Starting phenix.real_space_refine on Wed Mar 20 12:45:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py8_13716/03_2024/7py8_13716.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py8_13716/03_2024/7py8_13716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py8_13716/03_2024/7py8_13716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py8_13716/03_2024/7py8_13716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py8_13716/03_2024/7py8_13716.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py8_13716/03_2024/7py8_13716.pdb" } resolution = 3.8 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= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 75 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 16966 2.51 5 N 4863 2.21 5 O 5422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 835": "OE1" <-> "OE2" Residue "C PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1274": "OE1" <-> "OE2" Residue "D ASP 830": "OD1" <-> "OD2" Residue "D GLU 913": "OE1" <-> "OE2" Residue "D GLU 1349": "OE1" <-> "OE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27442 Number of models: 1 Model: "" Number of chains: 10 Chain: "N" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 620 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "T" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 690 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1706 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Chain: "B" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "C" Number of atoms: 10548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10548 Classifications: {'peptide': 1337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1280} Chain breaks: 1 Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 987 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15931 SG CYS D 70 23.369 51.294 97.478 1.00138.11 S ATOM 16077 SG CYS D 88 25.681 49.287 100.881 1.00144.60 S ATOM 21765 SG CYS D 814 42.560 117.348 89.819 1.00124.56 S ATOM 22330 SG CYS D 888 43.897 113.805 90.543 1.00105.12 S ATOM 22381 SG CYS D 895 42.567 114.708 87.045 1.00108.43 S ATOM 22402 SG CYS D 898 45.720 116.144 88.118 1.00105.52 S Time building chain proxies: 14.56, per 1000 atoms: 0.53 Number of scatterers: 27442 At special positions: 0 Unit cell: (134.2, 161.7, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 113 16.00 P 75 15.00 Mg 1 11.99 O 5422 8.00 N 4863 7.00 C 16966 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: 10.97 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " Number of angles added : 6 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6102 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 46 sheets defined 37.6% alpha, 13.7% beta 32 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 9.03 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.950A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.144A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.538A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 159' Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.781A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.551A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.987A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.609A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.929A 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 242 through 247 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.665A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.808A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.735A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.610A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.838A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 4.056A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 4.286A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 614' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.534A 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 removed outlier: 3.601A pdb=" N MET C 741 " --> pdb=" O GLU C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.961A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 906 removed outlier: 3.630A pdb=" N ILE C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 901 through 906' Processing helix chain 'C' and resid 942 through 981 removed outlier: 4.168A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 3.959A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.819A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.033A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.763A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.702A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C1242 " --> pdb=" O VAL C1239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1238 through 1242' Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1298 through 1309 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.853A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.716A pdb=" N PHE D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.511A pdb=" N HIS D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.631A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.617A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.715A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 408 through 416 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 452 through 458 removed outlier: 4.091A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.783A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.625A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 613 removed outlier: 3.545A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.627A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.517A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.086A 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 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.072A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.562A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 removed outlier: 4.024A pdb=" N GLU D 873 " --> pdb=" O CYS D 869 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU D 874 " --> pdb=" O ASP D 870 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.764A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1068 through 1073 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 4.078A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.412A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1294 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.697A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.879A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 74 removed outlier: 3.944A pdb=" N GLU E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 34 Processing helix chain 'G' and resid 77 through 86 removed outlier: 3.582A pdb=" N VAL G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 removed outlier: 3.556A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 186 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.526A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 59 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.530A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.968A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 15 removed outlier: 3.907A pdb=" N ARG B 12 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 8.412A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.798A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.661A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 188 through 190 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.664A 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: 3.570A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 68 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.609A 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 453 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.844A pdb=" N ASN C 173 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 185 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 228 through 231 Processing sheet with id=AB8, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.700A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.797A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.856A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.505A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 606 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.682A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 634 " --> pdb=" O PHE C 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.491A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 783 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 750 through 752 removed outlier: 6.922A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) 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 1076 through 1080 removed outlier: 7.512A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.526A pdb=" N LEU C1054 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.546A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET D 466 " --> pdb=" O SER D 353 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.657A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1337 removed outlier: 3.574A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 112 removed outlier: 4.053A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AD7, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.617A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.571A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.541A pdb=" N VAL D 882 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET D 822 " --> pdb=" O VAL D 880 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.032A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 991 through 996 removed outlier: 4.037A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.916A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1024 through 1026 removed outlier: 3.704A pdb=" N ARG D1123 " --> pdb=" O ILE D1106 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 4.092A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA D1077 " --> pdb=" O THR D1038 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1162 through 1165 removed outlier: 3.736A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.691A pdb=" N THR D1265 " --> pdb=" O SER D1303 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AF1, first strand: chain 'G' and resid 47 through 48 984 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 11.55 Time building geometry restraints manager: 11.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8860 1.34 - 1.46: 4024 1.46 - 1.58: 14779 1.58 - 1.70: 147 1.70 - 1.82: 198 Bond restraints: 28008 Sorted by residual: bond pdb=" C1' DC N 21 " pdb=" N1 DC N 21 " ideal model delta sigma weight residual 1.490 1.529 -0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" C THR C1184 " pdb=" O THR C1184 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.66e+00 bond pdb=" C3' DC N 35 " pdb=" O3' DC N 35 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CG GLU E 68 " pdb=" CD GLU E 68 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.40e+00 bond pdb=" CA PRO D 246 " pdb=" C PRO D 246 " ideal model delta sigma weight residual 1.514 1.521 -0.006 5.50e-03 3.31e+04 1.37e+00 ... (remaining 28003 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.07: 758 105.07 - 112.32: 14339 112.32 - 119.58: 9637 119.58 - 126.83: 12989 126.83 - 134.08: 418 Bond angle restraints: 38141 Sorted by residual: angle pdb=" N GLU E 68 " pdb=" CA GLU E 68 " pdb=" CB GLU E 68 " ideal model delta sigma weight residual 110.28 116.90 -6.62 1.55e+00 4.16e-01 1.82e+01 angle pdb=" C PRO C 43 " pdb=" N GLU C 44 " pdb=" CA GLU C 44 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 angle pdb=" N GLU C1279 " pdb=" CA GLU C1279 " pdb=" CB GLU C1279 " ideal model delta sigma weight residual 110.41 116.30 -5.89 1.68e+00 3.54e-01 1.23e+01 angle pdb=" N ILE D 915 " pdb=" CA ILE D 915 " pdb=" C ILE D 915 " ideal model delta sigma weight residual 113.53 110.19 3.34 9.80e-01 1.04e+00 1.16e+01 angle pdb=" C LEU C1278 " pdb=" N GLU C1279 " pdb=" CA GLU C1279 " ideal model delta sigma weight residual 121.58 114.99 6.59 1.95e+00 2.63e-01 1.14e+01 ... (remaining 38136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 16544 35.51 - 71.01: 502 71.01 - 106.52: 27 106.52 - 142.02: 1 142.02 - 177.53: 1 Dihedral angle restraints: 17075 sinusoidal: 7590 harmonic: 9485 Sorted by residual: dihedral pdb=" CA GLU D1146 " pdb=" C GLU D1146 " pdb=" N ALA D1147 " pdb=" CA ALA D1147 " ideal model delta harmonic sigma weight residual 180.00 150.42 29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" C4' DC N 35 " pdb=" C3' DC N 35 " pdb=" O3' DC N 35 " pdb=" P DA N 36 " ideal model delta sinusoidal sigma weight residual -140.00 37.53 -177.53 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC T 15 " pdb=" C3' DC T 15 " pdb=" O3' DC T 15 " pdb=" P DG T 16 " ideal model delta sinusoidal sigma weight residual 220.00 86.02 133.98 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 17072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3207 0.040 - 0.080: 808 0.080 - 0.120: 304 0.120 - 0.160: 28 0.160 - 0.200: 4 Chirality restraints: 4351 Sorted by residual: chirality pdb=" CB THR D1024 " pdb=" CA THR D1024 " pdb=" OG1 THR D1024 " pdb=" CG2 THR D1024 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CB ILE C 854 " pdb=" CA ILE C 854 " pdb=" CG1 ILE C 854 " pdb=" CG2 ILE C 854 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CB ILE C 572 " pdb=" CA ILE C 572 " pdb=" CG1 ILE C 572 " pdb=" CG2 ILE C 572 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 4348 not shown) Planarity restraints: 4731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A 30 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 29 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO B 30 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO D 851 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " 0.023 5.00e-02 4.00e+02 ... (remaining 4728 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 962 2.71 - 3.26: 27072 3.26 - 3.81: 42997 3.81 - 4.35: 50199 4.35 - 4.90: 83377 Nonbonded interactions: 204607 Sorted by model distance: nonbonded pdb=" OG SER D 977 " pdb=" OG1 THR D 980 " model vdw 2.163 2.440 nonbonded pdb=" O3' G R 14 " pdb="MG MG D1501 " model vdw 2.190 2.170 nonbonded