 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8009 (mm-30) REVERT: D 458 ASN cc_start: 0.7733 (t0) cc_final: 0.7516 (t0) REVERT: D 512 TYR cc_start: 0.7330 (t80) cc_final: 0.7130 (t80) REVERT: D 576 ARG cc_start: 0.6825 (mtt180) cc_final: 0.5780 (ttm170) REVERT: D 594 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.5813 (pm20) REVERT: D 719 PHE cc_start: 0.5349 (m-10) cc_final: 0.5094 (m-80) REVERT: D 724 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.6802 (mtm) REVERT: D 738 ARG cc_start: 0.6460 (ttt180) cc_final: 0.5924 (ttp80) REVERT: D 881 LYS cc_start: 0.5984 (tttm) cc_final: 0.5674 (tptt) REVERT: D 981 GLU cc_start: 0.6861 (tt0) cc_final: 0.6317 (tp30) REVERT: D 1151 LYS cc_start: 0.8117 (tmtt) cc_final: 0.7811 (ptpt) REVERT: D 1286 LYS cc_start: 0.7311 (mmtm) cc_final: 0.6852 (mtpt) REVERT: D 1368 ASP cc_start: 0.7656 (t0) cc_final: 0.7276 (t0) REVERT: E 72 GLN cc_start: 0.4955 (OUTLIER) cc_final: 0.4684 (mp10) REVERT: G 29 GLN cc_start: 0.7880 (mm-40) cc_final: 0.6909 (mm-40) REVERT: G 66 ASP cc_start: 0.7127 (t0) cc_final: 0.6787 (m-30) REVERT: G 110 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8530 (mm-30) REVERT: G 129 ARG cc_start: 0.4816 (OUTLIER) cc_final: 0.4529 (ppt170) outliers start: 95 outliers final: 62 residues processed: 389 average time/residue: 0.1697 time to fit residues: 104.5019 Evaluate side-chains 374 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 300 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1152 GLU Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 129 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 107 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 280 optimal weight: 50.0000 chunk 135 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 211 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 811 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.207161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.143984 restraints weight = 42213.581| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 4.04 r_work: 0.3624 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 28042 Z= 0.335 Angle : 0.794 11.966 38140 Z= 0.412 Chirality : 0.049 0.312 4349 Planarity : 0.006 0.068 4796 Dihedral : 13.746 136.334 4363 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.97 % Favored : 92.88 % Rotamer: Outliers : 3.50 % Allowed : 17.13 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: -1.39 (0.14), residues: 3341 helix: 0.08 (0.15), residues: 1213 sheet: -0.60 (0.28), residues: 334 loop : -1.74 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 473 TYR 0.036 0.002 TYR D 537 PHE 0.023 0.003 PHE C 38 TRP 0.083 0.003 TRP G 73 HIS 0.012 0.002 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00792 (28042) covalent geometry : angle 0.79442 (38140) hydrogen bonds : bond 0.05133 ( 1176) hydrogen bonds : angle 5.50609 ( 3307) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 306 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7950 (pm20) cc_final: 0.7572 (mp-120) REVERT: A 199 ASP cc_start: 0.7133 (m-30) cc_final: 0.6718 (m-30) REVERT: A 231 PHE cc_start: 0.7843 (m-10) cc_final: 0.7436 (m-10) REVERT: B 35 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7249 (t80) REVERT: B 182 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6803 (tpp80) REVERT: B 200 LYS cc_start: 0.6282 (mttm) cc_final: 0.6062 (mtpt) REVERT: C 41 GLN cc_start: 0.6872 (mm-40) cc_final: 0.6617 (mm-40) REVERT: C 185 ASP cc_start: 0.6528 (m-30) cc_final: 0.5704 (m-30) REVERT: C 216 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7628 (p) REVERT: C 369 MET cc_start: 0.7063 (ppp) cc_final: 0.6472 (ppp) REVERT: C 392 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8213 (tt0) REVERT: C 446 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: C 478 ARG cc_start: 0.7571 (mmt-90) cc_final: 0.7258 (tpt-90) REVERT: C 592 ARG cc_start: 0.8778 (mtp180) cc_final: 0.8106 (mtp85) REVERT: C 672 GLU cc_start: 0.6996 (pt0) cc_final: 0.6647 (pm20) REVERT: C 814 ASP cc_start: 0.7728 (m-30) cc_final: 0.7153 (m-30) REVERT: C 965 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7182 (mm-40) REVERT: C 1174 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7733 (tm-30) REVERT: C 1222 GLU cc_start: 0.7089 (tp30) cc_final: 0.6203 (mt-10) REVERT: C 1279 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6562 (mt-10) REVERT: C 1290 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6675 (mmt) REVERT: C 1315 MET cc_start: 0.4955 (OUTLIER) cc_final: 0.4685 (ttp) REVERT: C 1319 MET cc_start: 0.3923 (OUTLIER) cc_final: 0.3616 (mmm) REVERT: D 29 MET cc_start: 0.8425 (ppp) cc_final: 0.8194 (ppp) REVERT: D 166 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8470 (pp) REVERT: D 180 MET cc_start: 0.6449 (mmm) cc_final: 0.6106 (mmm) REVERT: D 198 CYS cc_start: 0.8723 (m) cc_final: 0.8251 (p) REVERT: D 236 TRP cc_start: 0.8431 (m-10) cc_final: 0.8025 (m-10) REVERT: D 278 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7092 (mtp-110) REVERT: D 297 ARG cc_start: 0.6368 (ttm170) cc_final: 0.6028 (tpt-90) REVERT: D 337 ARG cc_start: 0.4609 (tpt170) cc_final: 0.3624 (mpt-90) REVERT: D 525 MET cc_start: 0.7840 (pmm) cc_final: 0.6454 (tpt) REVERT: D 594 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6253 (pm20) REVERT: D 724 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.6861 (mtm) REVERT: D 751 ASP cc_start: 0.7014 (p0) cc_final: 0.6740 (p0) REVERT: D 881 LYS cc_start: 0.6106 (tttm) cc_final: 0.5754 (tptt) REVERT: D 981 GLU cc_start: 0.6824 (tt0) cc_final: 0.6189 (tp30) REVERT: D 1151 LYS cc_start: 0.8117 (tmtt) cc_final: 0.7895 (pttt) REVERT: D 1286 LYS cc_start: 0.7432 (mmtm) cc_final: 0.6937 (mtpt) REVERT: D 1355 ARG cc_start: 0.6913 (mtm180) cc_final: 0.6673 (mtm180) REVERT: D 1368 ASP cc_start: 0.7778 (t0) cc_final: 0.7439 (t70) REVERT: E 30 MET cc_start: 0.6532 (OUTLIER) cc_final: 0.5414 (pmm) REVERT: E 72 GLN cc_start: 0.4849 (OUTLIER) cc_final: 0.4598 (mp10) REVERT: G 29 GLN cc_start: 0.7890 (mm-40) cc_final: 0.6974 (mm-40) REVERT: G 129 ARG cc_start: 0.4713 (OUTLIER) cc_final: 0.4502 (ppt170) outliers start: 100 outliers final: 74 residues processed: 374 average time/residue: 0.1897 time to fit residues: 112.3055 Evaluate side-chains 373 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 285 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1152 GLU Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 129 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 57 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 40.0000 chunk 216 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 329 optimal weight: 7.9990 chunk 310 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 295 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.211944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.148548 restraints weight = 42442.230| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 3.71 r_work: 0.3725 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28042 Z= 0.157 Angle : 0.653 11.768 38140 Z= 0.338 Chirality : 0.044 0.200 4349 Planarity : 0.005 0.062 4796 Dihedral : 13.582 134.534 4363 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.06 % Favored : 94.73 % Rotamer: Outliers : 3.22 % Allowed : 17.90 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: -1.11 (0.14), residues: 3341 helix: 0.37 (0.15), residues: 1240 sheet: -0.56 (0.28), residues: 349 loop : -1.62 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 67 TYR 0.019 0.001 TYR D 537 PHE 0.021 0.002 PHE A 231 TRP 0.085 0.003 TRP G 73 HIS 0.014 