Starting phenix.real_space_refine on Fri Aug 9 23:56:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5a_36899/08_2024/8k5a_36899.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5a_36899/08_2024/8k5a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5a_36899/08_2024/8k5a_36899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5a_36899/08_2024/8k5a_36899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5a_36899/08_2024/8k5a_36899.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5a_36899/08_2024/8k5a_36899.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Residue "A GLU 67": "OE1" <-> "OE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C GLU 1083": "OE1" <-> "OE2" Residue "C ASP 1214": "OD1" <-> "OD2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 993": "OE1" <-> "OE2" Residue "D TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1278": "OE1" <-> "OE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 98": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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: 20.12, per 1000 atoms: 0.73 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 - 3.50 Amino acid : False - 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: 19.16 Conformation dependent library (CDL) restraints added in 7.6 seconds 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: 17.60 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: 22.01 Time building geometry restraints manager: 20.44 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: 96.03 - 103.65: 469 103.65 - 111.27: 11913 111.27 - 118.90: 11133 118.90 - 126.52: 14207 126.52 - 134.14: 418 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: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.150 Check model and map are aligned: 0.230 Set scattering table: 0.250 Process input model: 122.180 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:4.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.060 ------------------------------------------------------------------------------- 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= 0.261 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (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 TRP 0.047 0.002 TRP C1276 HIS 0.007 0.001 HIS C 343 PHE 0.031 0.002 PHE E 17 TYR 0.038 0.002 TYR C1285 ARG 0.010 0.001 ARG C1216 *********************** 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 fitting. rotamer outliers: 0 poor density : 611 time to evaluate : 3.053 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: 0.4388 time to fit residues: 404.7267 Evaluate side-chains 354 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 40.0000 chunk 256 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 306 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 808 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 320 ASN D 419 HIS D 435 GLN ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D1098 GLN D1218 HIS ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.105 28042 Z= 0.643 Angle : 0.944 13.100 38140 Z= 0.490 Chirality : 0.055 0.329 4349 Planarity : 0.008 0.128 4796 Dihedral : 13.899 143.315 4363 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.67 % Favored : 93.18 % Rotamer: Outliers : 3.19 % Allowed : 10.68 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3341 helix: -0.24 (0.14), residues: 1221 sheet: -1.22 (0.26), residues: 363 loop : -1.97 (0.13), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C1276 HIS 0.018 0.003 HIS B 132 PHE 0.030 0.004 PHE C 38 TYR 0.028 0.003 TYR A 68 ARG 0.018 0.001 ARG G 58 *********************** 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 451 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 360 time to evaluate : 3.325 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: 0.8030 (pm20) cc_final: 0.7251 (pp30) REVERT: A 233 ASP cc_start: 0.6900 (t70) cc_final: 0.6691 (p0) REVERT: B 95 LYS cc_start: 0.8059 (pptt) cc_final: 0.7567 (pptt) REVERT: B 152 TYR cc_start: 0.8086 (t80) cc_final: 0.7800 (t80) REVERT: C 22 LEU cc_start: 0.8525 (tp) cc_final: 0.8272 (tp) REVERT: C 41 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6951 (mm110) REVERT: C 50 GLU cc_start: 0.7164 (tp30) cc_final: 0.6889 (tp30) REVERT: C 73 TYR cc_start: 0.7777 (p90) cc_final: 0.7216 (p90) REVERT: C 85 CYS cc_start: 0.7858 (m) cc_final: 0.7561 (m) REVERT: C 213 LEU cc_start: 0.8280 (mt) cc_final: 0.8058 (mt) REVERT: C 369 MET cc_start: 0.7116 (ppp) cc_final: 0.6649 (ppp) REVERT: C 419 ILE cc_start: 0.7526 (pt) cc_final: 0.7149 (mt) REVERT: C 478 ARG cc_start: 0.7394 (mmt-90) cc_final: 0.7092 (tpt-90) REVERT: C 488 MET cc_start: 0.6135 (tpt) cc_final: 0.5864 (mtp) REVERT: C 490 GLN cc_start: 0.7999 (pp30) cc_final: 0.7716 (pp30) REVERT: C 512 SER cc_start: 0.8636 (t) cc_final: 0.8371 (t) REVERT: C 592 ARG cc_start: 0.8007 (mtp180) cc_final: 0.6783 (mtp85) REVERT: C 672 GLU cc_start: 0.6014 (pt0) cc_final: 0.5281 (pm20) REVERT: C 790 ASP cc_start: 0.7476 (t0) cc_final: 0.6991 (t70) REVERT: C 814 ASP cc_start: 0.6490 (m-30) cc_final: 0.5691 (m-30) REVERT: C 1012 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8632 (mt-10) REVERT: C 1078 LYS cc_start: 0.7307 (ttmt) cc_final: 0.7031 (tttt) REVERT: C 1089 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6426 (pm20) REVERT: C 1174 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6793 (tm-30) REVERT: C 1220 GLN cc_start: 0.7651 (pm20) cc_final: 0.7114 (pt0) REVERT: C 1222 GLU cc_start: 0.6798 (tp30) cc_final: 0.5714 (mt-10) REVERT: C 1269 ARG cc_start: 0.6289 (ttp80) cc_final: 0.5490 (ttm-80) REVERT: C 1279 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.5753 (mt-10) REVERT: C 1290 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5925 (mtt) REVERT: C 1319 MET cc_start: 0.3295 (mmt) cc_final: 0.2847 (mmm) REVERT: D 29 MET cc_start: 0.8465 (ppp) cc_final: 0.8207 (ppp) REVERT: D 166 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8492 (pp) REVERT: D 236 TRP cc_start: 0.8397 (m-10) cc_final: 0.8085 (m-10) REVERT: D 278 ARG cc_start: 0.7734 (mtt180) cc_final: 0.6974 (mtp180) REVERT: D 297 ARG cc_start: 0.6358 (ttm170) cc_final: 0.6022 (tpt-90) REVERT: D 330 MET cc_start: 0.5257 (tmm) cc_final: 0.4829 (tmm) REVERT: D 337 ARG cc_start: 0.4347 (tpt170) cc_final: 0.3524 (mpt-90) REVERT: D 414 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7302 (mt-10) REVERT: D 431 ARG cc_start: 0.7913 (ttp-170) cc_final: 0.7661 (ttp-170) REVERT: D 484 MET cc_start: 0.7519 (mmm) cc_final: 0.7210 (mmm) REVERT: D 572 THR cc_start: 0.6281 (p) cc_final: 0.5937 (p) REVERT: D 589 TYR cc_start: 0.7783 (t80) cc_final: 0.7518 (t80) REVERT: D 623 GLN cc_start: 0.5787 (mm-40) cc_final: 0.5335 (mt0) REVERT: D 776 THR cc_start: 0.6480 (OUTLIER) cc_final: 0.6265 (m) REVERT: D 780 ARG cc_start: 0.8301 (mmm-85) cc_final: 0.7921 (ttp80) REVERT: D 931 THR cc_start: 0.5404 (p) cc_final: 0.5203 (m) REVERT: D 1151 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7877 (pttt) REVERT: D 1214 PRO cc_start: 0.5123 (Cg_endo) cc_final: 0.4609 (Cg_exo) REVERT: D 1262 ARG cc_start: 0.7626 (ttp-170) cc_final: 0.7205 (ptm160) REVERT: D 1345 ARG cc_start: 0.7426 (ptm160) cc_final: 0.6914 (mmm-85) REVERT: D 1347 LEU cc_start: 0.7608 (mm) cc_final: 0.7269 (mm) REVERT: G 61 TYR cc_start: 0.8071 (t80) cc_final: 0.7821 (t80) REVERT: G 107 ASN cc_start: 0.6588 (t0) cc_final: 0.6010 (m110) outliers start: 91 outliers final: 59 residues processed: 416 average time/residue: 0.4158 time to fit residues: 