pdb=" O VAL G 49 " pdb=" OG SER G 60 " model vdw 2.192 2.440 nonbonded pdb=" OH TYR D 679 " pdb=" O ILE D 754 " model vdw 2.211 2.440 nonbonded pdb=" OE2 GLU D1146 " pdb=" NE ARG D1148 " model vdw 2.223 2.520 ... (remaining 204602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 158 or resid 170 through 232)) selection = (chain 'B' and resid 7 through 232) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.040 Extract box with map and model: 5.980 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 81.490 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28008 Z= 0.141 Angle : 0.523 8.608 38141 Z= 0.276 Chirality : 0.041 0.200 4351 Planarity : 0.003 0.056 4731 Dihedral : 15.674 177.526 10973 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3285 helix: 1.22 (0.16), residues: 1098 sheet: -0.65 (0.26), residues: 393 loop : -1.41 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 80 HIS 0.007 0.001 HIS G 33 PHE 0.014 0.001 PHE A 231 TYR 0.010 0.001 TYR D 631 ARG 0.010 0.000 ARG D1123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 955 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 16 ILE cc_start: 0.8607 (mt) cc_final: 0.8344 (tt) REVERT: A 33 ARG cc_start: 0.7792 (ptm160) cc_final: 0.7291 (ptm160) REVERT: A 46 ILE cc_start: 0.7685 (mm) cc_final: 0.7450 (tp) REVERT: A 67 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7168 (mt-10) REVERT: A 74 VAL cc_start: 0.8170 (m) cc_final: 0.7774 (p) REVERT: A 76 GLU cc_start: 0.7133 (pm20) cc_final: 0.6429 (pm20) REVERT: A 80 GLU cc_start: 0.7709 (tp30) cc_final: 0.7476 (tp30) REVERT: A 101 THR cc_start: 0.7914 (m) cc_final: 0.6885 (p) REVERT: A 104 LYS cc_start: 0.8243 (tptp) cc_final: 0.7861 (tptp) REVERT: A 122 GLU cc_start: 0.7306 (pp20) cc_final: 0.7084 (pp20) REVERT: A 148 ARG cc_start: 0.7454 (mtp180) cc_final: 0.7137 (mtp85) REVERT: A 188 GLU cc_start: 0.7487 (pm20) cc_final: 0.7284 (pm20) REVERT: A 204 GLU cc_start: 0.7932 (pt0) cc_final: 0.7233 (pt0) REVERT: A 205 MET cc_start: 0.7413 (ttp) cc_final: 0.6839 (ptp) REVERT: A 206 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6958 (tm-30) REVERT: A 226 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6620 (tm-30) REVERT: B 7 GLU cc_start: 0.6361 (pm20) cc_final: 0.5920 (pm20) REVERT: B 58 GLU cc_start: 0.7445 (pt0) cc_final: 0.7100 (pt0) REVERT: B 64 VAL cc_start: 0.7329 (t) cc_final: 0.7124 (p) REVERT: B 66 HIS cc_start: 0.7483 (t-90) cc_final: 0.6836 (t70) REVERT: B 80 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6442 (tm-30) REVERT: B 81 ILE cc_start: 0.7892 (pt) cc_final: 0.7347 (pt) REVERT: B 97 GLU cc_start: 0.7239 (pm20) cc_final: 0.6649 (pm20) REVERT: B 98 VAL cc_start: 0.7943 (p) cc_final: 0.7644 (m) REVERT: B 100 LEU cc_start: 0.8539 (mm) cc_final: 0.7853 (tp) REVERT: B 128 HIS cc_start: 0.8045 (t-90) cc_final: 0.7613 (t-90) REVERT: B 148 ARG cc_start: 0.6658 (ttm-80) cc_final: 0.6264 (mtm-85) REVERT: B 188 GLU cc_start: 0.7145 (pt0) cc_final: 0.6843 (pt0) REVERT: B 205 MET cc_start: 0.7621 (ppp) cc_final: 0.6581 (ppp) REVERT: C 8 LYS cc_start: 0.8166 (mttt) cc_final: 0.7788 (mtpp) REVERT: C 17 LYS cc_start: 0.8026 (mptt) cc_final: 0.7541 (mmtt) REVERT: C 69 GLN cc_start: 0.7120 (mt0) cc_final: 0.6908 (mt0) REVERT: C 87 ILE cc_start: 0.8185 (mt) cc_final: 0.7940 (pt) REVERT: C 92 TYR cc_start: 0.8494 (t80) cc_final: 0.8055 (t80) REVERT: C 99 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7457 (mtmm) REVERT: C 121 GLU cc_start: 0.6533 (mm-30) cc_final: 0.6186 (mm-30) REVERT: C 135 THR cc_start: 0.7529 (p) cc_final: 0.7077 (p) REVERT: C 142 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7195 (mt-10) REVERT: C 151 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7628 (ttm110) REVERT: C 180 ARG cc_start: 0.7051 (ttp80) cc_final: 0.6820 (ttp80) REVERT: C 185 ASP cc_start: 0.6597 (p0) cc_final: 0.5816 (p0) REVERT: C 187 GLU cc_start: 0.7342 (mp0) cc_final: 0.6230 (mp0) REVERT: C 214 ASN cc_start: 0.8687 (t0) cc_final: 0.8289 (t0) REVERT: C 339 ASN cc_start: 0.7493 (t0) cc_final: 0.7214 (t0) REVERT: C 349 GLU cc_start: 0.8125 (pm20) cc_final: 0.7761 (pm20) REVERT: C 368 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.7680 (mtm-85) REVERT: C 369 MET cc_start: 0.8216 (tpp) cc_final: 0.7989 (tpp) REVERT: C 374 GLU cc_start: 0.6515 (pt0) cc_final: 0.4701 (pt0) REVERT: C 387 ASN cc_start: 0.7749 (m-40) cc_final: 0.7240 (t0) REVERT: C 389 PHE cc_start: 0.8295 (m-80) cc_final: 0.8012 (m-10) REVERT: C 392 GLU cc_start: 0.7475 (mp0) cc_final: 0.7209 (mp0) REVERT: C 402 ARG cc_start: 0.8235 (tpt170) cc_final: 0.7999 (tpp-160) REVERT: C 404 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7698 (tttp) REVERT: C 427 ASP cc_start: 0.7289 (m-30) cc_final: 0.6953 (m-30) REVERT: C 430 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7864 (mttm) REVERT: C 459 MET cc_start: 0.6779 (mtm) cc_final: 0.6540 (mtp) REVERT: C 531 SER cc_start: 0.8688 (t) cc_final: 0.8264 (p) REVERT: C 549 ASP cc_start: 0.7130 (t0) cc_final: 0.6637 (t0) REVERT: C 572 ILE cc_start: 0.8430 (mm) cc_final: 0.8034 (mm) REVERT: C 592 ARG cc_start: 0.7667 (mtp180) cc_final: 0.6167 (ttm170) REVERT: C 593 LYS cc_start: 0.7973 (tptt) cc_final: 0.7658 (tptp) REVERT: C 611 GLU cc_start: 0.7505 (tt0) cc_final: 0.7250 (tt0) REVERT: C 616 ILE cc_start: 0.8555 (mp) cc_final: 0.8262 (mm) REVERT: C 633 LEU cc_start: 0.7807 (tp) cc_final: 0.6903 (tp) REVERT: C 653 MET cc_start: 0.7376 (ttm) cc_final: 0.7016 (ttp) REVERT: C 654 ASP cc_start: 0.7501 (m-30) cc_final: 0.6904 (m-30) REVERT: C 656 SER cc_start: 0.8501 (t) cc_final: 0.8051 (m) REVERT: C 685 MET cc_start: 0.7365 (mtm) cc_final: 0.7098 (mtm) REVERT: C 696 ASP cc_start: 0.7043 (t0) cc_final: 0.6742 (t0) REVERT: C 723 VAL cc_start: 0.8196 (t) cc_final: 0.7875 (m) REVERT: C 730 SER cc_start: 0.8701 (m) cc_final: 0.8199 (t) REVERT: C 778 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7323 (mp0) REVERT: C 788 SER cc_start: 0.8326 (m) cc_final: 0.7841 (p) REVERT: C 790 ASP cc_start: 0.7574 (t70) cc_final: 0.6699 (p0) REVERT: C 808 ASN cc_start: 0.8172 (t0) cc_final: 0.7946 (m-40) REVERT: C 930 ASP cc_start: 0.7825 (t0) cc_final: 0.7290 (m-30) REVERT: C 947 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7549 (tm-30) REVERT: C 950 GLU cc_start: 0.8435 (pt0) cc_final: 0.8234 (pt0) REVERT: C 960 LEU cc_start: 0.8176 (mp) cc_final: 0.7755 (pp) REVERT: C 1028 LYS cc_start: 0.8535 (ptpp) cc_final: 0.8125 (pttm) REVERT: C 1030 GLU cc_start: 0.8568 (tp30) cc_final: 0.7955 (tp30) REVERT: C 1032 LYS cc_start: 0.9235 (tptt) cc_final: 0.8780 (mttt) REVERT: C 1035 LYS cc_start: 0.8586 (tppt) cc_final: 0.7915 (tppt) REVERT: C 1090 ASN cc_start: 0.7772 (t0) cc_final: 0.7284 (t0) REVERT: C 1095 ASP cc_start: 0.7293 (m-30) cc_final: 0.6937 (m-30) REVERT: C 1114 GLU cc_start: 0.7443 (tt0) cc_final: 0.7213 (tt0) REVERT: C 1122 LYS cc_start: 0.8129 (tptm) cc_final: 0.7537 (tptp) REVERT: C 1126 ASP cc_start: 0.7314 (m-30) cc_final: 0.6732 (m-30) REVERT: C 1127 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8331 (tptp) REVERT: C 1131 MET cc_start: 0.8371 (ttt) cc_final: 0.7789 (ptp) REVERT: C 1143 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7329 (tm-30) REVERT: C 1177 ARG cc_start: 0.7723 (ptm160) cc_final: 0.7233 (ptp90) REVERT: C 1178 LYS cc_start: 0.8313 (tptm) cc_final: 0.8021 (mmmm) REVERT: C 1200 LYS cc_start: 0.8255 (tttt) cc_final: 0.7745 (mtpt) REVERT: C 1210 ILE cc_start: 0.8123 (tt) cc_final: 0.7852 (pt) REVERT: C 1216 ARG cc_start: 0.6907 (mtm180) cc_final: 0.5997 (mtm180) REVERT: C 1244 HIS cc_start: 0.7419 (t-90) cc_final: 0.7173 (t70) REVERT: C 1262 LYS cc_start: 0.7965 (tttt) cc_final: 0.7715 (ttpp) REVERT: C 1264 GLN cc_start: 0.8247 (mp10) cc_final: 0.7886 (mp10) REVERT: C 1279 GLU cc_start: 0.7215 (pm20) cc_final: 0.6835 (pm20) REVERT: C 1289 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6993 (mm-30) REVERT: C 1292 THR cc_start: 0.8121 (m) cc_final: 0.7920 (p) REVERT: C 1293 VAL cc_start: 0.7838 (t) cc_final: 0.6939 (m) REVERT: C 1321 GLU cc_start: 0.6564 (tt0) cc_final: 0.6261 (pp20) REVERT: C 1329 GLU cc_start: 0.6763 (tt0) cc_final: 0.6228 (tp30) REVERT: C 1331 ARG cc_start: 0.7117 (ttm170) cc_final: 0.6905 (ttm170) REVERT: D 21 LYS cc_start: 0.8223 (ptpt) cc_final: 0.7583 (ptmm) REVERT: D 33 TRP cc_start: 0.8072 (m-10) cc_final: 0.7748 (m-10) REVERT: D 39 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7916 (mtmm) REVERT: D 48 THR cc_start: 0.8194 (p) cc_final: 0.7805 (p) REVERT: D 50 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7824 (mtpt) REVERT: D 53 ARG cc_start: 0.7042 (ttt90) cc_final: 0.6839 (ttt90) REVERT: D 66 LYS cc_start: 0.7786 (mtpp) cc_final: 0.7519 (mtpp) REVERT: D 115 TRP cc_start: 0.8448 (m-10) cc_final: 0.8136 (m-10) REVERT: D 118 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7853 (mmmt) REVERT: D 128 LEU cc_start: 0.7932 (mt) cc_final: 0.7542 (mt) REVERT: D 137 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7269 (ttp-110) REVERT: D 141 PHE cc_start: 0.7978 (m-80) cc_final: 0.7581 (m-10) REVERT: D 148 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6343 (tm-30) REVERT: D 151 MET cc_start: 0.7789 (pmm) cc_final: 0.7298 (pmm) REVERT: D 159 ILE cc_start: 0.8141 (tt) cc_final: 0.7880 (mt) REVERT: D 167 ASP cc_start: 0.8341 (t0) cc_final: 0.8102 (t0) REVERT: D 198 CYS cc_start: 0.8362 (t) cc_final: 0.6566 (t) REVERT: D 199 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8134 (mm-30) REVERT: D 202 ARG cc_start: 0.8407 (mtp85) cc_final: 0.8019 (ptp-110) REVERT: D 215 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8607 (ptpt) REVERT: D 235 GLU cc_start: 0.7124 (pm20) cc_final: 0.6746 (pm20) REVERT: D 236 TRP cc_start: 0.8420 (m-10) cc_final: 0.7968 (m-10) REVERT: D 241 VAL cc_start: 0.8842 (t) cc_final: 0.8566 (m) REVERT: D 275 ARG cc_start: 0.7840 (tpp-160) cc_final: 0.7473 (tpp-160) REVERT: D 288 PRO cc_start: 0.6193 (Cg_endo) cc_final: 0.5518 (Cg_exo) REVERT: D 297 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7393 (tmm-80) REVERT: D 298 MET cc_start: 0.7754 (ttp) cc_final: 0.6369 (ttp) REVERT: D 325 LYS cc_start: 0.7925 (mmpt) cc_final: 0.7631 (tptt) REVERT: D 332 LYS cc_start: 0.7254 (mtmm) cc_final: 0.6765 (mtpp) REVERT: D 363 LEU cc_start: 0.6279 (pt) cc_final: 0.5934 (pp) REVERT: D 370 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7452 (ttpt) REVERT: D 375 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7180 (tm-30) REVERT: D 386 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6990 (mm-30) REVERT: D 400 MET cc_start: 0.7309 (tmm) cc_final: 0.6862 (tmm) REVERT: D 414 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7321 (tm-30) REVERT: D 475 GLU cc_start: 0.7456 (mp0) cc_final: 0.7116 (mp0) REVERT: D 495 ASN cc_start: 0.7180 (m-40) cc_final: 0.6804 (m-40) REVERT: D 497 GLU cc_start: 0.8077 (mp0) cc_final: 0.7846 (mp0) REVERT: D 500 ILE cc_start: 0.8249 (mm) cc_final: 0.7826 (tt) REVERT: D 504 GLN cc_start: 0.7700 (mt0) cc_final: 0.7491 (mt0) REVERT: D 511 TYR cc_start: 0.8391 (t80) cc_final: 0.7648 (t80) REVERT: D 521 LYS cc_start: 0.7963 (tttm) cc_final: 0.7754 (mtpp) REVERT: D 556 GLU cc_start: 0.7788 (tt0) cc_final: 0.7333 (tm-30) REVERT: D 589 TYR cc_start: 0.8502 (t80) cc_final: 0.8085 (t80) REVERT: D 610 ARG cc_start: 0.7935 (tpp-160) cc_final: 0.7637 (mmt-90) REVERT: D 644 MET cc_start: 0.7007 (mpp) cc_final: 0.6646 (mtt) REVERT: D 649 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8063 (mmmt) REVERT: D 684 ASP cc_start: 0.7402 (m-30) cc_final: 0.7072 (m-30) REVERT: D 691 ASP cc_start: 0.8006 (m-30) cc_final: 0.7691 (m-30) REVERT: D 695 LYS cc_start: 0.8483 (tmtt) cc_final: 0.7784 (ttpp) REVERT: D 703 THR cc_start: 0.8075 (m) cc_final: 0.7659 (t) REVERT: D 716 GLN cc_start: 0.7865 (pt0) cc_final: 0.7584 (pt0) REVERT: D 725 MET cc_start: 0.7406 (mtm) cc_final: 0.7119 (mtp) REVERT: D 770 LEU cc_start: 0.7687 (mm) cc_final: 0.7449 (mp) REVERT: D 789 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7516 (ptmm) REVERT: D 793 SER cc_start: 0.7658 (p) cc_final: 0.7446 (p) REVERT: D 806 ASP cc_start: 0.7216 (m-30) cc_final: 0.5790 (m-30) REVERT: D 838 ARG cc_start: 0.8361 (ttt180) cc_final: 0.7758 (tpp80) REVERT: D 842 ARG cc_start: 0.6574 (mtt180) cc_final: 0.5826 (mtt180) REVERT: D 865 HIS cc_start: 0.6518 (p90) cc_final: 0.6140 (p90) REVERT: D 869 CYS cc_start: 0.8369 (t) cc_final: 0.7769 (p) REVERT: D 870 ASP cc_start: 0.8110 (m-30) cc_final: 0.7122 (m-30) REVERT: D 910 ASN cc_start: 0.7481 (m110) cc_final: 0.7272 (m-40) REVERT: D 1025 MET cc_start: 0.8666 (mpp) cc_final: 0.8358 (mpp) REVERT: D 1143 ASP cc_start: 0.7698 (t70) cc_final: 0.7372 (t0) REVERT: D 1189 MET cc_start: 0.7013 (tpt) cc_final: 0.6638 (tpt) REVERT: D 1206 ARG cc_start: 0.7814 (ptm160) cc_final: 0.7606 (ttp80) REVERT: D 1218 HIS cc_start: 0.8217 (m90) cc_final: 0.7503 (m90) REVERT: D 1224 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7499 (mtm180) REVERT: D 1242 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6931 (ptp-110) REVERT: D 1254 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6848 (mt-10) REVERT: D 1262 ARG cc_start: 0.7386 (ttp-110) cc_final: 0.6857 (ttp80) REVERT: D 1281 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7051 (tm-30) REVERT: D 1305 ASP cc_start: 0.7752 (p0) cc_final: 0.7112 (t70) REVERT: D 1306 LEU cc_start: 0.8115 (tp) cc_final: 0.7734 (tp) REVERT: D 1343 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6358 (mp0) REVERT: D 1365 TYR cc_start: 0.8056 (t80) cc_final: 0.7553 (t80) REVERT: E 52 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7357 (ttp80) REVERT: E 53 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7961 (mm-30) REVERT: G 22 VAL cc_start: 0.9061 (t) cc_final: 0.8837 (p) REVERT: G 27 ARG cc_start: 0.8225 (mtm180) cc_final: 0.7798 (mtm-85) REVERT: G 43 MET cc_start: 0.7366 (tmm) cc_final: 0.6926 (tmm) REVERT: G 72 GLN cc_start: 0.7825 (mm110) cc_final: 0.7439 (mm110) REVERT: G 74 VAL cc_start: 0.7119 (p) cc_final: 0.6464 (m) REVERT: G 76 ASN cc_start: 0.4095 (p0) cc_final: 0.3873 (p0) REVERT: G 80 TRP cc_start: 0.7615 (t60) cc_final: 0.6651 (t60) REVERT: G 84 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7762 (tpt90) outliers start: 1 outliers final: 0 residues processed: 956 average time/residue: 0.4692 time to fit residues: 654.2530 Evaluate side-chains 808 