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00363 (28042) covalent geometry : angle 0.65289 (38140) hydrogen bonds : bond 0.04505 ( 1176) hydrogen bonds : angle 5.21695 ( 3307) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 306 time to evaluate : 0.818 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: A 93 GLN cc_start: 0.7912 (pm20) cc_final: 0.7499 (mp-120) REVERT: A 199 ASP cc_start: 0.7040 (m-30) cc_final: 0.6665 (m-30) REVERT: B 33 ARG cc_start: 0.8328 (ttt180) cc_final: 0.7635 (ttp-170) REVERT: B 35 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7099 (t80) REVERT: C 23 ASP cc_start: 0.8406 (p0) cc_final: 0.8165 (m-30) REVERT: C 124 MET cc_start: 0.7362 (pmm) cc_final: 0.7131 (pmm) REVERT: C 185 ASP cc_start: 0.6581 (m-30) cc_final: 0.5541 (m-30) REVERT: C 216 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7486 (p) REVERT: C 239 MET cc_start: 0.2240 (tpt) cc_final: 0.1212 (tmm) REVERT: C 369 MET cc_start: 0.7081 (ppp) cc_final: 0.6492 (ppp) REVERT: C 392 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8162 (tt0) REVERT: C 478 ARG cc_start: 0.7429 (mmt-90) cc_final: 0.7227 (tpt-90) REVERT: C 515 MET cc_start: 0.7965 (tpt) cc_final: 0.7511 (tpt) REVERT: C 524 ILE cc_start: 0.8799 (tt) cc_final: 0.8556 (tt) REVERT: C 592 ARG cc_start: 0.8759 (mtp180) cc_final: 0.8532 (mtp85) REVERT: C 704 MET cc_start: 0.7304 (mmp) cc_final: 0.6804 (mmm) REVERT: C 775 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7774 (tt0) REVERT: C 805 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7271 (ptp) REVERT: C 814 ASP cc_start: 0.7481 (m-30) cc_final: 0.6863 (m-30) REVERT: C 965 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7165 (mm-40) REVERT: C 1174 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7577 (tm-30) REVERT: C 1222 GLU cc_start: 0.6638 (tp30) cc_final: 0.5888 (mt-10) REVERT: C 1269 ARG cc_start: 0.7263 (ttp80) cc_final: 0.6324 (ttm-80) REVERT: C 1279 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6476 (mt-10) REVERT: C 1289 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: C 1290 MET cc_start: 0.6904 (mtp) cc_final: 0.6172 (mmt) REVERT: C 1315 MET cc_start: 0.4827 (OUTLIER) cc_final: 0.4300 (ttp) REVERT: C 1319 MET cc_start: 0.3890 (OUTLIER) cc_final: 0.3596 (mmm) REVERT: D 29 MET cc_start: 0.8408 (ppp) cc_final: 0.8172 (ppp) REVERT: D 45 ASN cc_start: -0.2730 (OUTLIER) cc_final: -0.4089 (t0) REVERT: D 166 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8460 (pp) REVERT: D 180 MET cc_start: 0.6239 (mmm) cc_final: 0.5876 (mmm) REVERT: D 195 GLU cc_start: 0.8505 (mp0) cc_final: 0.8165 (mp0) REVERT: D 198 CYS cc_start: 0.8690 (m) cc_final: 0.8209 (p) REVERT: D 236 TRP cc_start: 0.8455 (m-10) cc_final: 0.8124 (m-10) REVERT: D 278 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7099 (mtp180) REVERT: D 297 ARG cc_start: 0.6326 (ttm170) cc_final: 0.6010 (tpt-90) REVERT: D 330 MET cc_start: 0.5810 (tmm) cc_final: 0.5454 (tmm) REVERT: D 337 ARG cc_start: 0.4420 (tpt170) cc_final: 0.3669 (mmt90) REVERT: D 443 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8193 (mm-30) REVERT: D 525 MET cc_start: 0.7592 (pmm) cc_final: 0.6235 (tpt) REVERT: D 531 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8226 (mttm) REVERT: D 576 ARG cc_start: 0.6812 (mtt180) cc_final: 0.6124 (tpp80) REVERT: D 594 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.5839 (pm20) REVERT: D 719 PHE cc_start: 0.5321 (m-10) cc_final: 0.5103 (m-80) REVERT: D 724 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.6673 (mtm) REVERT: D 751 ASP cc_start: 0.7002 (p0) cc_final: 0.6731 (p0) REVERT: D 874 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8180 (pt0) REVERT: D 881 LYS cc_start: 0.6060 (tttm) cc_final: 0.5769 (tptt) REVERT: D 913 GLU cc_start: 0.7025 (mp0) cc_final: 0.6784 (mp0) REVERT: D 981 GLU cc_start: 0.6811 (tt0) cc_final: 0.6291 (tp30) REVERT: D 1286 LYS cc_start: 0.7360 (mmtm) cc_final: 0.6858 (mtpt) REVERT: D 1368 ASP cc_start: 0.7766 (t0) cc_final: 0.7365 (t0) REVERT: E 72 GLN cc_start: 0.4914 (OUTLIER) cc_final: 0.4656 (mp10) REVERT: G 29 GLN cc_start: 0.7906 (mm-40) cc_final: 0.6912 (mm-40) REVERT: G 66 ASP cc_start: 0.7171 (t0) cc_final: 0.6810 (m-30) REVERT: G 92 ILE cc_start: 0.4268 (mt) cc_final: 0.3814 (tp) REVERT: G 110 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8574 (mm-30) REVERT: G 129 ARG cc_start: 0.4636 (OUTLIER) cc_final: 0.4402 (ppt170) outliers start: 92 outliers final: 67 residues processed: 367 average time/residue: 0.1938 time to fit residues: 111.2661 Evaluate side-chains 373 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 291 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1152 GLU Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 129 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 51 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 185 optimal weight: 30.0000 chunk 84 optimal weight: 9.9990 chunk 115 optimal weight: 0.0980 chunk 252 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.211756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.147271 restraints weight = 41748.972| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 4.05 r_work: 0.3677 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 28042 Z= 0.255 Angle : 0.733 13.266 38140 Z= 0.378 Chirality : 0.047 0.249 4349 Planarity : 0.005 0.067 4796 Dihedral : 13.688 135.530 4363 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.94 % Favored : 92.88 % Rotamer: Outliers : 3.33 % Allowed : 17.93 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: -1.30 (0.14), residues: 3341 helix: 0.15 (0.15), residues: 1219 sheet: -0.54 (0.28), residues: 347 loop : -1.70 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 67 TYR 0.024 0.002 TYR D 537 PHE 0.026 0.002 PHE A 231 TRP 0.083 0.004 TRP G 73 HIS 0.020 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00602 (28042) covalent geometry : angle 0.73305 (38140) hydrogen bonds : bond 0.04826 ( 1176) hydrogen bonds : angle 5.38453 ( 3307) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 291 time to evaluate : 1.038 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: A 93 GLN cc_start: 0.7974 (pm20) cc_final: 0.7591 (mp-120) REVERT: A 199 ASP cc_start: 0.7111 (m-30) cc_final: 0.6753 (m-30) REVERT: B 35 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7186 (t80) REVERT: C 23 ASP cc_start: 0.8411 (p0) cc_final: 0.8154 (m-30) REVERT: C 41 GLN cc_start: 0.6831 (mm-40) cc_final: 0.6533 (mm-40) REVERT: C 124 MET cc_start: 0.7521 (pmm) cc_final: 0.7282 (pmm) REVERT: C 185 ASP cc_start: 0.6467 (m-30) cc_final: 0.5572 (m-30) REVERT: C 216 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7374 (p) REVERT: C 239 MET cc_start: 0.2296 (tpt) cc_final: 0.1258 (tmm) REVERT: C 369 MET cc_start: 0.7098 (ppp) cc_final: 0.6516 (ppp) REVERT: C 392 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8167 (tt0) REVERT: C 524 ILE cc_start: 0.8931 (tt) cc_final: 0.8608 (tt) REVERT: C 592 ARG cc_start: 0.8796 (mtp180) cc_final: 0.8157 (mtp85) REVERT: C 814 ASP cc_start: 0.7624 (m-30) cc_final: 0.7059 (m-30) REVERT: C 965 GLN cc_start: 0.7420 (mm-40) cc_final: 0.7164 (mm-40) REVERT: C 1174 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7665 (tm-30) REVERT: C 1222 GLU cc_start: 0.7016 (tp30) cc_final: 0.6205 (mt-10) REVERT: C 1269 ARG cc_start: 0.7391 (ttp80) cc_final: 0.6450 (ttm-80) REVERT: C 1279 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6516 (mt-10) REVERT: C 1289 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: C 1290 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6509 (mmt) REVERT: C 1319 