268.9350 Evaluate side-chains 352 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 289 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 77 ASP 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 48 LEU Chi-restraints excluded: chain B residue 132 HIS 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 90 VAL Chi-restraints excluded: chain C residue 142 GLU 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 563 THR Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 674 ASP Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1023 HIS 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 1161 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 1279 GLU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1325 VAL 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 569 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1353 VAL 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 Chi-restraints excluded: chain G residue 74 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 307 optimal weight: 0.6980 chunk 332 optimal weight: 9.9990 chunk 273 optimal weight: 2.9990 chunk 304 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS G 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28042 Z= 0.309 Angle : 0.708 11.955 38140 Z= 0.368 Chirality : 0.046 0.192 4349 Planarity : 0.005 0.074 4796 Dihedral : 13.677 138.405 4363 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.12 % Favored : 94.73 % Rotamer: Outliers : 3.19 % Allowed : 13.59 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3341 helix: 0.09 (0.15), residues: 1230 sheet: -1.05 (0.26), residues: 376 loop : -1.89 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 36 HIS 0.009 0.002 HIS B 37 PHE 0.021 0.002 PHE G 91 TYR 0.018 0.002 TYR C1213 ARG 0.018 0.001 ARG D1140 *********************** 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 442 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 351 time to evaluate : 3.067 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: A 93 GLN cc_start: 0.8063 (pm20) cc_final: 0.7449 (pp30) REVERT: A 199 ASP cc_start: 0.7901 (m-30) cc_final: 0.7296 (m-30) REVERT: B 35 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.6398 (t80) REVERT: B 152 TYR cc_start: 0.7972 (t80) cc_final: 0.7709 (t80) REVERT: C 22 LEU cc_start: 0.8530 (tp) cc_final: 0.8297 (tt) REVERT: C 85 CYS cc_start: 0.7696 (m) cc_final: 0.7358 (m) REVERT: C 86 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6229 (mt0) REVERT: C 124 MET cc_start: 0.7282 (ptp) cc_final: 0.7053 (ptp) REVERT: C 369 MET cc_start: 0.7091 (ppp) cc_final: 0.6592 (ppp) REVERT: C 419 ILE cc_start: 0.7595 (pt) cc_final: 0.7200 (mt) REVERT: C 478 ARG cc_start: 0.7334 (mmt-90) cc_final: 0.7059 (tpt-90) REVERT: C 479 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8101 (mp) REVERT: C 490 GLN cc_start: 0.7997 (pp30) cc_final: 0.7639 (pp30) REVERT: C 512 SER cc_start: 0.8533 (t) cc_final: 0.8251 (t) REVERT: C 524 ILE cc_start: 0.8054 (tt) cc_final: 0.7746 (tt) REVERT: C 592 ARG cc_start: 0.8059 (mtp180) cc_final: 0.6903 (mtp85) REVERT: C 672 GLU cc_start: 0.6244 (pt0) cc_final: 0.5552 (pm20) REVERT: C 704 MET cc_start: 0.6142 (mmp) cc_final: 0.5524 (mmm) REVERT: C 775 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7384 (tt0) REVERT: C 790 ASP cc_start: 0.7499 (t0) cc_final: 0.7073 (t70) REVERT: C 814 ASP cc_start: 0.6431 (m-30) cc_final: 0.5526 (m-30) REVERT: C 830 THR cc_start: 0.8000 (m) cc_final: 0.7679 (p) REVERT: C 943 LYS cc_start: 0.7780 (ttpt) cc_final: 0.7553 (tmtt) REVERT: C 1089 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6334 (pm20) REVERT: C 1174 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6657 (tm-30) REVERT: C 1213 TYR cc_start: 0.6936 (m-80) cc_final: 0.6624 (m-80) REVERT: C 1222 GLU cc_start: 0.6781 (tp30) cc_final: 0.5678 (mt-10) REVERT: C 1233 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6820 (mp) REVERT: C 1269 ARG cc_start: 0.6265 (ttp80) cc_final: 0.5360 (ttm-80) REVERT: C 1279 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.5663 (mt-10) REVERT: C 1319 MET cc_start: 0.3330 (mmt) cc_final: 0.2864 (mmm) REVERT: D 29 MET cc_start: 0.8398 (ppp) cc_final: 0.8057 (ppp) REVERT: D 102 MET cc_start: 0.7386 (ppp) cc_final: 0.6840 (ppp) REVERT: D 166 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8499 (pp) REVERT: D 180 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5530 (tpt) REVERT: D 198 CYS cc_start: 0.8708 (m) cc_final: 0.8390 (p) REVERT: D 236 TRP cc_start: 0.8389 (m-10) cc_final: 0.8079 (m-10) REVERT: D 278 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7078 (mtm-85) REVERT: D 297 ARG cc_start: 0.6348 (ttm170) cc_final: 0.6001 (tpt-90) REVERT: D 337 ARG cc_start: 0.4209 (tpt170) cc_final: 0.3482 (mpt-90) REVERT: D 400 MET cc_start: 0.5692 (tpt) cc_final: 0.5468 (mmm) REVERT: D 484 MET cc_start: 0.7666 (mmm) cc_final: 0.7430 (mmm) REVERT: D 594 GLN cc_start: 0.5662 (OUTLIER) cc_final: 0.4957 (pm20) REVERT: D 623 GLN cc_start: 0.5467 (mm-40) cc_final: 0.5064 (mt0) REVERT: D 724 MET cc_start: 0.7074 (mtm) cc_final: 0.6741 (mtm) REVERT: D 738 ARG cc_start: 0.5971 (ttt180) cc_final: 0.5368 (ttp-170) REVERT: D 751 ASP cc_start: 0.6979 (p0) cc_final: 0.6651 (p0) REVERT: D 780 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.7793 (ttp80) REVERT: D 874 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: D 881 LYS cc_start: 0.5333 (tttm) cc_final: 0.5099 (tptt) REVERT: D 981 GLU cc_start: 0.6867 (tt0) cc_final: 0.6412 (tp30) REVERT: D 1244 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8191 (mm-40) REVERT: D 1247 LYS cc_start: 0.7515 (pttm) cc_final: 0.6881 (tptp) REVERT: D 1255 VAL cc_start: 0.3823 (OUTLIER) cc_final: 0.3623 (m) REVERT: D 1347 LEU cc_start: 0.7600 (mm) cc_final: 0.7278 (mm) REVERT: D 1368 ASP cc_start: 0.7577 (t0) cc_final: 0.7253 (t0) REVERT: G 61 TYR cc_start: 0.7971 (t80) cc_final: 0.7728 (t80) REVERT: G 107 ASN cc_start: 0.6635 (t0) cc_final: 0.6304 (t0) outliers start: 91 outliers final: 56 residues processed: 410 average time/residue: 0.4002 time to fit residues: 259.2222 Evaluate side-chains 372 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 306 time to evaluate : 3.152 ------------------------------------------------------------------------------- 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 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 188 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 86 GLN 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 479 LEU Chi-restraints excluded: chain C residue 538 LEU 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 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 930 ASP 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 1080 ASN 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 1199 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1289 GLU 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 180 MET Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 279 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 545 HIS Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1255 VAL 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 54 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 7.9990 chunk 231 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 chunk 326 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 292 optimal weight: 40.0000 chunk 88 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 526 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** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 