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 808 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 0.8980 chunk 253 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 135 optimal weight: 0.2980 chunk 262 optimal weight: 4.9990 chunk 101 optimal weight: 0.1980 chunk 159 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 93 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 HIS D1218 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28008 Z= 0.179 Angle : 0.587 11.757 38141 Z= 0.302 Chirality : 0.043 0.251 4351 Planarity : 0.004 0.054 4731 Dihedral : 14.555 176.258 4488 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.02 % Allowed : 12.17 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 3285 helix: 1.20 (0.16), residues: 1112 sheet: -0.32 (0.27), residues: 393 loop : -1.37 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 409 HIS 0.007 0.001 HIS A 23 PHE 0.019 0.001 PHE B 8 TYR 0.022 0.001 TYR D 631 ARG 0.007 0.000 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 869 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8630 (mt) cc_final: 0.8355 (tt) REVERT: A 33 ARG cc_start: 0.7768 (ptm160) cc_final: 0.7223 (ptm160) REVERT: A 74 VAL cc_start: 0.8227 (m) cc_final: 0.7871 (p) REVERT: A 76 GLU cc_start: 0.7009 (pm20) cc_final: 0.6411 (pm20) REVERT: A 80 GLU cc_start: 0.7752 (tp30) cc_final: 0.7515 (tp30) REVERT: A 104 LYS cc_start: 0.8057 (tptp) cc_final: 0.7405 (tptp) REVERT: A 122 GLU cc_start: 0.7041 (pp20) cc_final: 0.6620 (pp20) REVERT: A 125 LYS cc_start: 0.8061 (ptpp) cc_final: 0.7804 (ttpp) REVERT: A 142 MET cc_start: 0.7824 (mtm) cc_final: 0.7517 (mtm) REVERT: A 153 VAL cc_start: 0.8831 (t) cc_final: 0.8547 (m) REVERT: A 170 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7497 (ttm-80) REVERT: A 204 GLU cc_start: 0.7759 (pt0) cc_final: 0.7435 (pt0) REVERT: A 205 MET cc_start: 0.7328 (ttp) cc_final: 0.7060 (ptp) REVERT: A 206 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7096 (tm-30) REVERT: A 226 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6581 (tm-30) REVERT: B 17 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6631 (tm-30) REVERT: B 32 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6806 (tm-30) REVERT: B 58 GLU cc_start: 0.7481 (pt0) cc_final: 0.7135 (pt0) REVERT: B 64 VAL cc_start: 0.7301 (t) cc_final: 0.7084 (p) REVERT: B 71 LYS cc_start: 0.8527 (tmtt) cc_final: 0.8319 (tmtt) REVERT: B 80 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6636 (tm-30) REVERT: B 81 ILE cc_start: 0.7883 (pt) cc_final: 0.7311 (pt) REVERT: B 82 LEU cc_start: 0.8349 (mt) cc_final: 0.8003 (pp) REVERT: B 97 GLU cc_start: 0.7209 (pm20) cc_final: 0.6462 (pm20) REVERT: B 100 LEU cc_start: 0.8473 (mm) cc_final: 0.8108 (tt) REVERT: B 142 MET cc_start: 0.7267 (mmm) cc_final: 0.6962 (mmm) REVERT: B 148 ARG cc_start: 0.6751 (ttm-80) cc_final: 0.6508 (tpp80) REVERT: B 188 GLU cc_start: 0.7134 (pt0) cc_final: 0.6820 (pt0) REVERT: B 205 MET cc_start: 0.7579 (ppp) cc_final: 0.6565 (ppp) REVERT: B 214 GLU cc_start: 0.6013 (tm-30) cc_final: 0.5748 (tm-30) REVERT: C 8 LYS cc_start: 0.8244 (mttt) cc_final: 0.7843 (mtpt) REVERT: C 17 LYS cc_start: 0.8053 (mptt) cc_final: 0.7448 (mmtp) REVERT: C 92 TYR cc_start: 0.8487 (t80) cc_final: 0.8020 (t80) REVERT: C 99 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7427 (mtmm) REVERT: C 101 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7639 (mtp85) REVERT: C 121 GLU cc_start: 0.6548 (mm-30) cc_final: 0.5996 (mm-30) REVERT: C 151 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7285 (mtm110) REVERT: C 180 ARG cc_start: 0.7181 (ttp80) cc_final: 0.6702 (ttp80) REVERT: C 183 TRP cc_start: 0.8020 (m-10) cc_final: 0.7585 (m-10) REVERT: C 185 ASP cc_start: 0.6175 (p0) cc_final: 0.5847 (p0) REVERT: C 186 PHE cc_start: 0.7819 (m-80) cc_final: 0.6942 (m-10) REVERT: C 187 GLU cc_start: 0.7207 (mp0) cc_final: 0.6469 (mp0) REVERT: C 195 PHE cc_start: 0.7661 (m-80) cc_final: 0.7459 (m-80) REVERT: C 203 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7311 (ttmm) REVERT: C 214 ASN cc_start: 0.8734 (t0) cc_final: 0.8324 (t0) REVERT: C 260 LYS cc_start: 0.8905 (pttm) cc_final: 0.8562 (tmtt) REVERT: C 346 TYR cc_start: 0.6990 (m-80) cc_final: 0.6647 (m-80) REVERT: C 349 GLU cc_start: 0.8200 (pm20) cc_final: 0.7778 (pm20) REVERT: C 365 GLU cc_start: 0.8120 (tp30) cc_final: 0.7845 (tp30) REVERT: C 368 ARG cc_start: 0.8195 (ttp-110) cc_final: 0.7759 (mtm-85) REVERT: C 374 GLU cc_start: 0.5865 (pt0) cc_final: 0.5394 (pt0) REVERT: C 392 GLU cc_start: 0.7600 (mp0) cc_final: 0.7138 (mp0) REVERT: C 404 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7833 (tptp) REVERT: C 427 ASP cc_start: 0.7335 (m-30) cc_final: 0.7039 (m-30) REVERT: C 430 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7922 (mttm) REVERT: C 499 SER cc_start: 0.7412 (p) cc_final: 0.7112 (p) REVERT: C 549 ASP cc_start: 0.7253 (t0) cc_final: 0.6715 (t0) REVERT: C 593 LYS cc_start: 0.8007 (tptt) cc_final: 0.7398 (tppt) REVERT: C 611 GLU cc_start: 0.7522 (tt0) cc_final: 0.6813 (tt0) REVERT: C 616 ILE cc_start: 0.8398 (mp) cc_final: 0.8078 (mm) REVERT: C 644 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7357 (tt) REVERT: C 651 ASP cc_start: 0.7868 (m-30) cc_final: 0.7485 (m-30) REVERT: C 653 MET cc_start: 0.7190 (ttm) cc_final: 0.6831 (ttp) REVERT: C 656 SER cc_start: 0.8572 (t) cc_final: 0.8022 (m) REVERT: C 685 MET cc_start: 0.7346 (mtm) cc_final: 0.7000 (mtm) REVERT: C 696 ASP cc_start: 0.7049 (t0) cc_final: 0.6820 (t0) REVERT: C 706 ARG cc_start: 0.6688 (mmm-85) cc_final: 0.6384 (tpp80) REVERT: C 720 ARG cc_start: 0.7600 (mtp85) cc_final: 0.7382 (mpp80) REVERT: C 723 VAL cc_start: 0.8051 (t) cc_final: 0.7671 (m) REVERT: C 730 SER cc_start: 0.8653 (m) cc_final: 0.8262 (t) REVERT: C 731 ARG cc_start: 0.7736 (ptp-110) cc_final: 0.7155 (ptm160) REVERT: C 734 ILE cc_start: 0.7768 (mt) cc_final: 0.7538 (mp) REVERT: C 775 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7166 (tp30) REVERT: C 778 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7350 (mp0) REVERT: C 785 ASP cc_start: 0.6751 (p0) cc_final: 0.6308 (p0) REVERT: C 788 SER cc_start: 0.8361 (m) cc_final: 0.7814 (p) REVERT: C 790 ASP cc_start: 0.7582 (t70) cc_final: 0.6590 (p0) REVERT: C 800 MET cc_start: 0.7386 (mmp) cc_final: 0.6961 (mmt) REVERT: C 808 ASN cc_start: 0.8171 (t0) cc_final: 0.7925 (m-40) REVERT: C 882 ILE cc_start: 0.8432 (mp) cc_final: 0.8207 (mm) REVERT: C 914 LYS cc_start: 0.8042 (tppt) cc_final: 0.7707 (tppt) REVERT: C 930 ASP cc_start: 0.7868 (t0) cc_final: 0.7246 (m-30) REVERT: C 943 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8305 (pttp) REVERT: C 946 LEU cc_start: 0.8588 (pp) cc_final: 0.8385 (pp) REVERT: C 947 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7693 (tm-30) REVERT: C 950 GLU cc_start: 0.8464 (pt0) cc_final: 0.8228 (pt0) REVERT: C 960 LEU cc_start: 0.8151 (mp) cc_final: 0.7759 (pp) REVERT: C 1028 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8287 (pttt) REVERT: C 1030 GLU cc_start: 0.8559 (tp30) cc_final: 0.7954 (tp30) REVERT: C 1032 LYS cc_start: 0.9251 (tptt) cc_final: 0.8787 (mttt) REVERT: C 1035 LYS cc_start: 0.8548 (tppt) cc_final: 0.7876 (tppt) REVERT: C 1088 ASP cc_start: 0.7151 (p0) cc_final: 0.6948 (p0) REVERT: C 1090 ASN cc_start: 0.7689 (t0) cc_final: 0.7364 (t0) REVERT: C 1122 LYS cc_start: 0.8183 (tptm) cc_final: 0.7294 (tppp) REVERT: C 1126 ASP cc_start: 0.7341 (m-30) cc_final: 0.6641 (m-30) REVERT: C 1140 LYS cc_start: 0.7956 (ptpt) cc_final: 0.7535 (ptpp) REVERT: C 1143 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7337 (tm-30) REVERT: C 1146 GLN cc_start: 0.7512 (tp40) cc_final: 0.6929 (tp-100) REVERT: C 1147 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.7729 (tmm-80) REVERT: C 1177 ARG cc_start: 0.7669 (ptm160) cc_final: 0.7160 (ptp90) REVERT: C 1178 LYS cc_start: 0.8356 (tptm) cc_final: 0.8023 (mmmm) REVERT: C 1200 LYS cc_start: 0.8347 (tttt) cc_final: 0.7782 (mtpt) REVERT: C 1210 ILE cc_start: 0.7872 (tt) cc_final: 0.7584 (pt) REVERT: C 1216 ARG cc_start: 0.7126 (mtm180) cc_final: 0.6212 (mtm180) REVERT: C 1229 TYR cc_start: 0.8284 (m-80) cc_final: 0.7879 (m-10) REVERT: C 1244 HIS cc_start: 0.7314 (t-90) cc_final: 0.7056 (t70) REVERT: C 1264 GLN cc_start: 0.8255 (mp10) cc_final: 0.7846 (mp10) REVERT: C 1278 LEU cc_start: 0.8208 (tp) cc_final: 0.8005 (tp) REVERT: C 1279 GLU cc_start: 0.7302 (pm20) cc_final: 0.6664 (pm20) REVERT: C 1289 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7135 (mm-30) REVERT: C 1290 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7098 (mpp) REVERT: C 1293 VAL cc_start: 0.7807 (t) cc_final: 0.7517 (p) REVERT: C 1296 ASP cc_start: 0.6752 (t0) cc_final: 0.6336 (t0) REVERT: C 1303 LYS cc_start: 0.7860 (mtmm) cc_final: 0.7655 (mtmm) REVERT: C 1321 GLU cc_start: 0.6489 (tt0) cc_final: 0.6150 (pp20) REVERT: C 1331 ARG cc_start: 0.7441 (ttm170) cc_final: 0.7234 (ttm170) REVERT: C 1340 GLU cc_start: 0.6323 (tp30) cc_final: 0.5909 (tp30) REVERT: D 17 PHE cc_start: 0.7770 (p90) cc_final: 0.7545 (p90) REVERT: D 21 LYS cc_start: 0.8115 (ptpt) cc_final: 0.7405 (ptmm) REVERT: D 33 TRP cc_start: 0.7926 (m-10) cc_final: 0.7663 (m-10) REVERT: D 39 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7870 (mtpt) REVERT: D 52 GLU cc_start: 0.6971 (tp30) cc_final: 0.6736 (tm-30) REVERT: D 53 ARG cc_start: 0.7095 (ttt90) cc_final: 0.6464 (ttt90) REVERT: D 54 ASP cc_start: 0.7573 (t0) cc_final: 0.7222 (t0) REVERT: D 60 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.6970 (mtp180) REVERT: D 66 LYS cc_start: 0.7796 (mtpp) cc_final: 0.7576 (mtpp) REVERT: D 96 LYS cc_start: 0.8331 (mtpp) cc_final: 0.8024 (mmtm) REVERT: D 115 TRP cc_start: 0.8468 (m-10) cc_final: 0.8231 (m-10) REVERT: D 118 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7722 (mmmt) REVERT: D 138 VAL cc_start: 0.8481 (t) cc_final: 0.8267 (t) REVERT: D 141 PHE cc_start: 0.7935 (m-80) cc_final: 0.7393 (m-10) REVERT: D 148 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6455 (tm-30) REVERT: D 151 MET cc_start: 0.7878 (pmm) cc_final: 0.7234 (pmm) REVERT: D 157 GLN cc_start: 0.7796 (mt0) cc_final: 0.7410 (mt0) REVERT: D 158 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7826 (mp10) REVERT: D 198 CYS cc_start: 0.8347 (t) cc_final: 0.6561 (t) REVERT: D 201 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8649 (mm) REVERT: D 215 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8598 (ptpt) REVERT: D 219 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8502 (ttpp) REVERT: D 235 GLU cc_start: 0.7274 (pm20) cc_final: 0.6861 (pm20) REVERT: D 236 TRP cc_start: 0.8275 (m-10) cc_final: 0.7914 (m-10) REVERT: D 275 ARG cc_start: 0.7886 (tpp-160) cc_final: 0.7332 (tpp-160) REVERT: D 282 LEU cc_start: 0.8475 (mt) cc_final: 0.8090 (tt) REVERT: D 293 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7472 (mtp180) REVERT: D 297 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7385 (tmm-80) REVERT: D 298 MET cc_start: 0.7806 (ttp) cc_final: 0.6228 (ttp) REVERT: D 332 LYS cc_start: 0.6953 (mtmm) cc_final: 0.6461 (mtpp) REVERT: D 375 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7335 (tm-30) REVERT: D 400 MET cc_start: 0.6878 (tmm) cc_final: 0.6335 (tmm) REVERT: D 475 GLU cc_start: 0.7526 (mp0) cc_final: 0.7070 (mp0) REVERT: D 495 ASN cc_start: 0.7012 (m-40) cc_final: 0.6478 (m110) REVERT: D 500 ILE cc_start: 0.8209 (mm) cc_final: 0.7845 (tt) REVERT: D 511 TYR cc_start: 0.8098 (t80) cc_final: 0.7521 (t80) REVERT: D 521 LYS cc_start: 0.8001 (tttm) cc_final: 0.7791 (mtpp) REVERT: D 549 LYS cc_start: 0.7642 (tptt) cc_final: 0.7416 (mmtt) REVERT: D 556 GLU cc_start: 0.7403 (tt0) cc_final: 0.6931 (tm-30) REVERT: D 589 TYR cc_start: 0.8242 (t80) cc_final: 0.7909 (t80) REVERT: D 610 ARG cc_start: 0.7924 (tpp-160) cc_final: 0.7654 (mmt-90) REVERT: D 649 LYS cc_start: 0.8544 (mmmt) cc_final: 0.7971 (mmmt) REVERT: D 652 GLU cc_start: 0.8615 (mp0) cc_final: 0.7514 (mp0) REVERT: D 665 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: D 684 ASP cc_start: 0.7447 (m-30) cc_final: 0.7121 (m-30) REVERT: D 691 ASP cc_start: 0.8016 (m-30) cc_final: 0.7718 (m-30) REVERT: D 692 ARG cc_start: 0.7453 (tmm-80) cc_final: 0.7232 (tmm-80) REVERT: D 695 LYS cc_start: 0.8525 (tmtt) cc_final: 0.7804 (ttpp) REVERT: D 714 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6723 (tm-30) REVERT: D 724 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7073 (mpp) REVERT: D 725 MET cc_start: 0.7461 (mtm) cc_final: 0.7150 (mtp) REVERT: D 765 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6785 (mm-30) REVERT: D 772 TYR cc_start: 0.8484 (t80) cc_final: 0.8069 (t80) REVERT: D 781 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8130 (tptp) REVERT: D 789 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7208 (ptmm) REVERT: D 793 SER cc_start: 0.7687 (p) cc_final: 0.7446 (p) REVERT: D 808 VAL cc_start: 0.8485 (t) cc_final: 0.8211 (m) REVERT: D 822 MET cc_start: 0.6551 (tmm) cc_final: 0.6106 (tmm) REVERT: D 838 ARG cc_start: 0.8016 (ttt180) cc_final: 0.7674 (tpp80) REVERT: D 842 ARG cc_start: 0.6464 (mtt180) cc_final: 0.5972 (mtt180) REVERT: D 865 HIS cc_start: 0.6458 (p90) cc_final: 0.5884 (p90) REVERT: D 880 VAL cc_start: 0.8481 (t) cc_final: 0.8267 (p) REVERT: D 1025 MET cc_start: 0.8722 (mpp) cc_final: 0.8429 (mpp) REVERT: D 1146 GLU cc_start: 0.7035 (pp20) cc_final: 0.6454 (pp20) REVERT: D 1173 ARG cc_start: 0.8248 (ptm160) cc_final: 0.7927 (ptm160) REVERT: D 1188 GLU cc_start: 0.6599 (pm20) cc_final: 0.5614 (pp20) REVERT: D 1218 HIS cc_start: 0.7955 (m-70) cc_final: 0.7677 (m-70) REVERT: D 1242 ARG cc_start: 0.7464 (ttm110) cc_final: 0.7205 (ptp-110) REVERT: D 1248 ILE cc_start: 0.7607 (mm) cc_final: 0.7266 (tp) REVERT: D 1262 ARG cc_start: 0.7319 (ttp-110) cc_final: 0.6914 (ttp80) REVERT: D 1343 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6452 (mp0) REVERT: D 1365 TYR cc_start: 0.8019 (t80) cc_final: 0.7555 (t80) REVERT: E 52 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7333 (ttp80) REVERT: E 53 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7731 (mm-30) REVERT: E 68 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7845 (pm20) REVERT: G 11 VAL cc_start: 0.8417 (t) cc_final: 0.8038 (p) REVERT: G 27 ARG cc_start: 0.8305 (mtm180) cc_final: 0.7838 (mtm-85) REVERT: G 43 MET cc_start: 0.7518 (tmm) cc_final: 0.6970 (tmm) REVERT: G 74 VAL