MET cc_start: 0.3932 (OUTLIER) cc_final: 0.3010 (mpp) REVERT: D 29 MET cc_start: 0.8411 (ppp) cc_final: 0.8191 (ppp) REVERT: D 45 ASN cc_start: -0.2681 (OUTLIER) cc_final: -0.4143 (t0) REVERT: D 102 MET cc_start: 0.7565 (ppp) cc_final: 0.7115 (ppp) REVERT: D 166 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8487 (pp) REVERT: D 180 MET cc_start: 0.6391 (mmm) cc_final: 0.6016 (mmm) REVERT: D 195 GLU cc_start: 0.8504 (mp0) cc_final: 0.8172 (mp0) REVERT: D 198 CYS cc_start: 0.8715 (m) cc_final: 0.8229 (p) REVERT: D 236 TRP cc_start: 0.8436 (m-10) cc_final: 0.8047 (m-10) REVERT: D 278 ARG cc_start: 0.7983 (mtt180) cc_final: 0.7071 (mtm-85) REVERT: D 297 ARG cc_start: 0.6330 (ttm170) cc_final: 0.5984 (tpt-90) REVERT: D 330 MET cc_start: 0.5964 (tmm) cc_final: 0.5648 (tmm) REVERT: D 337 ARG cc_start: 0.4497 (tpt170) cc_final: 0.3768 (mpt-90) REVERT: D 484 MET cc_start: 0.8019 (mmm) cc_final: 0.7768 (mmm) REVERT: D 525 MET cc_start: 0.7734 (pmm) cc_final: 0.6324 (tpt) REVERT: D 594 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6230 (pm20) REVERT: D 724 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.6776 (mtm) REVERT: D 751 ASP cc_start: 0.6917 (p0) cc_final: 0.6658 (p0) REVERT: D 874 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: D 881 LYS cc_start: 0.6136 (tttm) cc_final: 0.5817 (tptt) REVERT: D 913 GLU cc_start: 0.7107 (mp0) cc_final: 0.6850 (mp0) REVERT: D 932 MET cc_start: 0.3779 (mmm) cc_final: 0.2511 (ptp) REVERT: D 981 GLU cc_start: 0.6777 (tt0) cc_final: 0.6194 (tp30) REVERT: D 1286 LYS cc_start: 0.7422 (mmtm) cc_final: 0.6937 (mtmt) REVERT: D 1368 ASP cc_start: 0.7800 (t0) cc_final: 0.7455 (t70) REVERT: E 30 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.5246 (pmm) REVERT: E 72 GLN cc_start: 0.4931 (OUTLIER) cc_final: 0.4684 (mp10) REVERT: G 29 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7001 (mm-40) REVERT: G 92 ILE cc_start: 0.4204 (mt) cc_final: 0.3387 (tp) REVERT: G 110 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8548 (mm-30) outliers start: 95 outliers final: 70 residues processed: 355 average time/residue: 0.1785 time to fit residues: 100.3173 Evaluate side-chains 362 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 279 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 113 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 295 optimal weight: 0.9980 chunk 312 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 275 optimal weight: 7.9990 chunk 335 optimal weight: 20.0000 chunk 228 optimal weight: 0.9980 chunk 291 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 195 optimal weight: 30.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.215550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.162754 restraints weight = 41789.554| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 4.15 r_work: 0.3755 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28042 Z= 0.144 Angle : 0.655 12.914 38140 Z= 0.338 Chirality : 0.044 0.282 4349 Planarity : 0.005 0.069 4796 Dihedral : 13.561 134.012 4363 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.36 % Favored : 94.46 % Rotamer: Outliers : 2.98 % Allowed : 18.28 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: -1.04 (0.14), residues: 3341 helix: 0.42 (0.15), residues: 1233 sheet: -0.48 (0.27), residues: 361 loop : -1.58 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 67 TYR 0.016 0.001 TYR D 899 PHE 0.022 0.002 PHE A 231 TRP 0.068 0.003 TRP G 73 HIS 0.017 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00327 (28042) covalent geometry : angle 0.65506 (38140) hydrogen bonds : bond 0.04432 ( 1176) hydrogen bonds : angle 5.19263 ( 3307) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8762.72 seconds wall clock time: 150 minutes 25.39 seconds (9025.39 seconds total)