28042 Z= 0.478 Angle : 0.786 11.178 38140 Z= 0.410 Chirality : 0.048 0.267 4349 Planarity : 0.006 0.079 4796 Dihedral : 13.851 140.095 4363 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.97 % Favored : 92.94 % Rotamer: Outliers : 4.45 % Allowed : 15.38 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3341 helix: -0.09 (0.15), residues: 1214 sheet: -1.06 (0.26), residues: 371 loop : -2.01 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 36 HIS 0.028 0.002 HIS C 554 PHE 0.021 0.003 PHE C 38 TYR 0.022 0.002 TYR C1213 ARG 0.010 0.001 ARG D1140 *********************** 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 450 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 323 time to evaluate : 3.369 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: 0.8103 (pm20) cc_final: 0.7673 (mp-120) REVERT: A 199 ASP cc_start: 0.8151 (m-30) cc_final: 0.7556 (m-30) REVERT: B 35 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6368 (t80) REVERT: B 152 TYR cc_start: 0.8176 (t80) cc_final: 0.7902 (t80) REVERT: B 200 LYS cc_start: 0.5113 (mttm) cc_final: 0.4898 (mtpp) REVERT: C 22 LEU cc_start: 0.8664 (tp) cc_final: 0.8424 (tt) REVERT: C 85 CYS cc_start: 0.7779 (m) cc_final: 0.7415 (m) REVERT: C 86 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6397 (mt0) REVERT: C 369 MET cc_start: 0.7161 (ppp) cc_final: 0.6655 (ppp) REVERT: C 419 ILE cc_start: 0.7537 (pt) cc_final: 0.7149 (mt) REVERT: C 478 ARG cc_start: 0.7443 (mmt-90) cc_final: 0.7032 (tpt-90) REVERT: C 512 SER cc_start: 0.8715 (t) cc_final: 0.8458 (t) REVERT: C 524 ILE cc_start: 0.8212 (tt) cc_final: 0.7894 (tt) REVERT: C 592 ARG cc_start: 0.8094 (mtp180) cc_final: 0.6885 (mtp85) REVERT: C 672 GLU cc_start: 0.6196 (pt0) cc_final: 0.5528 (pm20) REVERT: C 790 ASP cc_start: 0.7527 (t0) cc_final: 0.7118 (t70) REVERT: C 814 ASP cc_start: 0.6716 (OUTLIER) cc_final: 0.5702 (m-30) REVERT: C 1080 ASN cc_start: 0.7839 (OUTLIER) cc_final: 0.7582 (t0) REVERT: C 1089 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6409 (pm20) REVERT: C 1171 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6613 (ttp-110) REVERT: C 1174 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6911 (tm-30) REVERT: C 1244 HIS cc_start: 0.6184 (p-80) cc_final: 0.5932 (p-80) REVERT: C 1279 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.5793 (mt-10) REVERT: C 1290 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.6050 (mtt) REVERT: C 1319 MET cc_start: 0.3548 (mmt) cc_final: 0.3132 (mmm) REVERT: D 29 MET cc_start: 0.8372 (ppp) cc_final: 0.8034 (ppp) REVERT: D 102 MET cc_start: 0.7383 (ppp) cc_final: 0.6879 (ppp) REVERT: D 166 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8524 (pp) REVERT: D 180 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.6055 (mmp) REVERT: D 198 CYS cc_start: 0.8747 (m) cc_final: 0.8408 (p) REVERT: D 236 TRP cc_start: 0.8413 (m-10) cc_final: 0.8077 (m-10) REVERT: D 278 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7124 (mtp180) REVERT: D 297 ARG cc_start: 0.6274 (ttm170) cc_final: 0.5979 (tpt-90) REVERT: D 330 MET cc_start: 0.5208 (tmm) cc_final: 0.4887 (tmm) REVERT: D 337 ARG cc_start: 0.4440 (tpt170) cc_final: 0.3559 (mpt-90) REVERT: D 466 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.6344 (mpt) REVERT: D 484 MET cc_start: 0.8084 (mmm) cc_final: 0.7529 (mmm) REVERT: D 594 GLN cc_start: 0.5772 (OUTLIER) cc_final: 0.5204 (pm20) REVERT: D 605 LEU cc_start: 0.4738 (OUTLIER) cc_final: 0.4337 (mt) REVERT: D 724 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.5689 (mtm) REVERT: D 751 ASP cc_start: 0.6909 (p0) cc_final: 0.6646 (p0) REVERT: D 776 THR cc_start: 0.6521 (OUTLIER) cc_final: 0.6294 (m) REVERT: D 780 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.7879 (tpp80) REVERT: D 981 GLU cc_start: 0.6745 (tt0) cc_final: 0.6265 (tp30) REVERT: D 1236 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8172 (mm-30) REVERT: D 1286 LYS cc_start: 0.7344 (mmtm) cc_final: 0.6866 (mtpt) REVERT: D 1347 LEU cc_start: 0.7748 (mm) cc_final: 0.7437 (mm) REVERT: D 1368 ASP cc_start: 0.7670 (t0) cc_final: 0.7369 (t70) REVERT: E 17 PHE cc_start: 0.5867 (m-80) cc_final: 0.5474 (m-80) REVERT: G 61 TYR cc_start: 0.7927 (t80) cc_final: 0.7688 (t80) REVERT: G 77 MET cc_start: 0.6335 (ptt) cc_final: 0.5864 (ptt) REVERT: G 107 ASN cc_start: 0.6597 (t0) cc_final: 0.6271 (t0) REVERT: G 110 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8934 (mm-30) outliers start: 127 outliers final: 87 residues processed: 408 average time/residue: 0.4102 time to fit residues: 266.3721 Evaluate side-chains 393 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 292 time to evaluate : 3.039 ------------------------------------------------------------------------------- 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 92 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 146 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 B residue 210 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 538 LEU 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 811 ASN Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1080 ASN 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 1171 ARG 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 1325 VAL 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 180 MET Chi-restraints excluded: chain D residue 211 GLU 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 408 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 453 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 594 GLN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 618 VAL 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 776 THR Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1261 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 54 ILE 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 Chi-restraints excluded: chain G residue 109 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 278 optimal weight: 30.0000 chunk 225 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 293 optimal weight: 40.0000 chunk 82 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** 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** C1008 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 ASN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28042 Z= 0.284 Angle : 0.675 10.414 38140 Z= 0.352 Chirality : 0.045 0.205 4349 Planarity : 0.005 0.066 4796 Dihedral : 13.720 137.795 4363 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.16 % Rotamer: Outliers : 3.50 % Allowed : 17.34 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3341 helix: 0.17 (0.15), residues: 1218 sheet: -1.09 (0.25), residues: 390 loop : -1.89 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 36 HIS 0.015 0.001 HIS C 554 PHE 0.019 0.002 PHE D 35 TYR 0.037 0.002 TYR D 589 ARG 0.010 0.001 ARG C 996 *********************** 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 fitting. rotamer outliers: 100 poor density : 328 time to evaluate : 3.299 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: A 93 GLN cc_start: 0.8072 (pm20) cc_final: 0.7541 (mp-120) REVERT: A 199 ASP cc_start: 0.7962 (m-30) cc_final: 0.7361 (m-30) REVERT: B 29 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7182 (tm-30) REVERT: B 35 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6265 (t80) REVERT: B 152 TYR cc_start: 0.8061 (t80) cc_final: 0.7832 (t80) REVERT: B 200 LYS cc_start: 0.4975 (mttm) cc_final: 0.4747 (mtpp) REVERT: C 50 