cc_start: 0.7189 (p) cc_final: 0.6851 (m) REVERT: G 80 TRP cc_start: 0.7574 (t60) cc_final: 0.6977 (t60) REVERT: G 84 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7378 (tpp-160) outliers start: 57 outliers final: 36 residues processed: 887 average time/residue: 0.4975 time to fit residues: 646.0682 Evaluate side-chains 841 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 798 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1078 LYS Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 304 optimal weight: 0.5980 chunk 329 optimal weight: 5.9990 chunk 271 optimal weight: 0.7980 chunk 302 optimal weight: 0.6980 chunk 103 optimal weight: 0.0970 chunk 244 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 686 GLN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS C1268 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN D1114 GLN E 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28008 Z= 0.169 Angle : 0.574 10.364 38141 Z= 0.295 Chirality : 0.042 0.244 4351 Planarity : 0.004 0.053 4731 Dihedral : 14.540 176.501 4488 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.48 % Allowed : 16.35 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3285 helix: 1.25 (0.16), residues: 1115 sheet: -0.32 (0.26), residues: 409 loop : -1.36 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1193 HIS 0.012 0.001 HIS C 343 PHE 0.019 0.001 PHE D 892 TYR 0.018 0.001 TYR C 172 ARG 0.012 0.000 ARG C 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 830 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8604 (mt) cc_final: 0.8311 (tt) REVERT: A 33 ARG cc_start: 0.7711 (ptm160) cc_final: 0.7184 (ptm160) REVERT: A 58 GLU cc_start: 0.7424 (pp20) cc_final: 0.6713 (pp20) REVERT: A 59 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7551 (p) REVERT: A 74 VAL cc_start: 0.8279 (m) cc_final: 0.7795 (p) REVERT: A 80 GLU cc_start: 0.7769 (tp30) cc_final: 0.7543 (tp30) REVERT: A 104 LYS cc_start: 0.8134 (tptp) cc_final: 0.7391 (tptp) REVERT: A 122 GLU cc_start: 0.6965 (pp20) cc_final: 0.6564 (pp20) REVERT: A 125 LYS cc_start: 0.8094 (ptpp) cc_final: 0.7856 (ttpp) REVERT: A 140 ILE cc_start: 0.5579 (OUTLIER) cc_final: 0.5312 (tp) REVERT: A 142 MET cc_start: 0.7868 (mtm) cc_final: 0.7592 (mtm) REVERT: A 153 VAL cc_start: 0.8831 (t) cc_final: 0.8550 (m) REVERT: A 170 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7099 (ttm-80) REVERT: A 171 LEU cc_start: 0.8457 (pp) cc_final: 0.7865 (pp) REVERT: A 198 LEU cc_start: 0.7461 (mm) cc_final: 0.6920 (mm) REVERT: A 204 GLU cc_start: 0.7750 (pt0) cc_final: 0.7443 (pt0) REVERT: A 206 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7058 (tm-30) REVERT: A 226 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6598 (tm-30) REVERT: B 17 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6582 (tm-30) REVERT: B 32 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6798 (tm-30) REVERT: B 51 MET cc_start: 0.7482 (mmm) cc_final: 0.7216 (mmm) REVERT: B 58 GLU cc_start: 0.7459 (pt0) cc_final: 0.7173 (pt0) REVERT: B 64 VAL cc_start: 0.7249 (t) cc_final: 0.7025 (p) REVERT: B 82 LEU cc_start: 0.8356 (mt) cc_final: 0.7991 (pp) REVERT: B 97 GLU cc_start: 0.7185 (pm20) cc_final: 0.6471 (pm20) REVERT: B 100 LEU cc_start: 0.8523 (mm) cc_final: 0.8201 (tt) REVERT: B 142 MET cc_start: 0.7342 (mmm) cc_final: 0.7062 (mmm) REVERT: B 188 GLU cc_start: 0.7146 (pt0) cc_final: 0.6804 (pt0) REVERT: B 205 MET cc_start: 0.7497 (ppp) cc_final: 0.6609 (ppp) REVERT: B 214 GLU cc_start: 0.6030 (tm-30) cc_final: 0.5149 (tm-30) REVERT: C 8 LYS cc_start: 0.8237 (mttt) cc_final: 0.7821 (mtpt) REVERT: C 17 LYS cc_start: 0.8020 (mptt) cc_final: 0.7551 (mmtp) REVERT: C 99 LYS cc_start: 0.7939 (ttmm) cc_final: 0.7399 (mtmm) REVERT: C 121 GLU cc_start: 0.6554 (mm-30) cc_final: 0.6008 (mm-30) REVERT: C 151 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7273 (mtm110) REVERT: C 180 ARG cc_start: 0.7269 (ttp80) cc_final: 0.6788 (ttp80) REVERT: C 183 TRP cc_start: 0.7997 (m-10) cc_final: 0.7632 (m-10) REVERT: C 185 ASP cc_start: 0.6141 (p0) cc_final: 0.5642 (p0) REVERT: C 186 PHE cc_start: 0.7866 (m-80) cc_final: 0.6933 (m-10) REVERT: C 187 GLU cc_start: 0.7206 (mp0) cc_final: 0.6511 (mp0) REVERT: C 195 PHE cc_start: 0.7867 (m-80) cc_final: 0.7548 (m-80) REVERT: C 203 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7319 (ttmm) REVERT: C 214 ASN cc_start: 0.8745 (t0) cc_final: 0.8348 (t0) REVERT: C 245 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8218 (mtt-85) REVERT: C 260 LYS cc_start: 0.8834 (pttm) cc_final: 0.8630 (pptt) REVERT: C 262 TYR cc_start: 0.7765 (m-80) cc_final: 0.7027 (m-80) REVERT: C 346 TYR cc_start: 0.7016 (m-80) cc_final: 0.6623 (m-80) REVERT: C 349 GLU cc_start: 0.8224 (pm20) cc_final: 0.7820 (pm20) REVERT: C 365 GLU cc_start: 0.8121 (tp30) cc_final: 0.7892 (tp30) REVERT: C 374 GLU cc_start: 0.5996 (pt0) cc_final: 0.5648 (pt0) REVERT: C 390 PHE cc_start: 0.6863 (m-80) cc_final: 0.6596 (m-80) REVERT: C 392 GLU cc_start: 0.7582 (mp0) cc_final: 0.7185 (mp0) REVERT: C 427 ASP cc_start: 0.7273 (m-30) cc_final: 0.6967 (m-30) REVERT: C 430 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7487 (mttm) REVERT: C 434 ASP cc_start: 0.7993 (m-30) cc_final: 0.7552 (m-30) REVERT: C 499 SER cc_start: 0.7369 (p) cc_final: 0.7061 (p) REVERT: C 523 GLU cc_start: 0.7514 (tp30) cc_final: 0.7222 (tp30) REVERT: C 549 ASP cc_start: 0.7318 (t0) cc_final: 0.6757 (t0) REVERT: C 593 LYS cc_start: 0.8005 (tptt) cc_final: 0.7406 (tppt) REVERT: C 611 GLU cc_start: 0.7485 (tt0) cc_final: 0.6787 (mt-10) REVERT: C 616 ILE cc_start: 0.8327 (mp) cc_final: 0.7994 (mm) REVERT: C 651 ASP cc_start: 0.7905 (m-30) cc_final: 0.7535 (m-30) REVERT: C 653 MET cc_start: 0.7182 (ttm) cc_final: 0.6728 (ttp) REVERT: C 656 SER cc_start: 0.8587 (t) cc_final: 0.7993 (m) REVERT: C 730 SER cc_start: 0.8678 (m) cc_final: 0.8267 (t) REVERT: C 731 ARG cc_start: 0.7734 (ptp-110) cc_final: 0.7198 (ptm160) REVERT: C 778 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7339 (mp0) REVERT: C 785 ASP cc_start: 0.6647 (p0) cc_final: 0.6250 (p0) REVERT: C 788 SER cc_start: 0.8354 (m) cc_final: 0.7751 (p) REVERT: C 790 ASP cc_start: 0.7559 (t70) cc_final: 0.6564 (p0) REVERT: C 800 MET cc_start: 0.7392 (mmp) cc_final: 0.6986 (mmt) REVERT: C 811 ASN cc_start: 0.7790 (p0) cc_final: 0.7290 (p0) REVERT: C 882 ILE cc_start: 0.8408 (mp) cc_final: 0.8202 (mm) REVERT: C 914 LYS cc_start: 0.7997 (tppt) cc_final: 0.7676 (tppt) REVERT: C 930 ASP cc_start: 0.7888 (t0) cc_final: 0.7192 (m-30) REVERT: C 947 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7667 (tm-30) REVERT: C 950 GLU cc_start: 0.8467 (pt0) cc_final: 0.8231 (pt0) REVERT: C 960 LEU cc_start: 0.8151 (mp) cc_final: 0.7773 (pp) REVERT: C 1028 LYS cc_start: 0.8589 (ptpp) cc_final: 0.8280 (pttt) REVERT: C 1030 GLU cc_start: 0.8557 (tp30) cc_final: 0.7953 (tp30) REVERT: C 1032 LYS cc_start: 0.9233 (tptt) cc_final: 0.8767 (mttt) REVERT: C 1035 LYS cc_start: 0.8566 (tppt) cc_final: 0.7894 (tppt) REVERT: C 1095 ASP cc_start: 0.7488 (m-30) cc_final: 0.7122 (m-30) REVERT: C 1122 LYS cc_start: 0.8206 (tptm) cc_final: 0.7567 (tptp) REVERT: C 1126 ASP cc_start: 0.7261 (m-30) cc_final: 0.6618 (m-30) REVERT: C 1140 LYS cc_start: 0.7956 (ptpt) cc_final: 0.7375 (ptpt) REVERT: C 1143 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7107 (tm-30) REVERT: C 1146 GLN cc_start: 0.7501 (tp40) cc_final: 0.6910 (tp-100) REVERT: C 1147 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.7787 (ttm-80) REVERT: C 1177 ARG cc_start: 0.7720 (ptm160) cc_final: 0.7152 (ptp90) REVERT: C 1178 LYS cc_start: 0.8367 (tptm) cc_final: 0.7973 (mmmm) REVERT: C 1194 GLU cc_start: 0.7062 (pm20) cc_final: 0.6760 (pm20) REVERT: C 1200 LYS cc_start: 0.8231 (tttt) cc_final: 0.7687 (mtpt) REVERT: C 1210 ILE cc_start: 0.7885 (tt) cc_final: 0.7552 (pt) REVERT: C 1229 TYR cc_start: 0.8257 (m-80) cc_final: 0.7776 (m-10) REVERT: C 1244 HIS cc_start: 0.7275 (t-90) cc_final: 0.6990 (t70) REVERT: C 1264 GLN cc_start: 0.8241 (mp10) cc_final: 0.7858 (mp10) REVERT: C 1268 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6611 (pp30) REVERT: C 1279 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6537 (pm20) REVERT: C 1290 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7298 (mpp) REVERT: C 1303 LYS cc_start: 0.7881 (mtmm) cc_final: 0.7633 (mtmm) REVERT: C 1340 GLU cc_start: 0.6345 (tp30) cc_final: 0.5930 (tp30) REVERT: D 21 LYS cc_start: 0.8159 (ptpt) cc_final: 0.7469 (ptmm) REVERT: D 29 MET cc_start: 0.7750 (ttt) cc_final: 0.7385 (ttt) REVERT: D 33 TRP cc_start: 0.7829 (m-10) cc_final: 0.7339 (m-10) REVERT: D 39 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7794 (mtmm) REVERT: D 50 LYS cc_start: 0.8288 (mtpt) cc_final: 0.8018 (mtpt) REVERT: D 52 GLU cc_start: 0.7040 (tp30) cc_final: 0.6629 (tm-30) REVERT: D 53 ARG cc_start: 0.7154 (ttt90) cc_final: 0.6715 (ttt90) REVERT: D 66 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7639 (mtpp) REVERT: D 96 LYS cc_start: 0.8290 (mtpp) cc_final: 0.8010 (mmtm) REVERT: D 115 TRP cc_start: 0.8476 (m-10) cc_final: 0.8231 (m-10) REVERT: D 118 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7834 (mmmt) REVERT: D 128 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7527 (mt) REVERT: D 148 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6382 (tm-30) REVERT: D 151 MET cc_start: 0.7879 (pmm) cc_final: 0.7350 (pmm) REVERT: D 158 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7334 (tm-30) REVERT: D 198 CYS cc_start: 0.7454 (t) cc_final: 0.6995 (t) REVERT: D 200 GLN cc_start: 0.8362 (pp30) cc_final: 0.8063 (pp30) REVERT: D 201 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8795 (mm) REVERT: D 213 LYS cc_start: 0.8080 (mmpt) cc_final: 0.7831 (mmpt) REVERT: D 215 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8600 (ptpt) REVERT: D 219 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8513 (ttpp) REVERT: D 221 ILE cc_start: 0.8580 (tp) cc_final: 0.8344 (tp) REVERT: D 235 GLU cc_start: 0.7321 (pm20) cc_final: 0.6890 (pm20) REVERT: D 236 TRP cc_start: 0.8288 (m-10) cc_final: 0.7949 (m-10) REVERT: D 282 LEU cc_start: 0.8463 (mt) cc_final: 0.8135 (tt) REVERT: D 297 ARG cc_start: 0.7841 (ttp80) cc_final: 0.7438 (tmm-80) REVERT: D 332 LYS cc_start: 0.6983 (mtmm) cc_final: 0.6519 (mtpp) REVERT: D 375 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7364 (tm-30) REVERT: D 400 MET cc_start: 0.6712 (tmm) cc_final: 0.6444 (tmm) REVERT: D 442 ILE cc_start: 0.8291 (tt) cc_final: 0.7892 (pt) REVERT: D 466 MET cc_start: 0.7455 (pmm) cc_final: 0.6689 (ptm) REVERT: D 475 GLU cc_start: 0.7543 (mp0) cc_final: 0.7043 (mp0) REVERT: D 495 ASN cc_start: 0.6937 (m-40) cc_final: 0.6581 (m110) REVERT: D 500 ILE cc_start: 0.8212 (mm) cc_final: 0.7872 (tt) REVERT: D 549 LYS cc_start: 0.7654 (tptt) cc_final: 0.7420 (mmtt) REVERT: D 554 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6571 (tm-30) REVERT: D 556 GLU cc_start: 0.7398 (tt0) cc_final: 0.7087 (tm-30) REVERT: D 579 LEU cc_start: 0.8316 (tp) cc_final: 0.8088 (tp) REVERT: D 589 TYR cc_start: 0.8249 (t80) cc_final: 0.8032 (t80) REVERT: D 610 ARG cc_start: 0.7977 (tpp-160) cc_final: 0.7666 (mmt-90) REVERT: D 649 LYS cc_start: 0.8518 (mmmt) cc_final: 0.7996 (mmmt) REVERT: D 652 GLU cc_start: 0.8599 (mp0) cc_final: 0.7537 (mp0) REVERT: D 665 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7361 (mp10) REVERT: D 684 ASP cc_start: 0.7471 (m-30) cc_final: 0.7186 (m-30) REVERT: D 691 ASP cc_start: 0.7940 (m-30) cc_final: 0.7649 (m-30) REVERT: D 695 LYS cc_start: 0.8526 (tmtt) cc_final: 0.8165 (tmtt) REVERT: D 714 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6676 (tm-30) REVERT: D 724 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7157 (mpp) REVERT: D 725 MET cc_start: 0.7513 (mtm) cc_final: 0.7298 (mtm) REVERT: D 772 TYR cc_start: 0.8331 (t80) cc_final: 0.7973 (t80) REVERT: D 781 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8118 (tptm) REVERT: D 789 LYS cc_start: 0.7708 (ttpt) cc_final: 0.7058 (ptmt) REVERT: D 793 SER cc_start: 0.7697 (p) cc_final: 0.7410 (p) REVERT: D 808 VAL cc_start: 0.8489 (t) cc_final: 0.8276 (m) REVERT: D 822 MET cc_start: 0.6527 (tmm) cc_final: 0.6050 (tmm) REVERT: D 842 ARG cc_start: 0.6388 (mtt180) cc_final: 0.6095 (mtt180) REVERT: D 915 ILE cc_start: 0.8202 (tt) cc_final: 0.7786 (pt) REVERT: D 992 LYS cc_start: 0.7338 (mmmm) cc_final: 0.7100 (mmmt) REVERT: D 1025 MET cc_start: 0.8744 (mpp) cc_final: 0.8401 (mpp) REVERT: D 1146 GLU cc_start: 0.7131 (pp20) cc_final: 0.6564 (pp20) REVERT: D 1173 ARG cc_start: 0.8341 (ptm160) cc_final: 0.8004 (ptm160) REVERT: D 1188 GLU cc_start: 0.6584 (pm20) cc_final: 0.5420 (pp20) REVERT: D 1218 HIS cc_start: 0.7981 (m-70) cc_final: 0.7621 (m-70) REVERT: D 1242 ARG cc_start: 0.7437 (ttm110) cc_final: 0.7208 (ptp-110) REVERT: D 1248 ILE cc_start: 0.7726 (mm) cc_final: 0.7313 (tp) REVERT: D 1250 ASP cc_start: 0.7404 (p0) cc_final: 0.7105 (p0) REVERT: D 1259 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7239 (mm-40) REVERT: D 1262 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.6491 (ttp80) REVERT: D 1286 LYS cc_start: 0.8271 (ttmm) cc_final: 0.8009 (tppp) REVERT: D 1343 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6488 (mp0) REVERT: D 1365 TYR cc_start: 0.8051 (t80) cc_final: 0.7589 (t80) REVERT: E 30 MET cc_start: 0.7409 (mmt) cc_final: 0.7206 (mmt) REVERT: E 31 GLN cc_start: 0.7775 (tp40) cc_final: 0.7528 (tp40) REVERT: E 52 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7342 (ttp80) REVERT: E 53 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7639 (mm-30) REVERT: E 62 GLN cc_start: 0.8333 (tp40) cc_final: 0.7801 (tp40) REVERT: G 11 VAL cc_start: 0.8415 (t) cc_final: 0.8046 (p) REVERT: G 27 ARG cc_start: 0.8309 (mtm180) cc_final: 0.7833 (mtm-85) REVERT: G 43 MET cc_start: 0.7491 (tmm) cc_final: 0.7148 (tmm) REVERT: G 72 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7708 (mm110) REVERT: G 74 VAL cc_start: 0.7027 (p) cc_final: 0.6803 (m) REVERT: G 80 TRP cc_start: 0.7709 (t60) cc_final: 0.6898 (t60) REVERT: G 84 ARG cc_start: 0.8190 (tpp80) cc_final: 0.7817 (tpt90) outliers start: 70 outliers final: 40 residues processed: 855 average time/residue: 0.4715 time to fit residues: 586.6919 Evaluate side-chains 835 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 786 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1268 