GLU cc_start: 0.7496 (tp30) cc_final: 0.6978 (tm-30) REVERT: C 85 CYS cc_start: 0.7678 (m) cc_final: 0.7353 (m) REVERT: C 86 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6205 (mt0) REVERT: C 124 MET cc_start: 0.6856 (ptp) cc_final: 0.6620 (ptp) REVERT: C 185 ASP cc_start: 0.6562 (m-30) cc_final: 0.5842 (m-30) REVERT: C 216 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7705 (p) REVERT: C 369 MET cc_start: 0.7125 (ppp) cc_final: 0.6604 (ppp) REVERT: C 419 ILE cc_start: 0.7525 (pt) cc_final: 0.7132 (mt) REVERT: C 478 ARG cc_start: 0.7328 (mmt-90) cc_final: 0.7009 (tpt-90) REVERT: C 524 ILE cc_start: 0.8087 (tt) cc_final: 0.7736 (tt) REVERT: C 592 ARG cc_start: 0.8152 (mtp180) cc_final: 0.7679 (mtp85) REVERT: C 672 GLU cc_start: 0.6133 (pt0) cc_final: 0.5539 (pm20) REVERT: C 775 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7296 (tt0) REVERT: C 790 ASP cc_start: 0.7498 (t0) cc_final: 0.7111 (t70) REVERT: C 814 ASP cc_start: 0.6537 (m-30) cc_final: 0.5530 (m-30) REVERT: C 830 THR cc_start: 0.8011 (m) cc_final: 0.7664 (p) REVERT: C 1034 ARG cc_start: 0.7964 (mmp80) cc_final: 0.7745 (mmt-90) REVERT: C 1080 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.7330 (t0) REVERT: C 1089 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6259 (pm20) REVERT: C 1171 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6450 (ttp-110) REVERT: C 1174 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6857 (tm-30) REVERT: C 1222 GLU cc_start: 0.6684 (tp30) cc_final: 0.5574 (mt-10) REVERT: C 1244 HIS cc_start: 0.6113 (p-80) cc_final: 0.5796 (p-80) REVERT: C 1279 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5858 (mt-10) REVERT: C 1319 MET cc_start: 0.3474 (mmt) cc_final: 0.3065 (mmm) REVERT: D 29 MET cc_start: 0.8364 (ppp) cc_final: 0.8048 (ppp) REVERT: D 102 MET cc_start: 0.7368 (ppp) cc_final: 0.6848 (ppp) REVERT: D 166 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8487 (pp) REVERT: D 180 MET cc_start: 0.5952 (OUTLIER) cc_final: 0.5716 (mmp) REVERT: D 195 GLU cc_start: 0.8536 (mp0) cc_final: 0.8212 (mp0) REVERT: D 198 CYS cc_start: 0.8754 (m) cc_final: 0.8416 (p) REVERT: D 236 TRP cc_start: 0.8421 (m-10) cc_final: 0.8095 (m-10) REVERT: D 278 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7152 (mtp180) REVERT: D 297 ARG cc_start: 0.6278 (ttm170) cc_final: 0.5957 (tpt-90) REVERT: D 330 MET cc_start: 0.5163 (tmm) cc_final: 0.4806 (tmm) REVERT: D 337 ARG cc_start: 0.4398 (tpt170) cc_final: 0.3566 (mmt90) REVERT: D 484 MET cc_start: 0.7979 (mmm) cc_final: 0.7421 (mmm) REVERT: D 594 GLN cc_start: 0.5693 (OUTLIER) cc_final: 0.5180 (pm20) REVERT: D 719 PHE cc_start: 0.5386 (m-80) cc_final: 0.5131 (m-80) REVERT: D 724 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.5600 (mtm) REVERT: D 751 ASP cc_start: 0.6869 (p0) cc_final: 0.6616 (p0) REVERT: D 780 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7872 (tpp80) REVERT: D 981 GLU cc_start: 0.6756 (tt0) cc_final: 0.6276 (tp30) REVERT: D 1286 LYS cc_start: 0.7304 (mmtm) cc_final: 0.6828 (mtpt) REVERT: D 1347 LEU cc_start: 0.7630 (mm) cc_final: 0.7247 (mm) REVERT: D 1349 GLU cc_start: 0.7402 (mp0) cc_final: 0.6935 (mp0) REVERT: D 1368 ASP cc_start: 0.7660 (t0) cc_final: 0.7344 (t70) REVERT: G 29 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7018 (mm-40) REVERT: G 98 GLU cc_start: 0.4882 (tm-30) cc_final: 0.4425 (mp0) REVERT: G 107 ASN cc_start: 0.6534 (t0) cc_final: 0.6213 (t0) REVERT: G 110 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8930 (mm-30) REVERT: G 129 ARG cc_start: 0.4537 (OUTLIER) cc_final: 0.4248 (ppt170) outliers start: 100 outliers final: 68 residues processed: 395 average time/residue: 0.3875 time to fit residues: 243.1188 Evaluate side-chains 372 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 293 time to evaluate : 2.955 ------------------------------------------------------------------------------- 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 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 47 TYR Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 VAL 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 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 826 ASP Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1080 ASN 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 1171 ARG 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 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 180 MET 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 453 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 574 VAL Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1152 GLU Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1261 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 54 ILE 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 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 109 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 327 optimal weight: 7.9990 chunk 271 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 28042 Z= 0.444 Angle : 0.754 11.261 38140 Z= 0.392 Chirality : 0.047 0.267 4349 Planarity : 0.006 0.074 4796 Dihedral : 13.846 138.355 4363 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.12 % Favored : 92.73 % Rotamer: Outliers : 5.22 % Allowed : 16.92 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3341 helix: -0.03 (0.15), residues: 1218 sheet: -1.02 (0.26), residues: 366 loop : -1.98 (0.13), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 73 HIS 0.020 0.002 HIS C 554 PHE 0.022 0.002 PHE E 17 TYR 0.021 0.002 TYR D 589 ARG 0.008 0.001 ARG C 678 *********************** 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 453 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 304 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8063 (pm20) cc_final: 0.7550 (mp-120) REVERT: A 199 ASP cc_start: 0.8137 (m-30) cc_final: 0.7527 (m-30) REVERT: B 35 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.6340 (t80) REVERT: B 200 LYS cc_start: 0.5101 (mttm) cc_final: 0.4900 (mtpt) REVERT: C 50 GLU cc_start: 0.7567 (tp30) cc_final: 0.7244 (tm-30) REVERT: C 54 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7076 (ttm-80) REVERT: C 86 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6393 (mt0) REVERT: C 185 ASP cc_start: 0.6447 (m-30) cc_final: 0.5812 (m-30) REVERT: C 216 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7582 (p) REVERT: C 369 MET cc_start: 0.7184 (ppp) cc_final: 0.6663 (ppp) REVERT: C 419 ILE cc_start: 0.7476 (pt) cc_final: 0.7112 (mt) REVERT: C 446 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: C 478 ARG cc_start: 0.7511 (mmt-90) cc_final: 0.7117 (tpt-90) REVERT: C 524 ILE cc_start: 0.8203 (tt) cc_final: 0.7864 (tt) REVERT: C 592 ARG cc_start: 0.8232 (mtp180) cc_final: 0.7137 (mtp85) REVERT: C 672 GLU cc_start: 0.6099 (pt0) cc_final: 0.5553 (pm20) REVERT: C 790 ASP cc_start: 0.7491 (t0) cc_final: 0.7104 (t70) REVERT: C 814 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.5610 (m-30) REVERT: C 841 ARG cc_start: 0.7138 (mmm-85) cc_final: 0.6602 (tpp-160) REVERT: C 1080 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7547 (t0) REVERT: C 1089 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6388 (pm20) REVERT: C 1171 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6638 (ttp-110) REVERT: C 1174 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6926 (tm-30) REVERT: C 1220 GLN cc_start: 0.7659 (pm20) cc_final: 0.6879 (pt0) REVERT: C 1279 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.5980 (mt-10) REVERT: C 1290 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.6019 (mtt) REVERT: C 1319 MET cc_start: 0.3580 (OUTLIER) cc_final: 0.3183 (mmm) REVERT: D 29 MET cc_start: 0.8339 (ppp) cc_final: 0.8058 (ppp) REVERT: D 102 MET cc_start: 0.7319 (ppp) cc_final: 0.6843 (ppp) REVERT: D 166 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8497 (pp) REVERT: D 180 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5816 (mmp) REVERT: D 198 CYS cc_start: 0.8733 (m) cc_final: 0.8348 (p) REVERT: D 236 TRP cc_start: 0.8447 (m-10) cc_final: 0.8098 (m-10) REVERT: D 278 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7139 (mtp180) REVERT: D 297 ARG cc_start: 0.6241 (ttm170) cc_final: 0.5949 (tpt-90) REVERT: D 337 ARG cc_start: 0.4477 (tpt170) cc_final: 0.3598 (mmt90) REVERT: D 466 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.6260 (mpt) REVERT: D 484 MET cc_start: 0.7968 (mmm) cc_final: 0.7356 (mmm) REVERT: D 594 GLN cc_start: 0.5671 (OUTLIER) cc_final: 0.5165 (pm20) REVERT: D 605 LEU cc_start: 0.4691 (OUTLIER) cc_final: 0.4282 (mt) REVERT: D 751 ASP cc_start: 0.6961 (p0) cc_final: 0.6711 (p0) REVERT: D 981 GLU cc_start: 0.6736 (tt0) cc_final: 0.6281 (tp30) REVERT: D 1218 HIS cc_start: 0.7525 (m90) cc_final: 0.7257 (m90) REVERT: D 1286 LYS cc_start: 0.7401 (mmtm) cc_final: 0.6883 (mtpt) REVERT: D 1347 LEU cc_start: 0.7676 (mm) cc_final: 0.7223 (mm) REVERT: D 1349 GLU cc_start: 0.7517 (mp0) cc_final: 0.7014 (mp0) REVERT: D 1368 ASP cc_start: 0.7684 (t0) cc_final: 0.7307 (t0) REVERT: E 30 MET cc_start: 0.5862 (OUTLIER) cc_final: 0.4839 (pmm) REVERT: G 29 GLN cc_start: 0.7903 (mm-40) cc_final: 0.6990 (mm-40) REVERT: G 77 MET cc_start: 0.6257 (ptt) cc_final: 0.6010 (ptt) REVERT: G 78 ARG cc_start: 0.8591 (ppt170) cc_final: 0.8218 (ttp80) REVERT: G 91 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6691 (t80) REVERT: G 98 GLU cc_start: 0.4975 (OUTLIER) cc_final: 0.4306 (mp0) REVERT: G 129 ARG cc_start: 0.4546 (OUTLIER) cc_final: 0.4246 (ppt170) outliers start: 149 outliers final: 101 residues processed: 410 average time/residue: 0.3978 time to fit residues: 258.1191 Evaluate side-chains 405 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 284 time to evaluate : 3.118 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 222 THR 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 130 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 ARG 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 11 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 91 THR 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 492 MET Chi-restraints excluded: chain C residue 525 THR 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 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1080 ASN 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 1171 ARG Chi-restraints excluded: chain C residue 1180 MET 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 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 180 MET 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 415 VAL Chi-restraints excluded: chain D residue 453 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 605 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 698 MET 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 743 MET Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1260 MET 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 54 ILE 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 91 PHE Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 109 ASP 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 315 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 275 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 198 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 28042 Z= 0.516 Angle : 0.812 12.673 38140 Z= 0.423 Chirality : 0.049 0.290 4349 Planarity : 0.006 0.070 4796 Dihedral : 13.980 137.941 4363 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.57 % Favored : 92.25 % Rotamer: Outliers : 5.43 % Allowed : 17.44 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.14), residues: 3341 helix: -0.24 (0.14), residues: 1217 sheet: -1.08 (0.26), residues: 361 loop : -2.11 (0.13), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP G 73 HIS 0.019 0.002 HIS C 554 PHE 0.024 0.003 PHE D 35 TYR 0.022 0.002 TYR C1213 ARG 0.011 0.001 ARG G 67 *********************** 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 463 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 308 time to evaluate : 3.058 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: A 93 GLN cc_start: 0.8052 (pm20) cc_final: 0.7559 (mp-120) REVERT: A 199 ASP cc_start: 0.8186 (m-30) cc_final: 0.7594 (m-30) REVERT: B 35 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.6332 (t80) REVERT: B 200 LYS cc_start: 0.5161 (mttm) cc_final: 0.4921 (mtmt) REVERT: C 50 GLU cc_start: 0.7591 (tp30) cc_final: 0.6914 (tm-30) REVERT: C 54 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6231 (mtt90) REVERT: C 86 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6474 (mt0) REVERT: C 216 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7581 (p) REVERT: C 369 MET cc_start: 0.7154 (ppp) cc_final: 0.6619 (ppp) REVERT: C 419 ILE cc_start: 0.7459 (pt) cc_final: 0.7127 (mt) REVERT: C 478 ARG cc_start: 0.7364 (mmt-90) cc_final: 0.7060 (tpt-90) REVERT: C 592 ARG cc_start: 0.8265 (mtp180) cc_final: 0.7911 (mtp180) REVERT: C 672 GLU cc_start: 0.5961 (pt0) cc_final: 0.5462 (pm20) REVERT: C 790 ASP cc_start: 0.7468 (t0) cc_final: 0.7063 (t70) REVERT: C 814 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.5578 (m-30) REVERT: C 829 THR cc_start: 0.8713 (m) cc_final: 0.8189 (p) REVERT: C 841 ARG cc_start: 0.7192 (mmm-85) cc_final: 0.6589 (tpp-160) REVERT: C 1080 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7755 (t0) REVERT: C 1089 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6398 (pm20) REVERT: C 1171 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6610 (ttp-110) REVERT: C 1174 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7021 (tm-30) REVERT: C 1220 GLN cc_start: 0.7650 (pm20) cc_final: 0.6977 (pt0) REVERT: C 1244 HIS cc_start: 0.6437 (p-80) cc_final: 0.6235 (p-80) REVERT: C 1279 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6123 (mt-10) REVERT: C 1290 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5991 (mtt) REVERT: C 1319 MET cc_start: 0.3583 (OUTLIER) cc_final: 0.2753 (mpp) REVERT: D 29 MET cc_start: 0.8328 (ppp) cc_final: 0.8073 (ppp) REVERT: D 166 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8527 (pp) REVERT: D 180 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5991 (mmp) REVERT: D 198 CYS cc_start: 0.8852 (m) cc_final: 0.8480 (p) REVERT: D 236 TRP cc_start: 0.8481 (m-10) cc_final: 0.8127 (m-10) REVERT: D 278 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7066 (mtp180) REVERT: D 282 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.5231 (mp) REVERT: D 337 ARG cc_start: 0.4693 (tpt170) cc_final: 0.3806 (mpt-90) REVERT: D 466 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.6262 (mpt) REVERT: D 594 GLN cc_start: 0.5787 (OUTLIER) cc_final: 0.5211 (pm20) REVERT: D 605 LEU cc_start: 0.4746 (OUTLIER) cc_final: 0.4324 (mt) REVERT: D 751 ASP cc_start: 0.7008 (p0) cc_final: 0.6775 (p0) REVERT: D 913 GLU cc_start: 0.6568 (mp0) cc_final: 0.6184 (mp0) REVERT: D 981 GLU cc_start: 0.6717 (tt0) cc_final: 0.6248 (tp30) REVERT: D 1140 ARG cc_start: 0.6555 (tpt170) cc_final: 0.6321 (tpt170) REVERT: D 1146 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7986 (mm-30) REVERT: D 1218 HIS cc_start: 0.7620 (m90) cc_final: 0.7312 (m90) REVERT: D 1286 LYS cc_start: 0.7444 (mmtm) cc_final: 0.6926 (mtpt) REVERT: D 1347 LEU cc_start: 0.7798 (mm) cc_final: 0.7337 (mm) REVERT: D 1349 GLU cc_start: 0.7474 (mp0) cc_final: 0.6986 (mp0) REVERT: D 1368 ASP cc_start: 0.7758 (t0) cc_final: 0.7382 (t0) REVERT: E 30 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.5045 (pmm) REVERT: G 29 GLN cc_start: 0.7832 (mm-40) cc_final: 0.6836 (mm-40) REVERT: G 78 ARG cc_start: 0.8560 (ppt170) cc_final: 0.8321 (ttp80) REVERT: G 91 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6745 (t80) REVERT: G 129 ARG cc_start: 0.4546 (OUTLIER) cc_final: 0.4280 (ppt170) outliers start: 155 outliers final: 113 residues processed: 416 average time/residue: 0.3912 time to fit residues: 259.3460 Evaluate side-chains 420 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 288 time to evaluate : 3.026 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 222 THR 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 130 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 91 THR 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 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 525 THR 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 668 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 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 817 LEU 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 971 LEU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1080 ASN 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 1171 ARG Chi-restraints excluded: chain C residue 1180 MET 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 1243 MET 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 1319 MET Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 124 ILE 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 180 MET Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 282 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 415 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 466 MET 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 563 LEU 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 604 MET Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1291 GLU 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 47 THR Chi-restraints excluded: chain E residue 54 ILE 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 74 ILE Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain G residue 109 ASP 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 201 optimal weight: 0.0170 chunk 130 optimal weight: 0.6980 chunk 194 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 221 optimal weight: 0.0970 chunk 161 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** 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** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS D 762 ASN E 43 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28042 Z= 0.207 Angle : 0.664 13.236 38140 Z= 0.343 Chirality : 0.045 0.248 4349 Planarity : 0.005 0.065 4796 Dihedral : 13.674 134.950 4363 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 3.26 % Allowed : 20.07 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3341 helix: 0.22 (0.15), residues: 1223 sheet: -0.79 (0.26), residues: 381 loop : -1.81 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP G 73 HIS 0.009 0.001 HIS C 554 PHE 0.019 0.002 PHE A 231 TYR 0.013 0.001 TYR D 589 ARG 0.013 0.001 ARG G 67 *********************** 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 424 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 331 time to evaluate : 3.227 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: 0.8058 (pm20) cc_final: 0.7517 (mp-120) REVERT: A 199 ASP cc_start: 0.7936 (m-30) cc_final: 0.7334 (m-30) REVERT: B 29 GLU cc_start: 0.7317 (tm-30) cc_final: 0.7114 (tm-30) REVERT: B 35 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6260 (t80) REVERT: C 23 ASP cc_start: 0.8291 (p0) cc_final: 0.7700 (m-30) REVERT: C 50 GLU cc_start: 0.7609 (tp30) cc_final: 0.7147 (tm-30) REVERT: C 73 TYR cc_start: 0.7782 (p90) cc_final: 0.7455 (p90) REVERT: C 216 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7405 (p) REVERT: C 369 MET cc_start: 0.7104 (ppp) cc_final: 0.6582 (ppp) REVERT: C 419 ILE cc_start: 0.7473 (pt) cc_final: 0.7097 (mt) REVERT: C 478 ARG cc_start: 0.7363 (mmt-90) cc_final: 0.7068 (tpt-90) REVERT: C 524 ILE cc_start: 0.8005 (tt) cc_final: 0.7778 (tt) REVERT: C 592 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7027 (mtp85) REVERT: C 615 VAL cc_start: 0.6753 (OUTLIER) cc_final: 0.6485 (m) REVERT: C 775 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7347 (tt0) REVERT: C 790 ASP cc_start: 0.7529 (t0) cc_final: 0.7178 (t70) REVERT: C 814 ASP cc_start: 0.6128 (OUTLIER) cc_final: 0.5402 (m-30) REVERT: C 829 THR cc_start: 0.8692 (m) cc_final: 0.8408 (p) REVERT: C 830 THR cc_start: 0.8046 (m) cc_final: 0.7700 (p) REVERT: C 844 LYS cc_start: 0.7744 (pttm) cc_final: 0.7461 (mttp) REVERT: C 1080 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6752 (t0) REVERT: C 1089 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6255 (pm20) REVERT: C 1174 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6763 (tm-30) REVERT: C 1213 TYR cc_start: 0.6693 (m-80) cc_final: 0.6416 (m-80) REVERT: C 1220 GLN cc_start: 0.7444 (pm20) cc_final: 0.6986 (pt0) REVERT: C 1244 HIS cc_start: 0.6188 (p-80) cc_final: 0.5873 (p90) REVERT: C 1279 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.5804 (mt-10) REVERT: C 1290 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.5913 (mtt) REVERT: C 1319 MET cc_start: 0.3488 (OUTLIER) cc_final: 0.2641 (mpp) REVERT: D 29 MET cc_start: 0.8296 (ppp) cc_final: 0.8062 (ppp) REVERT: D 102 MET cc_start: 0.7165 (ppp) cc_final: 0.6584 (ppp) REVERT: D 166 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8532 (pp) REVERT: D 195 GLU cc_start: 0.8555 (mp0) cc_final: 0.8276 (mp0) REVERT: D 198 CYS cc_start: 0.8719 (m) cc_final: 0.8299 (p) REVERT: D 236 TRP cc_start: 0.8474 (m-10) cc_final: 0.8178 (m-10) REVERT: D 278 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7123 (mtp180) REVERT: D 337 ARG cc_start: 0.4208 (tpt170) cc_final: 0.3569 (mmt90) REVERT: D 340 GLN cc_start: 0.4510 (mm-40) cc_final: 0.4288 (mm-40) REVERT: D 458 ASN cc_start: 0.7085 (t0) cc_final: 0.6804 (t0) REVERT: D 484 MET cc_start: 0.7430 (mmm) cc_final: 0.6708 (mmt) REVERT: D 594 GLN cc_start: 0.5750 (OUTLIER) cc_final: 0.5228 (pm20) REVERT: D 644 MET cc_start: 0.6841 (mtt) cc_final: 0.6283 (mtt) REVERT: D 679 TYR cc_start: 0.3136 (t80) cc_final: 0.2931 (t80) REVERT: D 698 MET cc_start: 0.4827 (OUTLIER) cc_final: 0.3734 (mmt) REVERT: D 712 GLN cc_start: 0.8164 (pm20) cc_final: 0.7365 (pm20) REVERT: D 724 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.5539 (mtm) REVERT: D 738 ARG cc_start: 0.6335 (OUTLIER) cc_final: 0.5430 (ttp80) REVERT: D 751 ASP cc_start: 0.7049 (p0) cc_final: 0.6796 (p0) REVERT: D 780 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7951 (tpp80) REVERT: D 981 GLU cc_start: 0.6828 (tt0) cc_final: 0.6374 (tp30) REVERT: D 1146 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8106 (mm-30) REVERT: D 1286 LYS cc_start: 0.7344 (mmtm) cc_final: 0.6802 (mtpt) REVERT: D 1347 LEU cc_start: 0.7601 (mm) cc_final: 0.7326 (mm) REVERT: D 1349 GLU cc_start: 0.7307 (mp0) cc_final: 0.6849 (mp0) REVERT: D 1368 ASP cc_start: 0.7701 (t0) cc_final: 0.7369 (t70) REVERT: G 29 GLN cc_start: 