GLN Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 65 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 204 optimal weight: 0.4980 chunk 305 optimal weight: 0.0980 chunk 323 optimal weight: 0.0030 chunk 159 optimal weight: 0.7980 chunk 289 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 811 ASN ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 469 HIS ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28008 Z= 0.148 Angle : 0.558 11.723 38141 Z= 0.286 Chirality : 0.042 0.295 4351 Planarity : 0.004 0.051 4731 Dihedral : 14.521 176.350 4488 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.94 % Allowed : 17.99 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3285 helix: 1.26 (0.16), residues: 1118 sheet: -0.28 (0.27), residues: 384 loop : -1.32 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1193 HIS 0.011 0.001 HIS C 343 PHE 0.021 0.001 PHE D1319 TYR 0.020 0.001 TYR D1186 ARG 0.008 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 811 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8614 (mt) cc_final: 0.8303 (tt) REVERT: A 33 ARG cc_start: 0.7654 (ptm160) cc_final: 0.7150 (ptm160) REVERT: A 58 GLU cc_start: 0.7431 (pp20) cc_final: 0.6662 (pp20) REVERT: A 59 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7479 (p) REVERT: A 74 VAL cc_start: 0.8238 (m) cc_final: 0.7792 (p) REVERT: A 80 GLU cc_start: 0.7738 (tp30) cc_final: 0.7520 (tp30) REVERT: A 104 LYS cc_start: 0.8047 (tptp) cc_final: 0.7215 (tptp) REVERT: A 122 GLU cc_start: 0.6911 (pp20) cc_final: 0.6554 (pp20) REVERT: A 125 LYS cc_start: 0.8096 (ptpp) cc_final: 0.7873 (ttpp) REVERT: A 140 ILE cc_start: 0.5410 (OUTLIER) cc_final: 0.5131 (tp) REVERT: A 142 MET cc_start: 0.7852 (mtm) cc_final: 0.7606 (mtm) REVERT: A 153 VAL cc_start: 0.8811 (t) cc_final: 0.8518 (m) REVERT: A 170 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7448 (ttm-80) REVERT: A 171 LEU cc_start: 0.8426 (pp) cc_final: 0.7798 (pp) REVERT: A 198 LEU cc_start: 0.7410 (mm) cc_final: 0.6906 (mm) REVERT: A 204 GLU cc_start: 0.7773 (pt0) cc_final: 0.7457 (pt0) REVERT: A 206 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7063 (tm-30) REVERT: A 212 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6811 (m-30) REVERT: A 226 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6608 (tm-30) REVERT: B 16 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7654 (mt) REVERT: B 17 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6849 (tm-30) REVERT: B 32 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6748 (tm-30) REVERT: B 51 MET cc_start: 0.7420 (mmm) cc_final: 0.7198 (mmm) REVERT: B 58 GLU cc_start: 0.7319 (pt0) cc_final: 0.7105 (pt0) REVERT: B 64 VAL cc_start: 0.7327 (t) cc_final: 0.7063 (p) REVERT: B 80 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6586 (tm-30) REVERT: B 82 LEU cc_start: 0.8406 (mt) cc_final: 0.7976 (pp) REVERT: B 97 GLU cc_start: 0.7198 (pm20) cc_final: 0.6561 (pm20) REVERT: B 100 LEU cc_start: 0.8626 (mm) cc_final: 0.8101 (tp) REVERT: B 142 MET cc_start: 0.7391 (mmm) cc_final: 0.7157 (mmm) REVERT: B 188 GLU cc_start: 0.6980 (pt0) cc_final: 0.6644 (pt0) REVERT: B 205 MET cc_start: 0.7542 (ppp) cc_final: 0.6598 (ppp) REVERT: B 214 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5672 (tm-30) REVERT: C 8 LYS cc_start: 0.8218 (mttt) cc_final: 0.7805 (mtpt) REVERT: C 17 LYS cc_start: 0.7990 (mptt) cc_final: 0.7462 (mmtp) REVERT: C 87 ILE cc_start: 0.8212 (tp) cc_final: 0.7702 (pt) REVERT: C 92 TYR cc_start: 0.8491 (t80) cc_final: 0.7994 (t80) REVERT: C 151 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7648 (ttm110) REVERT: C 180 ARG cc_start: 0.7239 (ttp80) cc_final: 0.6759 (ttp80) REVERT: C 183 TRP cc_start: 0.7963 (m-10) cc_final: 0.7475 (m-10) REVERT: C 185 ASP cc_start: 0.6044 (p0) cc_final: 0.5177 (p0) REVERT: C 186 PHE cc_start: 0.7758 (m-80) cc_final: 0.7215 (m-80) REVERT: C 187 GLU cc_start: 0.7177 (mp0) cc_final: 0.6227 (mp0) REVERT: C 195 PHE cc_start: 0.7832 (m-80) cc_final: 0.7410 (m-80) REVERT: C 203 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7338 (ttmm) REVERT: C 211 ARG cc_start: 0.7582 (mtp85) cc_final: 0.6836 (mtp85) REVERT: C 214 ASN cc_start: 0.8717 (t0) cc_final: 0.8347 (t0) REVERT: C 218 GLU cc_start: 0.8152 (pm20) cc_final: 0.7694 (pm20) REVERT: C 245 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8177 (mtt-85) REVERT: C 262 TYR cc_start: 0.7740 (m-80) cc_final: 0.6941 (m-80) REVERT: C 346 TYR cc_start: 0.6999 (m-80) cc_final: 0.6583 (m-80) REVERT: C 349 GLU cc_start: 0.8214 (pm20) cc_final: 0.7785 (pm20) REVERT: C 368 ARG cc_start: 0.8255 (ttp-170) cc_final: 0.7762 (mtm110) REVERT: C 371 ARG cc_start: 0.6464 (mtp-110) cc_final: 0.6211 (ptm160) REVERT: C 374 GLU cc_start: 0.5913 (pt0) cc_final: 0.4868 (pt0) REVERT: C 392 GLU cc_start: 0.7476 (mp0) cc_final: 0.7105 (mp0) REVERT: C 427 ASP cc_start: 0.7249 (m-30) cc_final: 0.6949 (m-30) REVERT: C 430 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7491 (mttm) REVERT: C 434 ASP cc_start: 0.7919 (m-30) cc_final: 0.7488 (m-30) REVERT: C 499 SER cc_start: 0.7331 (p) cc_final: 0.7017 (p) REVERT: C 549 ASP cc_start: 0.7327 (t0) cc_final: 0.6752 (t0) REVERT: C 593 LYS cc_start: 0.7954 (tptt) cc_final: 0.7385 (tppt) REVERT: C 602 GLU cc_start: 0.7256 (tp30) cc_final: 0.7005 (tp30) REVERT: C 611 GLU cc_start: 0.7485 (tt0) cc_final: 0.7007 (tt0) REVERT: C 653 MET cc_start: 0.7197 (ttm) cc_final: 0.6738 (ttp) REVERT: C 656 SER cc_start: 0.8557 (t) cc_final: 0.7986 (m) REVERT: C 720 ARG cc_start: 0.7585 (mtp180) cc_final: 0.7381 (mpp80) REVERT: C 730 SER cc_start: 0.8679 (m) cc_final: 0.8153 (t) REVERT: C 731 ARG cc_start: 0.7731 (ptp-110) cc_final: 0.7198 (ptm160) REVERT: C 740 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6819 (mt-10) REVERT: C 778 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7322 (mp0) REVERT: C 788 SER cc_start: 0.8294 (m) cc_final: 0.7643 (p) REVERT: C 790 ASP cc_start: 0.7559 (t70) cc_final: 0.6521 (p0) REVERT: C 800 MET cc_start: 0.7342 (mmp) cc_final: 0.6952 (mmt) REVERT: C 811 ASN cc_start: 0.7788 (p0) cc_final: 0.7191 (p0) REVERT: C 814 ASP cc_start: 0.7479 (m-30) cc_final: 0.6859 (m-30) REVERT: C 825 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6993 (tm-30) REVERT: C 882 ILE cc_start: 0.8406 (mp) cc_final: 0.8198 (mm) REVERT: C 914 LYS cc_start: 0.8007 (tppt) cc_final: 0.7674 (tppt) REVERT: C 930 ASP cc_start: 0.7813 (t0) cc_final: 0.7205 (m-30) REVERT: C 947 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 950 GLU cc_start: 0.8457 (pt0) cc_final: 0.8210 (pt0) REVERT: C 960 LEU cc_start: 0.8197 (mp) cc_final: 0.7804 (pp) REVERT: C 1028 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8245 (pttt) REVERT: C 1030 GLU cc_start: 0.8567 (tp30) cc_final: 0.7980 (tp30) REVERT: C 1032 LYS cc_start: 0.9224 (tptt) cc_final: 0.8764 (mttt) REVERT: C 1035 LYS cc_start: 0.8542 (tppt) cc_final: 0.7892 (tppt) REVERT: C 1095 ASP cc_start: 0.7453 (m-30) cc_final: 0.7146 (m-30) REVERT: C 1122 LYS cc_start: 0.8268 (tptm) cc_final: 0.7598 (tptp) REVERT: C 1126 ASP cc_start: 0.7229 (m-30) cc_final: 0.6613 (m-30) REVERT: C 1140 LYS cc_start: 0.7914 (ptpt) cc_final: 0.7631 (ptpt) REVERT: C 1143 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7084 (tm-30) REVERT: C 1146 GLN cc_start: 0.7462 (tp40) cc_final: 0.6872 (tp-100) REVERT: C 1147 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.7753 (ttm-80) REVERT: C 1178 LYS cc_start: 0.8391 (tptm) cc_final: 0.7945 (mmmm) REVERT: C 1194 GLU cc_start: 0.6930 (pm20) cc_final: 0.6658 (pm20) REVERT: C 1200 LYS cc_start: 0.8219 (tttt) cc_final: 0.7660 (mtpt) REVERT: C 1210 ILE cc_start: 0.7874 (tt) cc_final: 0.7555 (pt) REVERT: C 1229 TYR cc_start: 0.8184 (m-80) cc_final: 0.7764 (m-80) REVERT: C 1244 HIS cc_start: 0.7252 (t-90) cc_final: 0.7048 (t70) REVERT: C 1264 GLN cc_start: 0.8190 (mp10) cc_final: 0.7794 (mp10) REVERT: C 1279 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6523 (pm20) REVERT: C 1289 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6978 (mm-30) REVERT: C 1290 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7347 (mpp) REVERT: C 1293 VAL cc_start: 0.7497 (t) cc_final: 0.6889 (t) REVERT: C 1303 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7617 (mtmm) REVERT: C 1304 MET cc_start: 0.7622 (tpp) cc_final: 0.6967 (tmm) REVERT: D 21 LYS cc_start: 0.8032 (ptpt) cc_final: 0.7369 (ptmm) REVERT: D 29 MET cc_start: 0.7807 (ttt) cc_final: 0.7406 (ttt) REVERT: D 33 TRP cc_start: 0.7584 (m-10) cc_final: 0.7195 (m-10) REVERT: D 39 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7786 (mtmt) REVERT: D 50 LYS cc_start: 0.8246 (mtpt) cc_final: 0.8001 (mmmt) REVERT: D 52 GLU cc_start: 0.7031 (tp30) cc_final: 0.6614 (tm-30) REVERT: D 53 ARG cc_start: 0.7148 (ttt90) cc_final: 0.6712 (ttt90) REVERT: D 66 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7677 (mtpp) REVERT: D 96 LYS cc_start: 0.8284 (mtpp) cc_final: 0.8031 (mmtm) REVERT: D 115 TRP cc_start: 0.8464 (m-10) cc_final: 0.8244 (m-10) REVERT: D 118 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7815 (mmmt) REVERT: D 128 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7369 (mt) REVERT: D 138 VAL cc_start: 0.8422 (t) cc_final: 0.8167 (m) REVERT: D 148 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6354 (tm-30) REVERT: D 151 MET cc_start: 0.8072 (pmm) cc_final: 0.7388 (pmm) REVERT: D 158 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7336 (tm-30) REVERT: D 198 CYS cc_start: 0.7846 (t) cc_final: 0.6951 (t) REVERT: D 200 GLN cc_start: 0.8416 (pp30) cc_final: 0.8150 (pp30) REVERT: D 201 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8781 (mm) REVERT: D 202 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8126 (mtm-85) REVERT: D 213 LYS cc_start: 0.8111 (mmpt) cc_final: 0.7857 (mmpt) REVERT: D 215 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8588 (ptpt) REVERT: D 219 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8514 (ttpp) REVERT: D 221 ILE cc_start: 0.8668 (tp) cc_final: 0.8377 (tp) REVERT: D 235 GLU cc_start: 0.7342 (pm20) cc_final: 0.7028 (pm20) REVERT: D 275 ARG cc_start: 0.7715 (tpp-160) cc_final: 0.7195 (tpp-160) REVERT: D 282 LEU cc_start: 0.8451 (mt) cc_final: 0.8151 (tt) REVERT: D 297 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7499 (tmm-80) REVERT: D 298 MET cc_start: 0.7559 (ttp) cc_final: 0.6932 (ttp) REVERT: D 303 VAL cc_start: 0.7932 (t) cc_final: 0.6988 (m) REVERT: D 332 LYS cc_start: 0.6864 (mtmm) cc_final: 0.6426 (mtpp) REVERT: D 375 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7394 (tm-30) REVERT: D 402 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7036 (tm-30) REVERT: D 442 ILE cc_start: 0.8302 (tt) cc_final: 0.7945 (pt) REVERT: D 466 MET cc_start: 0.7396 (pmm) cc_final: 0.6751 (ptm) REVERT: D 475 GLU cc_start: 0.7477 (mp0) cc_final: 0.7047 (mp0) REVERT: D 500 ILE cc_start: 0.8198 (mm) cc_final: 0.7890 (tt) REVERT: D 504 GLN cc_start: 0.7670 (mt0) cc_final: 0.7427 (mt0) REVERT: D 549 LYS cc_start: 0.7564 (tptt) cc_final: 0.7329 (mmtt) REVERT: D 554 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6531 (tm-30) REVERT: D 556 GLU cc_start: 0.7484 (tt0) cc_final: 0.7280 (tm-30) REVERT: D 573 THR cc_start: 0.8203 (m) cc_final: 0.7747 (p) REVERT: D 579 LEU cc_start: 0.8231 (tp) cc_final: 0.7958 (tp) REVERT: D 589 TYR cc_start: 0.8233 (t80) cc_final: 0.7944 (t80) REVERT: D 610 ARG cc_start: 0.7987 (tpp-160) cc_final: 0.7627 (mmt-90) REVERT: D 649 LYS cc_start: 0.8551 (mmmt) cc_final: 0.7910 (mmmt) REVERT: D 652 GLU cc_start: 0.8584 (mp0) cc_final: 0.7545 (mp0) REVERT: D 665 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: D 684 ASP cc_start: 0.7461 (m-30) cc_final: 0.7143 (m-30) REVERT: D 691 ASP cc_start: 0.7993 (m-30) cc_final: 0.7703 (m-30) REVERT: D 695 LYS cc_start: 0.8512 (tmtt) cc_final: 0.8164 (tmtt) REVERT: D 714 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6584 (tm-30) REVERT: D 724 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7120 (mpp) REVERT: D 725 MET cc_start: 0.7525 (mtm) cc_final: 0.7030 (mtp) REVERT: D 770 LEU cc_start: 0.7754 (mm) cc_final: 0.7354 (mt) REVERT: D 772 TYR cc_start: 0.8320 (t80) cc_final: 0.7871 (t80) REVERT: D 781 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8146 (tptm) REVERT: D 789 LYS cc_start: 0.7635 (ttpt) cc_final: 0.7207 (ttpp) REVERT: D 793 SER cc_start: 0.7644 (p) cc_final: 0.7414 (p) REVERT: D 807 LEU cc_start: 0.8264 (tp) cc_final: 0.7928 (tt) REVERT: D 808 VAL cc_start: 0.8488 (t) cc_final: 0.8260 (m) REVERT: D 822 MET cc_start: 0.6484 (tmm) cc_final: 0.5991 (tmm) REVERT: D 842 ARG cc_start: 0.6461 (mtt180) cc_final: 0.5851 (mtt180) REVERT: D 992 LYS cc_start: 0.7298 (mmmm) cc_final: 0.7085 (mmmt) REVERT: D 1025 MET cc_start: 0.8760 (mpp) cc_final: 0.8530 (mpp) REVERT: D 1099 TYR cc_start: 0.7779 (m-80) cc_final: 0.6744 (m-80) REVERT: D 1146 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6643 (pp20) REVERT: D 1173 ARG cc_start: 0.8391 (ptm160) cc_final: 0.8056 (ptm160) REVERT: D 1188 GLU cc_start: 0.6400 (pm20) cc_final: 0.5475 (pp20) REVERT: D 1218 HIS cc_start: 0.7948 (m-70) cc_final: 0.7618 (m-70) REVERT: D 1248 ILE cc_start: 0.7700 (mm) cc_final: 0.7309 (tp) REVERT: D 1250 ASP cc_start: 0.7352 (p0) cc_final: 0.7029 (p0) REVERT: D 1286 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7980 (tppp) REVERT: D 1343 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6548 (mp0) REVERT: D 1365 TYR cc_start: 0.8045 (t80) cc_final: 0.7623 (t80) REVERT: E 30 MET cc_start: 0.7382 (mmt) cc_final: 0.7133 (mmt) REVERT: E 52 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7345 (ttp80) REVERT: E 53 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7646 (mm-30) REVERT: E 55 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: E 62 GLN cc_start: 0.8287 (tp40) cc_final: 0.7764 (tp40) REVERT: G 27 ARG cc_start: 0.8257 (mtm180) cc_final: 0.7807 (mtm-85) REVERT: G 72 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7839 (mm110) REVERT: G 73 MET cc_start: 0.6370 (ppp) cc_final: 0.6083 (ppp) REVERT: G 80 TRP cc_start: 0.7587 (t60) cc_final: 0.6949 (t60) REVERT: G 84 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7824 (tpt90) outliers start: 83 outliers final: 47 residues processed: 844 average time/residue: 0.4726 time to fit residues: 583.8806 Evaluate side-chains 835 