0.7866 (mm-40) cc_final: 0.6711 (mm-40) REVERT: G 66 ASP cc_start: 0.7017 (t0) cc_final: 0.6639 (m-30) REVERT: G 77 MET cc_start: 0.5911 (ptt) cc_final: 0.5694 (ptt) REVERT: G 78 ARG cc_start: 0.8593 (ppt170) cc_final: 0.8335 (ttp80) REVERT: G 98 GLU cc_start: 0.4912 (OUTLIER) cc_final: 0.4579 (mp0) REVERT: G 129 ARG cc_start: 0.4469 (OUTLIER) cc_final: 0.4122 (ppt170) outliers start: 93 outliers final: 59 residues processed: 392 average time/residue: 0.4060 time to fit residues: 252.3433 Evaluate side-chains 368 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 294 time to evaluate : 3.003 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 547 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 615 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1161 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 1319 MET Chi-restraints excluded: chain C residue 1337 ILE 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 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 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 5 THR 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 71 GLU 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 98 GLU 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 296 optimal weight: 6.9990 chunk 312 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 chunk 303 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 238 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 287 optimal weight: 0.0170 chunk 302 optimal weight: 1.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN ** C 526 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** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28042 Z= 0.254 Angle : 0.673 12.293 38140 Z= 0.347 Chirality : 0.045 0.286 4349 Planarity : 0.005 0.065 4796 Dihedral : 13.660 136.191 4363 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.78 % Favored : 94.04 % Rotamer: Outliers : 3.26 % Allowed : 20.28 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 3341 helix: 0.20 (0.15), residues: 1234 sheet: -0.77 (0.26), residues: 386 loop : -1.79 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.004 TRP G 73 HIS 0.012 0.001 HIS C 554 PHE 0.015 0.002 PHE D 176 TYR 0.017 0.001 TYR C1053 ARG 0.011 0.000 ARG G 67 *********************** 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 405 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 312 time to evaluate : 2.919 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: A 199 ASP cc_start: 0.7946 (m-30) cc_final: 0.7311 (m-30) REVERT: B 35 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.6315 (t80) REVERT: C 50 GLU cc_start: 0.7565 (tp30) cc_final: 0.7022 (tm-30) REVERT: C 151 ARG cc_start: 0.6492 (ttp-110) cc_final: 0.5948 (ttt90) REVERT: C 216 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7354 (p) REVERT: C 239 MET cc_start: 0.2334 (tpt) cc_final: 0.1439 (tmm) REVERT: C 369 MET cc_start: 0.7151 (ppp) cc_final: 0.6619 (ppp) REVERT: C 419 ILE cc_start: 0.7525 (pt) cc_final: 0.7137 (mt) REVERT: C 459 MET cc_start: 0.5045 (mtp) cc_final: 0.4802 (mtp) REVERT: C 478 ARG cc_start: 0.7396 (mmt-90) cc_final: 0.7087 (tpt-90) REVERT: C 515 MET cc_start: 0.6505 (tpt) cc_final: 0.5898 (tpt) REVERT: C 524 ILE cc_start: 0.8056 (tt) cc_final: 0.7812 (tt) REVERT: C 592 ARG cc_start: 0.8281 (mtp180) cc_final: 0.7749 (mtp85) REVERT: C 615 VAL cc_start: 0.6737 (OUTLIER) cc_final: 0.6460 (m) REVERT: C 672 GLU cc_start: 0.6134 (pt0) cc_final: 0.5491 (pm20) REVERT: C 775 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7335 (tt0) REVERT: C 790 ASP cc_start: 0.7507 (t0) cc_final: 0.7184 (t70) REVERT: C 814 ASP cc_start: 0.6367 (OUTLIER) cc_final: 0.5634 (m-30) REVERT: C 830 THR cc_start: 0.8096 (m) cc_final: 0.7723 (p) REVERT: C 841 ARG cc_start: 0.6972 (mmm-85) cc_final: 0.6380 (tpp-160) REVERT: C 1089 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6302 (pm20) REVERT: C 1171 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.6449 (ttp-110) REVERT: C 1174 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6807 (tm-30) REVERT: C 1220 GLN cc_start: 0.7427 (pm20) cc_final: 0.6993 (pt0) REVERT: C 1244 HIS cc_start: 0.6227 (p-80) cc_final: 0.5840 (p90) REVERT: C 1279 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5952 (mt-10) REVERT: C 1290 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.5942 (mtt) REVERT: C 1319 MET cc_start: 0.3471 (OUTLIER) cc_final: 0.2624 (mpp) REVERT: D 102 MET cc_start: 0.7151 (ppp) cc_final: 0.6598 (ppp) REVERT: D 166 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8528 (pp) REVERT: D 195 GLU cc_start: 0.8545 (mp0) cc_final: 0.8265 (mp0) REVERT: D 198 CYS cc_start: 0.8727 (m) cc_final: 0.8313 (p) REVERT: D 236 TRP cc_start: 0.8495 (m-10) cc_final: 0.8176 (m-10) REVERT: D 278 ARG cc_start: 0.7833 (mtt180) cc_final: 0.7082 (mtp180) REVERT: D 282 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5446 (mp) REVERT: D 337 ARG cc_start: 0.4164 (tpt170) cc_final: 0.3590 (mpt-90) REVERT: D 458 ASN cc_start: 0.7103 (t0) cc_final: 0.6803 (t0) REVERT: D 484 MET cc_start: 0.7388 (mmm) cc_final: 0.6697 (mmt) REVERT: D 576 ARG cc_start: 0.6253 (mtt180) cc_final: 0.5571 (ttm170) REVERT: D 594 GLN cc_start: 0.5678 (OUTLIER) cc_final: 0.4780 (pm20) REVERT: D 644 MET cc_start: 0.6653 (mtt) cc_final: 0.5995 (mtt) REVERT: D 698 MET cc_start: 0.4729 (OUTLIER) cc_final: 0.3707 (mmt) REVERT: D 724 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.5518 (mtm) REVERT: D 751 ASP cc_start: 0.7059 (p0) cc_final: 0.6807 (p0) REVERT: D 913 GLU cc_start: 0.6466 (mp0) cc_final: 0.6228 (mp0) REVERT: D 981 GLU cc_start: 0.6853 (tt0) cc_final: 0.6425 (tp30) REVERT: D 1146 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8099 (mm-30) REVERT: D 1286 LYS cc_start: 0.7331 (mmtm) cc_final: 0.6832 (mtpt) REVERT: D 1347 LEU cc_start: 0.7596 (mm) cc_final: 0.7329 (mm) REVERT: D 1349 GLU cc_start: 0.7361 (mp0) cc_final: 0.6952 (mp0) REVERT: D 1368 ASP cc_start: 0.7663 (t0) cc_final: 0.7301 (t0) REVERT: G 66 ASP cc_start: 0.7060 (t0) cc_final: 0.6786 (m-30) REVERT: G 91 PHE cc_start: 0.7741 (t80) cc_final: 0.7419 (t80) REVERT: G 98 GLU cc_start: 0.4718 (OUTLIER) cc_final: 0.4484 (mp0) REVERT: G 129 ARG cc_start: 0.4544 (OUTLIER) cc_final: 0.4200 (ppt170) outliers start: 93 outliers final: 67 residues processed: 378 average time/residue: 0.4012 time to fit residues: 241.4048 Evaluate side-chains 379 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 297 time to evaluate : 3.302 ------------------------------------------------------------------------------- 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 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 137 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 547 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 615 VAL 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 814 ASP Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1021 LEU 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 1171 ARG 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 1243 MET 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 1319 MET Chi-restraints excluded: chain C residue 1337 ILE 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 279 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 453 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 545 HIS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 5 THR 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 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 