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 775 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1048 LYS Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 65 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 276 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 290 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28008 Z= 0.253 Angle : 0.617 11.988 38141 Z= 0.319 Chirality : 0.043 0.302 4351 Planarity : 0.005 0.058 4731 Dihedral : 14.595 176.618 4488 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.76 % Allowed : 19.12 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3285 helix: 1.17 (0.16), residues: 1108 sheet: -0.25 (0.26), residues: 388 loop : -1.40 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 183 HIS 0.012 0.001 HIS C 343 PHE 0.024 0.002 PHE D1319 TYR 0.017 0.002 TYR A 152 ARG 0.009 0.001 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 809 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8480 (mt) cc_final: 0.8166 (tt) REVERT: A 33 ARG cc_start: 0.7638 (ptm160) cc_final: 0.7107 (ptm160) REVERT: A 59 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7984 (t) REVERT: A 74 VAL cc_start: 0.8243 (m) cc_final: 0.7842 (p) REVERT: A 80 GLU cc_start: 0.7814 (tp30) cc_final: 0.7560 (tp30) REVERT: A 104 LYS cc_start: 0.7861 (tptp) cc_final: 0.7181 (tptp) REVERT: A 114 ASP cc_start: 0.7922 (t0) cc_final: 0.7653 (t0) REVERT: A 122 GLU cc_start: 0.6768 (pp20) cc_final: 0.6519 (pp20) REVERT: A 125 LYS cc_start: 0.8194 (ptpp) cc_final: 0.7960 (ttpp) REVERT: A 142 MET cc_start: 0.7917 (mtm) cc_final: 0.7642 (mtm) REVERT: A 145 LYS cc_start: 0.7501 (mtpp) cc_final: 0.7262 (mtpp) REVERT: A 170 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7512 (ttm-80) REVERT: A 171 LEU cc_start: 0.8451 (pp) cc_final: 0.8246 (pp) REVERT: A 181 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7444 (mm-30) REVERT: A 188 GLU cc_start: 0.7592 (pm20) cc_final: 0.7141 (pm20) REVERT: A 198 LEU cc_start: 0.7573 (mm) cc_final: 0.7047 (mm) REVERT: A 204 GLU cc_start: 0.7710 (pt0) cc_final: 0.7437 (pt0) REVERT: A 206 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7042 (tm-30) REVERT: A 212 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6990 (m-30) REVERT: A 226 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6619 (tm-30) REVERT: A 233 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.7060 (t70) REVERT: B 16 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7766 (mt) REVERT: B 32 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6728 (tm-30) REVERT: B 51 MET cc_start: 0.7497 (mmm) cc_final: 0.7285 (mmm) REVERT: B 64 VAL cc_start: 0.7421 (t) cc_final: 0.7153 (p) REVERT: B 67 GLU cc_start: 0.7866 (pm20) cc_final: 0.7328 (pm20) REVERT: B 82 LEU cc_start: 0.8433 (mt) cc_final: 0.8031 (pp) REVERT: B 97 GLU cc_start: 0.7170 (pm20) cc_final: 0.6495 (pm20) REVERT: B 100 LEU cc_start: 0.8620 (mm) cc_final: 0.8061 (tp) REVERT: B 142 MET cc_start: 0.7505 (mmm) cc_final: 0.7268 (mmm) REVERT: B 143 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7156 (ptt180) REVERT: B 188 GLU cc_start: 0.6978 (pt0) cc_final: 0.6661 (pt0) REVERT: B 205 MET cc_start: 0.7638 (ppp) cc_final: 0.6692 (ppp) REVERT: B 214 GLU cc_start: 0.6139 (OUTLIER) cc_final: 0.5674 (tm-30) REVERT: C 8 LYS cc_start: 0.8289 (mttt) cc_final: 0.7839 (mtpt) REVERT: C 17 LYS cc_start: 0.8056 (mptt) cc_final: 0.7512 (mmtp) REVERT: C 87 ILE cc_start: 0.8217 (tp) cc_final: 0.7680 (pt) REVERT: C 151 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7644 (ptp-110) REVERT: C 185 ASP cc_start: 0.6194 (p0) cc_final: 0.5375 (p0) REVERT: C 186 PHE cc_start: 0.7865 (m-80) cc_final: 0.7382 (m-10) REVERT: C 187 GLU cc_start: 0.7189 (mp0) cc_final: 0.6214 (mp0) REVERT: C 195 PHE cc_start: 0.7784 (m-80) cc_final: 0.7318 (m-80) REVERT: C 203 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7471 (ttmm) REVERT: C 214 ASN cc_start: 0.8786 (t0) cc_final: 0.8371 (t0) REVERT: C 245 ARG cc_start: 0.8662 (mtt180) cc_final: 0.8220 (mtp180) REVERT: C 346 TYR cc_start: 0.7065 (m-80) cc_final: 0.6787 (m-80) REVERT: C 349 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: C 368 ARG cc_start: 0.8407 (ttp-170) cc_final: 0.7932 (mtm-85) REVERT: C 392 GLU cc_start: 0.7484 (mp0) cc_final: 0.6978 (mp0) REVERT: C 427 ASP cc_start: 0.7298 (m-30) cc_final: 0.7025 (m-30) REVERT: C 430 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7585 (mttp) REVERT: C 434 ASP cc_start: 0.7995 (m-30) cc_final: 0.7591 (m-30) REVERT: C 499 SER cc_start: 0.7373 (p) cc_final: 0.7107 (p) REVERT: C 523 GLU cc_start: 0.7667 (tp30) cc_final: 0.7409 (tp30) REVERT: C 538 LEU cc_start: 0.8253 (tp) cc_final: 0.8042 (tp) REVERT: C 549 ASP cc_start: 0.7418 (t0) cc_final: 0.7167 (t0) REVERT: C 583 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7368 (pp20) REVERT: C 593 LYS cc_start: 0.8062 (tptt) cc_final: 0.7448 (tppt) REVERT: C 611 GLU cc_start: 0.7439 (tt0) cc_final: 0.6828 (mt-10) REVERT: C 653 MET cc_start: 0.7365 (ttm) cc_final: 0.6977 (ttp) REVERT: C 656 SER cc_start: 0.8653 (t) cc_final: 0.8067 (m) REVERT: C 730 SER cc_start: 0.8708 (m) cc_final: 0.8311 (t) REVERT: C 731 ARG cc_start: 0.7814 (ptp-110) cc_final: 0.7387 (ptm160) REVERT: C 740 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6876 (mt-10) REVERT: C 778 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7385 (mp0) REVERT: C 779 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7884 (ttp80) REVERT: C 788 SER cc_start: 0.8414 (m) cc_final: 0.7683 (p) REVERT: C 790 ASP cc_start: 0.7446 (t70) cc_final: 0.7206 (t70) REVERT: C 800 MET cc_start: 0.7403 (mmp) cc_final: 0.7145 (mmm) REVERT: C 811 ASN cc_start: 0.7715 (p0) cc_final: 0.6633 (p0) REVERT: C 814 ASP cc_start: 0.7478 (m-30) cc_final: 0.6882 (m-30) REVERT: C 825 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6820 (tm-30) REVERT: C 882 ILE cc_start: 0.8449 (mp) cc_final: 0.8219 (mm) REVERT: C 914 LYS cc_start: 0.8038 (tppt) cc_final: 0.7711 (tppt) REVERT: C 930 ASP cc_start: 0.7798 (t0) cc_final: 0.7421 (m-30) REVERT: C 947 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7748 (tm-30) REVERT: C 948 ILE cc_start: 0.8797 (mm) cc_final: 0.8373 (mm) REVERT: C 950 GLU cc_start: 0.8535 (pt0) cc_final: 0.8289 (pt0) REVERT: C 960 LEU cc_start: 0.8163 (mp) cc_final: 0.7750 (pp) REVERT: C 1028 LYS cc_start: 0.8591 (ptpp) cc_final: 0.8248 (pttt) REVERT: C 1030 GLU cc_start: 0.8618 (tp30) cc_final: 0.8016 (tp30) REVERT: C 1032 LYS cc_start: 0.9222 (tptt) cc_final: 0.8820 (mttt) REVERT: C 1035 LYS cc_start: 0.8655 (tppt) cc_final: 0.7994 (tppt) REVERT: C 1095 ASP cc_start: 0.7590 (m-30) cc_final: 0.7291 (m-30) REVERT: C 1099 ASN cc_start: 0.8029 (t0) cc_final: 0.7176 (t0) REVERT: C 1119 MET cc_start: 0.8158 (tpp) cc_final: 0.7709 (tpt) REVERT: C 1122 LYS cc_start: 0.8306 (tptm) cc_final: 0.7439 (tppt) REVERT: C 1126 ASP cc_start: 0.7349 (m-30) cc_final: 0.6716 (m-30) REVERT: C 1131 MET cc_start: 0.8191 (ttt) cc_final: 0.7923 (ttt) REVERT: C 1133 LYS cc_start: 0.7704 (tppt) cc_final: 0.7425 (ttmm) REVERT: C 1140 LYS cc_start: 0.8100 (ptpt) cc_final: 0.7527 (ptpt) REVERT: C 1143 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7343 (tm-30) REVERT: C 1146 GLN cc_start: 0.7695 (tp40) cc_final: 0.7236 (tp-100) REVERT: C 1147 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8165 (mmm-85) REVERT: C 1174 GLU cc_start: 0.7722 (tp30) cc_final: 0.7221 (tp30) REVERT: C 1194 GLU cc_start: 0.7232 (pm20) cc_final: 0.6824 (pm20) REVERT: C 1200 LYS cc_start: 0.8341 (tttt) cc_final: 0.7981 (tttt) REVERT: C 1210 ILE cc_start: 0.7929 (tt) cc_final: 0.7674 (pt) REVERT: C 1229 TYR cc_start: 0.8226 (m-80) cc_final: 0.7754 (m-10) REVERT: C 1264 GLN cc_start: 0.8127 (mp10) cc_final: 0.7767 (mp10) REVERT: C 1268 GLN cc_start: 0.7163 (pp30) cc_final: 0.6940 (pp30) REVERT: C 1289 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7205 (mm-30) REVERT: C 1293 VAL cc_start: 0.7618 (t) cc_final: 0.7285 (t) REVERT: C 1303 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7688 (mtmm) REVERT: C 1332 SER cc_start: 0.7836 (p) cc_final: 0.7628 (p) REVERT: D 21 LYS cc_start: 0.8071 (ptpt) cc_final: 0.7456 (ptmm) REVERT: D 29 MET cc_start: 0.7953 (ttt) cc_final: 0.7316 (ttm) REVERT: D 31 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7614 (mtt-85) REVERT: D 33 TRP cc_start: 0.7829 (m-10) cc_final: 0.7141 (m-10) REVERT: D 39 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7846 (mtpt) REVERT: D 52 GLU cc_start: 0.7044 (tp30) cc_final: 0.6806 (tm-30) REVERT: D 53 ARG cc_start: 0.7420 (ttt90) cc_final: 0.6900 (ttt90) REVERT: D 60 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7168 (ttm-80) REVERT: D 115 TRP cc_start: 0.8528 (m-10) cc_final: 0.8280 (m-10) REVERT: D 118 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7875 (mmmt) REVERT: D 128 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7439 (mt) REVERT: D 138 VAL cc_start: 0.8558 (t) cc_final: 0.8276 (m) REVERT: D 148 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6398 (tm-30) REVERT: D 151 MET cc_start: 0.8100 (pmm) cc_final: 0.7394 (pmm) REVERT: D 158 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7731 (mp10) REVERT: D 177 ASP cc_start: 0.7477 (p0) cc_final: 0.7026 (p0) REVERT: D 179 LYS cc_start: 0.7318 (mtmm) cc_final: 0.7035 (mtmm) REVERT: D 180 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6526 (ppp) REVERT: D 192 MET cc_start: 0.7859 (tpp) cc_final: 0.7613 (tpp) REVERT: D 193 ASP cc_start: 0.6412 (t0) cc_final: 0.5891 (t0) REVERT: D 196 GLN cc_start: 0.8271 (mp10) cc_final: 0.7843 (mp10) REVERT: D 199 GLU cc_start: 0.8364 (pp20) cc_final: 0.8104 (pp20) REVERT: D 200 GLN cc_start: 0.8494 (pp30) cc_final: 0.8256 (pp30) REVERT: D 201 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8699 (mm) REVERT: D 213 LYS cc_start: 0.8186 (mmpt) cc_final: 0.7957 (mmpt) REVERT: D 215 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8602 (ptpt) REVERT: D 219 LYS cc_start: 0.8973 (ttmt) cc_final: 0.8545 (ttpp) REVERT: D 235 GLU cc_start: 0.7424 (pm20) cc_final: 0.7123 (pm20) REVERT: D 275 ARG cc_start: 0.7752 (tpp-160) cc_final: 0.7254 (tpp-160) REVERT: D 279 LEU cc_start: 0.8160 (tp) cc_final: 0.7955 (tp) REVERT: D 282 LEU cc_start: 0.8552 (mt) cc_final: 0.8300 (tt) REVERT: D 295 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7311 (tm-30) REVERT: D 297 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7362 (tmm-80) REVERT: D 298 MET cc_start: 0.7586 (ttp) cc_final: 0.6853 (ttp) REVERT: D 332 LYS cc_start: 0.7203 (mtmm) cc_final: 0.6893 (mtmm) REVERT: D 360 TYR cc_start: 0.8308 (p90) cc_final: 0.7648 (p90) REVERT: D 399 LYS cc_start: 0.7704 (mtmt) cc_final: 0.7217 (mtmt) REVERT: D 402 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7100 (tm-30) REVERT: D 442 ILE cc_start: 0.8371 (tt) cc_final: 0.7967 (pt) REVERT: D 466 MET cc_start: 0.7401 (pmm) cc_final: 0.7156 (ptm) REVERT: D 475 GLU cc_start: 0.7687 (mp0) cc_final: 0.7158 (mp0) REVERT: D 500 ILE cc_start: 0.8193 (mm) cc_final: 0.7907 (tt) REVERT: D 514 THR cc_start: 0.8089 (p) cc_final: 0.7873 (p) REVERT: D 554 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6672 (tm-30) REVERT: D 573 THR cc_start: 0.8242 (m) cc_final: 0.7795 (p) REVERT: D 579 LEU cc_start: 0.8451 (tp) cc_final: 0.8141 (tp) REVERT: D 589 TYR cc_start: 0.8268 (t80) cc_final: 0.7941 (t80) REVERT: D 610 ARG cc_start: 0.7866 (tpp-160) cc_final: 0.7524 (mmt90) REVERT: D 622 ASP cc_start: 0.7436 (m-30) cc_final: 0.7113 (m-30) REVERT: D 649 LYS cc_start: 0.8565 (mmmt) cc_final: 0.7912 (mmmt) REVERT: D 652 GLU cc_start: 0.8603 (mp0) cc_final: 0.7599 (mp0) REVERT: D 665 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: D 684 ASP cc_start: 0.7577 (m-30) cc_final: 0.7270 (m-30) REVERT: D 691 ASP cc_start: 0.7959 (m-30) cc_final: 0.7632 (m-30) REVERT: D 695 LYS cc_start: 0.8548 (tmtt) cc_final: 0.8197 (tmtt) REVERT: D 714 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6716 (tm-30) REVERT: D 744 ARG cc_start: 0.7716 (ptm160) cc_final: 0.7374 (ttm110) REVERT: D 772 TYR cc_start: 0.8363 (t80) cc_final: 0.7806 (t80) REVERT: D 781 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8162 (tptm) REVERT: D 789 LYS cc_start: 0.7713 (ttpt) cc_final: 0.7107 (ptmm) REVERT: D 793 SER cc_start: 0.7827 (p) cc_final: 0.7612 (p) REVERT: D 822 MET cc_start: 0.6464 (tmm) cc_final: 0.5961 (tmm) REVERT: D 860 ARG cc_start: 0.6145 (ptm-80) cc_final: 0.5751 (ttt180) REVERT: D 865 HIS cc_start: 0.6662 (p-80) cc_final: 0.6330 (p-80) REVERT: D 913 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7217 (mm-30) REVERT: D 915 ILE cc_start: 0.8175 (tt) cc_final: 0.7878 (pt) REVERT: D 922 SER cc_start: 0.8214 (m) cc_final: 0.7677 (p) REVERT: D 992 LYS cc_start: 0.7301 (mmmm) cc_final: 0.7084 (mmmt) REVERT: D 1025 MET cc_start: 0.8834 (mpp) cc_final: 0.8572 (mpp) REVERT: D 1099 TYR cc_start: 0.7809 (m-80) cc_final: 0.6803 (m-80) REVERT: D 1120 THR cc_start: 0.7968 (t) cc_final: 0.7267 (p) REVERT: D 1146 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6783 (pp20) REVERT: D 1188 GLU cc_start: 0.6483 (pm20) cc_final: 0.5437 (pp20) REVERT: D 1248 ILE cc_start: 0.7664 (mm) cc_final: 0.7449 (mt) REVERT: D 1250 ASP cc_start: 0.7310 (p0) cc_final: 0.6869 (p0) REVERT: D 1327 GLU cc_start: 0.7104 (pm20) cc_final: 0.5884 (mp0) REVERT: E 52 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7422 (ttp80) REVERT: E 53 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7707 (mm-30) REVERT: E 55 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: G 11 VAL cc_start: 0.8545 (m) cc_final: 0.8200 (p) REVERT: G 27 ARG cc_start: 0.8299 (mtm180) cc_final: 0.7819 (mtm-85) REVERT: G 43 MET cc_start: 0.7440 (tmm) cc_final: 0.7110 (tmm) REVERT: G 74 VAL cc_start: 0.7468 (p) cc_final: 0.7241 (m) REVERT: G 93 ILE cc_start: 0.8045 (mm) cc_final: 0.7629 (mm) outliers start: 106 outliers final: 67 residues processed: 860 average time/residue: 0.4683 time to fit residues: 589.1426 Evaluate side-chains 860 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 780 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 105 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 0.9980 chunk 291 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 324 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 26 optimal weight: 0.0470 chunk 107 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C1237 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 28008 Z= 0.188 Angle : 0.594 13.097 38141 Z= 0.305 Chirality : 0.042 0.347 4351 Planarity : 0.004 0.054 4731 Dihedral : 14.586 175.885 4488 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.87 % Allowed : 20.82 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3285 helix: 1.22 (0.16), residues: 1111 sheet: -0.20 (0.26), residues: 414 loop : -1.40 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1193 HIS 0.009 0.001 HIS C 343 PHE 0.037 0.001 PHE D1319 TYR 0.022 0.001 TYR D 609 ARG 0.008 0.000 ARG C 352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 811 time to evaluate : 3.222 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 16 ILE cc_start: 0.8455 (mt) cc_final: 0.8141 (tt) REVERT: A 33 ARG cc_start: 0.7610 (ptm160) cc_final: 0.7097 (ptm160) REVERT: A 51 MET cc_start: 0.8105 (mmm) cc_final: 0.7856 (mmp) REVERT: A 58 GLU cc_start: 0.7631 (pp20) cc_final: 0.6870 (pp20) REVERT: A 59 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7514 (t) REVERT: A 74 VAL cc_start: 0.8226 (m) cc_final: 0.7869 (p) REVERT: A 104 LYS cc_start: 0.7989 (tptp) cc_final: 0.7405 (tptp) REVERT: A 114 ASP cc_start: 0.7932 (t0) cc_final: 0.7525 (t0) REVERT: A 125 LYS cc_start: 0.8178 (ptpp) cc_final: 0.7943 (ttpp) REVERT: A 142 MET cc_start: 0.7939 (mtm) cc_final: 0.7650 (mtm) REVERT: A 170 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7230 (ttm-80) REVERT: A 171 LEU cc_start: 0.8467 (pp) cc_final: 0.7834 (pp) REVERT: A 188 GLU cc_start: 0.7580 (pm20) cc_final: 0.7102 (pm20) REVERT: A 198 LEU cc_start: 0.7456 (mm) cc_final: 0.6943 (mm) REVERT: A 204 GLU cc_start: 0.7700 (pt0) cc_final: 0.7435 (pt0) REVERT: A 206 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7049 (tm-30) REVERT: A 212 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6904 (m-30) REVERT: A 226 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6602 (tm-30) REVERT: A 227 GLN cc_start: 0.7758 (tp40) cc_final: 0.7530 (tp40) REVERT: A 233 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7137 (t70) REVERT: B 16 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7785 (mt) REVERT: B 32 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6709 (tm-30) REVERT: B 51 MET cc_start: 0.7457 (mmm) cc_final: 0.7228 (mmm) REVERT: B 64 VAL cc_start: 0.7336 (t) cc_final: 0.7074 (p) REVERT: B 80 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6551 (tm-30) REVERT: B 82 LEU cc_start: 0.8423 (mt) cc_final: 0.8028 (pp) REVERT: B 97 GLU cc_start: 0.7147 (pm20) cc_final: 0.6510 (pm20) REVERT: B 100 LEU cc_start: 0.8633 (mm) cc_final: 0.8081 (tp) REVERT: B 142 MET cc_start: 0.7594 (mmm) cc_final: 0.7369 (mmm) REVERT: B 143 ARG cc_start: 0.7493 (mtt180) cc_final: 0.7172 (ptt180) REVERT: B 205 MET cc_start: 0.7553 (ppp) cc_final: 0.6768 (ppp) REVERT: B 214 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5739 (tm-30) REVERT: C 8 LYS cc_start: 0.8306 (mttt) cc_final: 0.7839 (mtpt) REVERT: C 17 LYS cc_start: 0.8014 (mptt) cc_final: 0.7424 (mmtp) REVERT: C 87 ILE cc_start: 0.8183 (tp) cc_final: 0.7663 (pt) REVERT: C 99 LYS cc_start: 0.8072 (ttmm) cc_final: 0.7305 (tptm) REVERT: C 151 ARG cc_start: 0.8013 (ttm110) cc_final: 0.7655 (ptp-110) REVERT: C 180 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6890 (ttp80) REVERT: C 185 ASP cc_start: 0.6092 (p0) cc_final: 0.5262 (p0) REVERT: C 186 PHE cc_start: 0.7819 (m-80) cc_final: 0.7303 (m-10) REVERT: C 187 GLU cc_start: 0.7162 (mp0) cc_final: 0.6185 (mp0) REVERT: C 195 PHE cc_start: 0.7797 (m-80) cc_final: 0.7309 (m-80) REVERT: C 203 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7415 (ttmm) REVERT: C 214 ASN cc_start: 0.8790 (t0) cc_final: 0.8399 (t0) REVERT: C 245 ARG cc_start: 0.8698 (mtt180) cc_final: 0.8387 (mtt180) REVERT: C 330 HIS cc_start: 0.8089 (m90) cc_final: 0.7724 (m-70) REVERT: C 349 GLU cc_start: 0.8229 (pm20) cc_final: 0.7824 (mp0) REVERT: C 365 GLU cc_start: 0.8114 (tp30) cc_final: 0.7818 (tp30) REVERT: C 368 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7926 (mtm-85) REVERT: C 371 ARG cc_start: 0.6665 (mtp-110) cc_final: 0.6187 (ptm160) REVERT: C 389 PHE cc_start: 0.8019 (m-10) cc_final: 0.7671 (m-80) REVERT: C 392 GLU cc_start: 0.7452 (mp0) cc_final: 0.7087 (mp0) REVERT: C 394 ARG cc_start: 0.7103 (ttm110) cc_final: 0.6874 (ttm110) REVERT: C 427 ASP cc_start: 0.7282 (m-30) cc_final: 0.7026 (m-30) REVERT: C 430 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7568 (mttp) REVERT: C 434 ASP cc_start: 0.7980 (m-30) cc_final: 0.7557 (m-30) REVERT: C 499 SER cc_start: 0.7390 (p) cc_final: 0.7107 (p) REVERT: C 523 GLU cc_start: 0.7611 (tp30) cc_final: 0.7317 (tp30) REVERT: C 538 LEU cc_start: 0.8234 (tp) cc_final: 0.8007 (tp) REVERT: C 549 ASP cc_start: 0.7312 (t0) cc_final: 0.7032 (t0) REVERT: C 593 LYS cc_start: 0.8054 (tptt) cc_final: 0.7416 (tppt) REVERT: C 611 GLU cc_start: 0.7422 (tt0) cc_final: 0.6977 (tt0) REVERT: C 651 ASP cc_start: 0.7986 (m-30) cc_final: 0.6915 (p0) REVERT: C 653 MET cc_start: 0.7336 (ttm) cc_final: 0.6937 (ttp) REVERT: C 656 SER cc_start: 0.8693 (t) cc_final: 0.8182 (m) REVERT: C 714 VAL cc_start: 0.8446 (p) cc_final: 0.8215 (t) REVERT: C 730 SER cc_start: 0.8721 (m) cc_final: 0.8306 (t) REVERT: C 731 ARG cc_start: 0.7813 (ptp-110) cc_final: 0.7461 (ptm160) REVERT: C 757 THR cc_start: 0.8787 (t) cc_final: 0.8580 (p) REVERT: C 778 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7351 (mp0) REVERT: C 779 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7869 (ttp80) REVERT: C 788 SER cc_start: 0.8376 (m) cc_final: 0.7678 (p) REVERT: C 790 ASP cc_start: 0.7442 (t70) cc_final: 0.7208 (t70) REVERT: C 800 MET cc_start: 0.7355 (mmp) cc_final: 0.6932 (mtp) REVERT: C 811 ASN cc_start: 0.7684 (p0) cc_final: 0.6556 (p0) REVERT: C 814 ASP cc_start: 0.7474 (m-30) cc_final: 0.6931 (m-30) REVERT: C 825 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6753 (tm-30) REVERT: C 914 LYS cc_start: 0.8029 (tppt) cc_final: 0.7682 (tppt) REVERT: C 930 ASP cc_start: 0.7756 (t0) cc_final: 0.7187 (m-30) REVERT: C 947 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7663 (tm-30) REVERT: C 948 ILE cc_start: 0.8764 (mm) cc_final: 0.8376 (mm) REVERT: C 950 GLU cc_start: 0.8513 (pt0) cc_final: 0.8263 (pt0) REVERT: C 960 LEU cc_start: 0.8185 (mp) cc_final: 0.7767 (pp) REVERT: C 1028 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8285 (pttt) REVERT: C 1030 GLU cc_start: 0.8615 (tp30) cc_final: 0.8000 (tp30) REVERT: C 1032 LYS cc_start: 0.9210 (tptt) cc_final: 0.8795 (mttt) REVERT: C 1035 LYS cc_start: 0.8641 (tppt) cc_final: 0.7982 (tppt) REVERT: C 1095 ASP cc_start: 0.7553 (m-30) cc_final: 0.7304 (m-30) REVERT: C 1099 ASN cc_start: 0.7986 (t0) cc_final: 0.7093 (t0) REVERT: C 1119 MET cc_start: 0.8141 (tpp) cc_final: 0.7705 (tpt) REVERT: C 1122 LYS cc_start: 0.8297 (tptm) cc_final: 0.7606 (tptp) REVERT: C 1126 ASP cc_start: 0.7279 (m-30) cc_final: 0.6672 (m-30) REVERT: C 1131 MET cc_start: 0.8211 (ttt) cc_final: 0.7837 (ttt) REVERT: C 1140 LYS cc_start: 0.8035 (ptpt) cc_final: 0.7750 (ptpt) REVERT: C 1143 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7335 (tm-30) REVERT: C 1146 GLN cc_start: 0.7559 (tp40) cc_final: 0.7042 (tp-100) REVERT: C 1147 ARG cc_start: 0.8397 (mmm-85) cc_final: 0.8085 (mmm-85) REVERT: C 1194 GLU cc_start: 0.7245 (pm20) cc_final: 0.6852 (pm20) REVERT: C 1200 LYS cc_start: 0.8331 (tttt) cc_final: 0.7991 (tttt) REVERT: C 1229 TYR cc_start: 0.8195 (m-80) cc_final: 0.7744 (m-10) REVERT: C 1264 GLN cc_start: 0.8275 (mp10) cc_final: 0.7609 (mp10) REVERT: C 1268 GLN cc_start: 0.7080 (pp30) cc_final: 0.6705 (pp30) REVERT: C 1274 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: C 1289 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7231 (mm-30) REVERT: C 1293 VAL cc_start: 0.7566 (t) cc_final: 0.7313 (t) REVERT: C 1303 LYS cc_start: 0.7935 (mtmm) cc_final: 0.7655 (mtmm) REVERT: D 17 PHE cc_start: 0.7882 (p90) cc_final: 0.7675 (p90) REVERT: D 21 LYS cc_start: 0.7978 (ptpt) cc_final: 0.7378 (ptmm) REVERT: D 29 MET cc_start: 0.7967 (ttt) cc_final: 0.7083 (tpp) REVERT: D 33 TRP cc_start: 0.7546 (m-10) cc_final: 0.6996 (m-10) REVERT: D 39 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7824 (mtmt) REVERT: D 52 GLU cc_start: 0.7067 (tp30) cc_final: 0.6802 (tm-30) REVERT: D 53 ARG cc_start: 0.7414 (ttt90) cc_final: 0.6945 (ttt90) REVERT: D 60 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7157 (ttm-80) REVERT: D 90 VAL cc_start: 0.7676 (t) cc_final: 0.7444 (p) REVERT: D 115 TRP cc_start: 0.8504 (m-10) cc_final: 0.8252 (m-10) REVERT: D 118 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7876 (mmmt) REVERT: D 128 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7370 (mt) REVERT: D 138 VAL cc_start: 0.8549 (t) cc_final: 0.8263 (m) REVERT: D 148 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6406 (tm-30) REVERT: D 151 MET cc_start: 0.8012 (pmm) cc_final: 0.7353 (pmm) REVERT: D 158 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7675 (mp10) REVERT: D 177 ASP cc_start: 0.7460 (p0) cc_final: 0.7006 (p0) REVERT: D 180 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6604 (ppp) REVERT: D 192 MET cc_start: 0.7814 (tpp) cc_final: 0.7594 (tpp) REVERT: D 193 ASP cc_start: 0.6401 (t0) cc_final: 0.5902 (t0) REVERT: D 196 GLN cc_start: 0.8287 (mp10) cc_final: 0.7848 (mp10) REVERT: D 202 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8135 (mtm-85) REVERT: D 213 LYS cc_start: 0.8186 (mmpt) cc_final: 0.7956 (mmpt) REVERT: D 215 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8591 (ptpt) REVERT: D 219 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8538 (ttpp) REVERT: D 235 GLU cc_start: 0.7384 (pm20) cc_final: 0.7106 (pm20) REVERT: D 251 PRO cc_start: 0.7763 (Cg_endo) cc_final: 0.7465 (Cg_exo) REVERT: D 275 ARG cc_start: 0.7846 (tpp-160) cc_final: 0.7189 (tpp-160) REVERT: D 282 LEU cc_start: 0.8522 (mt) cc_final: 0.8271 (tt) REVERT: D 295 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7158 (tm-30) REVERT: D 298 MET cc_start: 0.7571 (ttp) cc_final: 0.6715 (ttp) REVERT: D 332 LYS cc_start: 0.7076 (mtmm) cc_final: 0.6529 (mtpp) REVERT: D 368 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7750 (tp) REVERT: D 375 GLU cc_start: 0.7298 (tp30) cc_final: 0.6863 (tm-30) REVERT: D 399 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7199 (mtmt) REVERT: D 402 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7032 (tm-30) REVERT: D 441 LEU cc_start: 0.8398 (mm) cc_final: 0.8063 (mp) REVERT: D 442 ILE cc_start: 0.8346 (tt) cc_final: 0.7934 (pt) REVERT: D 475 GLU cc_start: 0.7730 (mp0) cc_final: 0.7241 (mp0) REVERT: D 500 ILE cc_start: 0.8189 (mm) cc_final: 0.7901 (tt) REVERT: D 549 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7680 (mmmt) REVERT: D 554 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6956 (tm-30) REVERT: D 572 THR cc_start: 0.7991 (p) cc_final: 0.7562 (p) REVERT: D 573 THR cc_start: 0.8102 (m) cc_final: 0.7560 (p) REVERT: D 579 LEU cc_start: 0.8277 (tp) cc_final: 0.7980 (tp) REVERT: D 589 TYR cc_start: 0.8189 (t80) cc_final: 0.7946 (t80) REVERT: D 622 ASP cc_start: 0.7295 (m-30) cc_final: 0.6947 (m-30) REVERT: D 649 LYS cc_start: 0.8575 (mmmt) cc_final: 0.7872 (mmmt) REVERT: D 652 GLU cc_start: 0.8588 (mp0) cc_final: 0.7490 (mp0) REVERT: D 665 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: D 678 ARG cc_start: 0.8220 (ttp-110) cc_final: 0.7869 (ttp80) REVERT: D 684 ASP cc_start: 0.7585 (m-30) cc_final: 0.7228 (m-30) REVERT: D 691 ASP cc_start: 0.7911 (m-30) cc_final: 0.7631 (m-30) REVERT: D 695 LYS cc_start: 0.8505 (tmtt) cc_final: 0.8156 (tmtt) REVERT: D 703 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7859 (t) REVERT: D 714 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6659 (tm-30) REVERT: D 723 TYR cc_start: 0.8149 (t80) cc_final: 0.7901 (t80) REVERT: D 739 GLN cc_start: 0.8033 (tt0) cc_final: 0.7761 (tt0) REVERT: D 772 TYR cc_start: 0.8348 (t80) cc_final: 0.8012 (t80) REVERT: D 781 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8130 (tptm) REVERT: D 789 LYS cc_start: 0.7727 (ttpt) cc_final: 0.7179 (ptmm) REVERT: D 793 SER cc_start: 0.7831 (p) cc_final: 0.7616 (p) REVERT: D 822 MET cc_start: 0.6332 (tmm) cc_final: 0.5900 (tmm) REVERT: D 860 ARG cc_start: 0.6241 (ptm-80) cc_final: 0.5826 (ttt180) REVERT: D 913 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7191 (mm-30) REVERT: D 915 ILE cc_start: 0.8162 (tt) cc_final: 0.7904 (pt) REVERT: D 922 SER cc_start: 0.8241 (m) cc_final: 0.7703 (p) REVERT: D 950 ILE cc_start: 0.7677 (tp) cc_final: 0.7387 (tp) REVERT: D 992 LYS cc_start: 0.7307 (mmmm) cc_final: 0.7020 (mmmt) REVERT: D 1020 TRP cc_start: 0.8002 (p90) cc_final: 0.7711 (p90) REVERT: D 1025 MET cc_start: 0.8823 (mpp) cc_final: 0.8559 (mpp) REVERT: D 1099 TYR cc_start: 0.7799 (m-80) cc_final: 0.6782 (m-80) REVERT: D 1146 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6798 (pp20) REVERT: D 1218 HIS cc_start: 0.8020 (m-70) cc_final: 0.7611 (m-70) REVERT: D 1250 ASP cc_start: 0.7267 (p0) cc_final: 0.6896 (p0) REVERT: D 1320 ILE cc_start: 0.7952 (mm) cc_final: 0.7724 (mm) REVERT: D 1327 GLU cc_start: 0.7012 (pm20) cc_final: 0.5806 (mp0) REVERT: D 1345 ARG cc_start: 0.8285 (mtp85) cc_final: 0.7615 (mmm-85) REVERT: E 52 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7391 (ttp80) REVERT: E 53 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7644 (mm-30) REVERT: E 55 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7139 (tp30) REVERT: E 58 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8160 (pp) REVERT: E 62 GLN cc_start: 0.8289 (tp40) cc_final: 0.7787 (tp40) REVERT: G 11 VAL cc_start: 0.8500 (m) cc_final: 0.8183 (p) REVERT: G 27 ARG cc_start: 0.8287 (mtm180) cc_final: 0.7801 (mtm-85) REVERT: G 83 VAL cc_start: 0.8836 (t) cc_final: 0.8630 (p) REVERT: G 88 ARG cc_start: 0.8063 (mtp180) cc_final: 0.7543 (mtm180) REVERT: G 93 ILE cc_start: 0.7945 (mm) cc_final: 0.7534 (mm) outliers start: 109 outliers final: 64 residues processed: 863 average time/residue: 0.4741 time to fit residues: 605.6017 Evaluate side-chains 869 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 790 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1048 LYS Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 65 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 272 optimal weight: 0.0970 chunk 180 optimal weight: 0.9990 chunk 322 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 chunk 196 optimal weight: 6.