98 GLU 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 199 optimal weight: 30.0000 chunk 321 optimal weight: 20.0000 chunk 195 optimal weight: 40.0000 chunk 152 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 336 optimal weight: 20.0000 chunk 309 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.159 28042 Z= 0.375 Angle : 0.794 59.195 38140 Z= 0.430 Chirality : 0.047 0.494 4349 Planarity : 0.005 0.099 4796 Dihedral : 13.659 136.182 4363 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.75 % Favored : 94.07 % Rotamer: Outliers : 3.19 % Allowed : 20.42 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3341 helix: 0.17 (0.15), residues: 1234 sheet: -0.76 (0.26), residues: 386 loop : -1.79 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.119 0.006 TRP G 73 HIS 0.011 0.001 HIS C 554 PHE 0.016 0.002 PHE D 176 TYR 0.016 0.002 TYR C 810 ARG 0.026 0.001 ARG C 678 ********************** 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 394 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 303 time to evaluate : 3.718 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 199 ASP cc_start: 0.7948 (m-30) cc_final: 0.7315 (m-30) REVERT: B 35 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6281 (t80) REVERT: C 50 GLU cc_start: 0.7579 (tp30) cc_final: 0.7025 (tm-30) REVERT: C 121 GLU cc_start: 0.7727 (pt0) cc_final: 0.7230 (pm20) REVERT: C 151 ARG cc_start: 0.6567 (ttp-110) cc_final: 0.6233 (ttm-80) REVERT: C 216 THR cc_start: 0.7578 (OUTLIER) cc_final: 0.7314 (p) REVERT: C 239 MET cc_start: 0.2334 (tpt) cc_final: 0.1448 (tmm) REVERT: C 369 MET cc_start: 0.7152 (ppp) cc_final: 0.6619 (ppp) REVERT: C 419 ILE cc_start: 0.7529 (pt) cc_final: 0.7141 (mt) REVERT: C 459 MET cc_start: 0.5033 (mtp) cc_final: 0.4787 (mtp) REVERT: C 478 ARG cc_start: 0.7344 (mmt-90) cc_final: 0.7091 (tpt-90) REVERT: C 515 MET cc_start: 0.6530 (tpt) cc_final: 0.5890 (tpt) REVERT: C 524 ILE cc_start: 0.8081 (tt) cc_final: 0.7764 (tt) REVERT: C 592 ARG cc_start: 0.8287 (mtp180) cc_final: 0.7756 (mtp85) REVERT: C 615 VAL cc_start: 0.6718 (OUTLIER) cc_final: 0.6434 (m) REVERT: C 672 GLU cc_start: 0.6096 (pt0) cc_final: 0.5469 (pm20) REVERT: C 775 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7344 (tt0) REVERT: C 790 ASP cc_start: 0.7490 (t0) cc_final: 0.7166 (t70) REVERT: C 814 ASP cc_start: 0.6405 (OUTLIER) cc_final: 0.5667 (m-30) REVERT: C 830 THR cc_start: 0.8114 (m) cc_final: 0.7763 (p) REVERT: C 841 ARG cc_start: 0.6979 (mmm-85) cc_final: 0.6388 (tpp-160) REVERT: C 1089 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6297 (pm20) REVERT: C 1171 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6489 (ttp-110) REVERT: C 1174 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6814 (tm-30) REVERT: C 1220 GLN cc_start: 0.7464 (pm20) cc_final: 0.7006 (pt0) REVERT: C 1222 GLU cc_start: 0.6364 (tp30) cc_final: 0.5367 (mt-10) REVERT: C 1244 HIS cc_start: 0.6212 (p-80) cc_final: 0.5818 (p90) REVERT: C 1279 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.5967 (mt-10) REVERT: C 1290 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5928 (mtt) REVERT: C 1319 MET cc_start: 0.3472 (OUTLIER) cc_final: 0.2629 (mpp) REVERT: D 102 MET cc_start: 0.7147 (ppp) cc_final: 0.6598 (ppp) REVERT: D 166 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8528 (pp) REVERT: D 195 GLU cc_start: 0.8546 (mp0) cc_final: 0.8265 (mp0) REVERT: D 198 CYS cc_start: 0.8729 (m) cc_final: 0.8316 (p) REVERT: D 236 TRP cc_start: 0.8496 (m-10) cc_final: 0.8173 (m-10) REVERT: D 278 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7085 (mtp180) REVERT: D 282 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5447 (mp) REVERT: D 337 ARG cc_start: 0.4199 (tpt170) cc_final: 0.3595 (mpt-90) REVERT: D 458 ASN cc_start: 0.7109 (t0) cc_final: 0.6799 (t0) REVERT: D 484 MET cc_start: 0.7393 (mmm) cc_final: 0.6704 (mmt) REVERT: D 576 ARG cc_start: 0.6276 (mtt180) cc_final: 0.5611 (ttm170) REVERT: D 594 GLN cc_start: 0.5676 (OUTLIER) cc_final: 0.4772 (pm20) REVERT: D 644 MET cc_start: 0.6644 (mtt) cc_final: 0.6048 (mtt) REVERT: D 698 MET cc_start: 0.4795 (OUTLIER) cc_final: 0.3718 (mmt) REVERT: D 724 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.5600 (mtm) REVERT: D 751 ASP cc_start: 0.7062 (p0) cc_final: 0.6810 (p0) REVERT: D 913 GLU cc_start: 0.6532 (mp0) cc_final: 0.6120 (mp0) REVERT: D 981 GLU cc_start: 0.6852 (tt0) cc_final: 0.6425 (tp30) REVERT: D 1146 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8099 (mm-30) REVERT: D 1286 LYS cc_start: 0.7338 (mmtm) cc_final: 0.6844 (mtpt) REVERT: D 1347 LEU cc_start: 0.7604 (mm) cc_final: 0.7336 (mm) REVERT: D 1349 GLU cc_start: 0.7369 (mp0) cc_final: 0.6955 (mp0) REVERT: D 1368 ASP cc_start: 0.7695 (t0) cc_final: 0.7329 (t0) REVERT: G 66 ASP cc_start: 0.7065 (t0) cc_final: 0.6791 (m-30) REVERT: G 91 PHE cc_start: 0.7742 (t80) cc_final: 0.7419 (t80) REVERT: G 98 GLU cc_start: 0.4808 (OUTLIER) cc_final: 0.4529 (mp0) REVERT: G 129 ARG cc_start: 0.4544 (OUTLIER) cc_final: 0.4200 (ppt170) outliers start: 91 outliers final: 71 residues processed: 363 average time/residue: 0.4362 time to fit residues: 252.0221 Evaluate side-chains 383 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 297 time to evaluate : 3.155 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 47 TYR 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 492 MET Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 547 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 615 VAL 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 814 ASP Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1021 LEU 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 1171 ARG Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1243 MET 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 1319 MET Chi-restraints excluded: chain C residue 1337 ILE 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 279 LEU Chi-restraints excluded: chain D residue 282 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 545 HIS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 5 THR 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 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 98 GLU 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 212 optimal weight: 0.6980 chunk 285 optimal weight: 0.0030 chunk 82 optimal weight: 0.7980 chunk 247 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 275 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** 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 = 0.4700 r_free = 0.4700 target = 0.210008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.142957 restraints weight = 42599.661| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.87 r_work: 0.3714 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.159 28042 Z= 0.375 Angle : 0.794 59.195 38140 Z= 0.430 Chirality : 0.047 0.494 4349 Planarity : 0.005 0.101 4796 Dihedral : 13.659 136.182 4363 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.75 % Favored : 94.07 % Rotamer: Outliers : 3.01 % Allowed : 20.67 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3341 helix: 0.17 (0.15), residues: 1234 sheet: -0.76 (0.26), residues: 386 loop : -1.79 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.119 0.006 TRP G 73 HIS 0.011 0.001 HIS C 554 PHE 0.016 0.002 PHE D 176 TYR 0.016 0.002 TYR C 810 ARG 0.026 0.001 ARG C 678 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6891.33 seconds wall clock time: 123 minutes 46.55 seconds (7426.55 seconds total)