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 28008 Z= 0.182 Angle : 0.597 13.743 38141 Z= 0.305 Chirality : 0.042 0.371 4351 Planarity : 0.004 0.056 4731 Dihedral : 14.561 175.463 4488 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.58 % Allowed : 22.38 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3285 helix: 1.25 (0.16), residues: 1112 sheet: -0.18 (0.26), residues: 398 loop : -1.36 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D1193 HIS 0.008 0.001 HIS C 343 PHE 0.020 0.001 PHE D 892 TYR 0.033 0.001 TYR D 995 ARG 0.008 0.000 ARG D1231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 796 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8449 (mt) cc_final: 0.8137 (tt) REVERT: A 33 ARG cc_start: 0.7602 (ptm160) cc_final: 0.7080 (ptm160) REVERT: A 51 MET cc_start: 0.8090 (mmm) cc_final: 0.7839 (mmp) REVERT: A 74 VAL cc_start: 0.8339 (m) cc_final: 0.7953 (p) REVERT: A 104 LYS cc_start: 0.7987 (tptp) cc_final: 0.7406 (tptp) REVERT: A 114 ASP cc_start: 0.7975 (t0) cc_final: 0.7512 (t0) REVERT: A 125 LYS cc_start: 0.8209 (ptpp) cc_final: 0.7952 (ttpp) REVERT: A 142 MET cc_start: 0.7906 (mtm) cc_final: 0.7656 (mtm) REVERT: A 145 LYS cc_start: 0.7477 (mtpp) cc_final: 0.6937 (mtpp) REVERT: A 170 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7856 (ttm-80) REVERT: A 171 LEU cc_start: 0.8451 (pp) cc_final: 0.8220 (pp) REVERT: A 181 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 188 GLU cc_start: 0.7579 (pm20) cc_final: 0.7087 (pm20) REVERT: A 198 LEU cc_start: 0.7434 (mm) cc_final: 0.6925 (mm) REVERT: A 204 GLU cc_start: 0.7702 (pt0) cc_final: 0.7422 (pt0) REVERT: A 206 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 212 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6934 (m-30) REVERT: A 226 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6544 (tm-30) REVERT: B 16 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7698 (mt) REVERT: B 32 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6669 (tm-30) REVERT: B 51 MET cc_start: 0.7447 (mmm) cc_final: 0.7170 (mmm) REVERT: B 64 VAL cc_start: 0.7296 (t) cc_final: 0.7040 (p) REVERT: B 80 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6494 (tm-30) REVERT: B 97 GLU cc_start: 0.7133 (pm20) cc_final: 0.6505 (pm20) REVERT: B 100 LEU cc_start: 0.8634 (mm) cc_final: 0.8095 (tp) REVERT: B 142 MET cc_start: 0.7561 (mmm) cc_final: 0.7354 (mmm) REVERT: B 205 MET cc_start: 0.7503 (ppp) cc_final: 0.6749 (ppp) REVERT: B 214 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5692 (tm-30) REVERT: B 219 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7595 (mtm-85) REVERT: C 8 LYS cc_start: 0.8295 (mttt) cc_final: 0.7808 (mtpt) REVERT: C 17 LYS cc_start: 0.8020 (mptt) cc_final: 0.7368 (mmtp) REVERT: C 151 ARG cc_start: 0.8004 (ttm110) cc_final: 0.7627 (ptp-110) REVERT: C 180 ARG cc_start: 0.7268 (ttp80) cc_final: 0.6874 (ttp80) REVERT: C 185 ASP cc_start: 0.6071 (p0) cc_final: 0.5233 (p0) REVERT: C 186 PHE cc_start: 0.7761 (m-80) cc_final: 0.7153 (m-10) REVERT: C 187 GLU cc_start: 0.7135 (mp0) cc_final: 0.6174 (mp0) REVERT: C 195 PHE cc_start: 0.7853 (m-80) cc_final: 0.7419 (m-80) REVERT: C 203 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7395 (ttmm) REVERT: C 214 ASN cc_start: 0.8792 (t0) cc_final: 0.8408 (t0) REVERT: C 330 HIS cc_start: 0.8129 (m90) cc_final: 0.7738 (m-70) REVERT: C 349 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: C 368 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7911 (mtm-85) REVERT: C 371 ARG cc_start: 0.6574 (mtp-110) cc_final: 0.6085 (ptm160) REVERT: C 389 PHE cc_start: 0.7916 (m-10) cc_final: 0.7568 (m-80) REVERT: C 392 GLU cc_start: 0.7418 (mp0) cc_final: 0.6916 (mp0) REVERT: C 394 ARG cc_start: 0.7103 (ttm110) cc_final: 0.6858 (ttm110) REVERT: C 427 ASP cc_start: 0.7247 (m-30) cc_final: 0.6965 (m-30) REVERT: C 430 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7950 (mttp) REVERT: C 499 SER cc_start: 0.7332 (p) cc_final: 0.7033 (p) REVERT: C 523 GLU cc_start: 0.7586 (tp30) cc_final: 0.7272 (tp30) REVERT: C 538 LEU cc_start: 0.8255 (tp) cc_final: 0.8022 (tp) REVERT: C 549 ASP cc_start: 0.7316 (t0) cc_final: 0.7026 (t0) REVERT: C 593 LYS cc_start: 0.8032 (tptt) cc_final: 0.7422 (tppt) REVERT: C 611 GLU cc_start: 0.7425 (tt0) cc_final: 0.7004 (tt0) REVERT: C 653 MET cc_start: 0.7328 (ttm) cc_final: 0.6921 (ttp) REVERT: C 656 SER cc_start: 0.8664 (t) cc_final: 0.8025 (m) REVERT: C 714 VAL cc_start: 0.8440 (p) cc_final: 0.8213 (t) REVERT: C 730 SER cc_start: 0.8721 (m) cc_final: 0.8285 (t) REVERT: C 731 ARG cc_start: 0.7805 (ptp-110) cc_final: 0.7453 (ptm160) REVERT: C 778 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7392 (mp0) REVERT: C 788 SER cc_start: 0.8363 (m) cc_final: 0.7675 (p) REVERT: C 790 ASP cc_start: 0.7476 (t70) cc_final: 0.7214 (t70) REVERT: C 800 MET cc_start: 0.7351 (mmp) cc_final: 0.6930 (mtp) REVERT: C 811 ASN cc_start: 0.7635 (p0) cc_final: 0.6521 (p0) REVERT: C 814 ASP cc_start: 0.7449 (m-30) cc_final: 0.6946 (m-30) REVERT: C 825 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6779 (tm-30) REVERT: C 882 ILE cc_start: 0.8462 (mp) cc_final: 0.8207 (mm) REVERT: C 914 LYS cc_start: 0.8005 (tppt) cc_final: 0.7666 (tppt) REVERT: C 930 ASP cc_start: 0.7736 (t0) cc_final: 0.7208 (m-30) REVERT: C 947 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7697 (tm-30) REVERT: C 948 ILE cc_start: 0.8769 (mm) cc_final: 0.8381 (mm) REVERT: C 950 GLU cc_start: 0.8512 (pt0) cc_final: 0.8255 (pt0) REVERT: C 960 LEU cc_start: 0.8196 (mp) cc_final: 0.7832 (pp) REVERT: C 1028 LYS cc_start: 0.8594 (ptpp) cc_final: 0.8257 (pttt) REVERT: C 1030 GLU cc_start: 0.8610 (tp30) cc_final: 0.7995 (tp30) REVERT: C 1032 LYS cc_start: 0.9205 (tptt) cc_final: 0.8792 (mttt) REVERT: C 1035 LYS cc_start: 0.8630 (tppt) cc_final: 0.7975 (tppt) REVERT: C 1095 ASP cc_start: 0.7545 (m-30) cc_final: 0.7307 (m-30) REVERT: C 1099 ASN cc_start: 0.7990 (t0) cc_final: 0.7073 (t0) REVERT: C 1119 MET cc_start: 0.8097 (tpp) cc_final: 0.7680 (tpt) REVERT: C 1122 LYS cc_start: 0.8276 (tptm) cc_final: 0.7576 (tptp) REVERT: C 1126 ASP cc_start: 0.7276 (m-30) cc_final: 0.6667 (m-30) REVERT: C 1131 MET cc_start: 0.8213 (ttt) cc_final: 0.7810 (ttt) REVERT: C 1143 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7336 (tm-30) REVERT: C 1146 GLN cc_start: 0.7535 (tp40) cc_final: 0.6996 (tp-100) REVERT: C 1147 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.8061 (mmm-85) REVERT: C 1194 GLU cc_start: 0.7232 (pm20) cc_final: 0.6769 (pm20) REVERT: C 1200 LYS cc_start: 0.8329 (tttt) cc_final: 0.7986 (tttt) REVERT: C 1229 TYR cc_start: 0.8161 (m-80) cc_final: 0.7705 (m-80) REVERT: C 1264 GLN cc_start: 0.8225 (mp10) cc_final: 0.7570 (mp10) REVERT: C 1268 GLN cc_start: 0.6985 (pp30) cc_final: 0.6508 (pp30) REVERT: C 1274 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6518 (mp0) REVERT: C 1293 VAL cc_start: 0.7635 (t) cc_final: 0.7297 (t) REVERT: D 21 LYS cc_start: 0.8029 (ptpt) cc_final: 0.7391 (ptmm) REVERT: D 29 MET cc_start: 0.7949 (ttt) cc_final: 0.7013 (tpp) REVERT: D 33 TRP cc_start: 0.7543 (m-10) cc_final: 0.6975 (m-10) REVERT: D 39 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7822 (mtmm) REVERT: D 52 GLU cc_start: 0.7046 (tp30) cc_final: 0.6788 (tm-30) REVERT: D 53 ARG cc_start: 0.7395 (ttt90) cc_final: 0.6840 (ttt90) REVERT: D 60 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7149 (ttm-80) REVERT: D 90 VAL cc_start: 0.7603 (t) cc_final: 0.7294 (p) REVERT: D 96 LYS cc_start: 0.8357 (mtpp) cc_final: 0.8116 (mmtm) REVERT: D 115 TRP cc_start: 0.8488 (m-10) cc_final: 0.8201 (m-10) REVERT: D 118 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7888 (mmmt) REVERT: D 128 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7379 (mt) REVERT: D 138 VAL cc_start: 0.8551 (t) cc_final: 0.8265 (m) REVERT: D 148 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6406 (tm-30) REVERT: D 151 MET cc_start: 0.7978 (pmm) cc_final: 0.7368 (pmm) REVERT: D 157 GLN cc_start: 0.7690 (mt0) cc_final: 0.7108 (mp10) REVERT: D 158 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7693 (mp10) REVERT: D 177 ASP cc_start: 0.7471 (p0) cc_final: 0.7029 (p0) REVERT: D 180 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6595 (ppp) REVERT: D 192 MET cc_start: 0.7756 (tpp) cc_final: 0.7550 (tpp) REVERT: D 193 ASP cc_start: 0.6419 (t0) cc_final: 0.5931 (t0) REVERT: D 196 GLN cc_start: 0.8175 (mp10) cc_final: 0.7883 (mp10) REVERT: D 201 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8889 (mm) REVERT: D 202 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.8059 (mtm-85) REVERT: D 213 LYS cc_start: 0.8203 (mmpt) cc_final: 0.7981 (mmpt) REVERT: D 215 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8571 (ptpt) REVERT: D 219 LYS cc_start: 0.8974 (ttmt) cc_final: 0.8542 (ttpp) REVERT: D 235 GLU cc_start: 0.7413 (pm20) cc_final: 0.7183 (pm20) REVERT: D 251 PRO cc_start: 0.7729 (Cg_endo) cc_final: 0.7435 (Cg_exo) REVERT: D 275 ARG cc_start: 0.7816 (tpp-160) cc_final: 0.7036 (tpp-160) REVERT: D 279 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7625 (tp) REVERT: D 282 LEU cc_start: 0.8506 (mt) cc_final: 0.8261 (tt) REVERT: D 295 GLU cc_start: 0.7695 (tm-30) cc_final: 0.6769 (tm-30) REVERT: D 298 MET cc_start: 0.7572 (ttp) cc_final: 0.6652 (ttp) REVERT: D 332 LYS cc_start: 0.6976 (mtmm) cc_final: 0.6468 (mtpp) REVERT: D 368 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7766 (tp) REVERT: D 375 GLU cc_start: 0.7270 (tp30) cc_final: 0.6817 (tm-30) REVERT: D 399 LYS cc_start: 0.7696 (mtmt) cc_final: 0.7163 (mtmt) REVERT: D 402 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7057 (tm-30) REVERT: D 441 LEU cc_start: 0.8398 (mm) cc_final: 0.8085 (mp) REVERT: D 442 ILE cc_start: 0.8335 (tt) cc_final: 0.7952 (pt) REVERT: D 475 GLU cc_start: 0.7769 (mp0) cc_final: 0.7248 (mp0) REVERT: D 500 ILE cc_start: 0.8175 (mm) cc_final: 0.7895 (tt) REVERT: D 554 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7087 (tm-30) REVERT: D 573 THR cc_start: 0.8032 (m) cc_final: 0.7594 (p) REVERT: D 579 LEU cc_start: 0.8263 (tp) cc_final: 0.7945 (tp) REVERT: D 589 TYR cc_start: 0.8136 (t80) cc_final: 0.7886 (t80) REVERT: D 649 LYS cc_start: 0.8570 (mmmt) cc_final: 0.7860 (mmmt) REVERT: D 652 GLU cc_start: 0.8593 (mp0) cc_final: 0.7478 (mp0) REVERT: D 665 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: D 684 ASP cc_start: 0.7607 (m-30) cc_final: 0.7235 (m-30) REVERT: D 691 ASP cc_start: 0.7911 (m-30) cc_final: 0.7623 (m-30) REVERT: D 695 LYS cc_start: 0.8500 (tmtt) cc_final: 0.8153 (tmtt) REVERT: D 703 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7802 (t) REVERT: D 714 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6605 (tm-30) REVERT: D 770 LEU cc_start: 0.7603 (mm) cc_final: 0.7293 (mt) REVERT: D 772 TYR cc_start: 0.8350 (t80) cc_final: 0.7964 (t80) REVERT: D 781 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8127 (tptm) REVERT: D 789 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7179 (ptmm) REVERT: D 793 SER cc_start: 0.7838 (p) cc_final: 0.7605 (p) REVERT: D 822 MET cc_start: 0.6338 (tmm) cc_final: 0.5831 (tmm) REVERT: D 860 ARG cc_start: 0.6142 (ptm-80) cc_final: 0.5748 (ttt180) REVERT: D 913 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7180 (mm-30) REVERT: D 915 ILE cc_start: 0.8185 (tt) cc_final: 0.7962 (pt) REVERT: D 922 SER cc_start: 0.8210 (m) cc_final: 0.7709 (p) REVERT: D 959 LYS cc_start: 0.8348 (mmtt) cc_final: 0.7977 (mmtp) REVERT: D 992 LYS cc_start: 0.7441 (mmmm) cc_final: 0.7134 (mmmt) REVERT: D 1020 TRP cc_start: 0.8031 (p90) cc_final: 0.7742 (p90) REVERT: D 1025 MET cc_start: 0.8813 (mpp) cc_final: 0.8546 (mpp) REVERT: D 1099 TYR cc_start: 0.7779 (m-80) cc_final: 0.6761 (m-80) REVERT: D 1146 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6768 (pp20) REVERT: D 1194 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7881 (mmm-85) REVERT: D 1218 HIS cc_start: 0.8026 (m-70) cc_final: 0.7623 (m-70) REVERT: D 1250 ASP cc_start: 0.7254 (p0) cc_final: 0.6858 (p0) REVERT: D 1320 ILE cc_start: 0.7936 (mm) cc_final: 0.7726 (mm) REVERT: D 1327 GLU cc_start: 0.7003 (pm20) cc_final: 0.5800 (mp0) REVERT: E 52 ARG cc_start: 0.7653 (ttp80) cc_final: 0.7370 (ttp80) REVERT: E 53 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7657 (mm-30) REVERT: E 55 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: E 58 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8148 (pp) REVERT: E 62 GLN cc_start: 0.8281 (tp40) cc_final: 0.7790 (tp40) REVERT: G 27 ARG cc_start: 0.8280 (mtm180) cc_final: 0.7787 (mtm-85) REVERT: G 43 MET cc_start: 0.7399 (tmm) cc_final: 0.6453 (tmm) REVERT: G 80 TRP cc_start: 0.7805 (t60) cc_final: 0.7090 (t60) REVERT: G 83 VAL cc_start: 0.8801 (t) cc_final: 0.8593 (p) REVERT: G 84 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7809 (tpp-160) REVERT: G 88 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7465 (mtm180) REVERT: G 93 ILE cc_start: 0.7897 (mm) cc_final: 0.7490 (mm) outliers start: 101 outliers final: 63 residues processed: 845 average time/residue: 0.4591 time to fit residues: 572.2599 Evaluate side-chains 862 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 783 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1048 LYS Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 65 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 205 optimal weight: 0.2980 chunk 219 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 686 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 28008 Z= 0.206 Angle : 0.611 14.340 38141 Z= 0.314 Chirality : 0.043 0.374 4351 Planarity : 0.004 0.057 4731 Dihedral : 14.570 175.327 4488 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.69 % Allowed : 22.67 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3285 helix: 1.23 (0.16), residues: 1111 sheet: -0.20 (0.26), residues: 405 loop : -1.37 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D1193 HIS 0.009 0.001 HIS C 343 PHE 0.020 0.001 PHE D 892 TYR 0.025 0.001 TYR B 185 ARG 0.010 0.000 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 796 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8430 (mt) cc_final: 0.8107 (tt) REVERT: A 33 ARG cc_start: 0.7599 (ptm160) cc_final: 0.7106 (ptm160) REVERT: A 51 MET cc_start: 0.8118 (mmm) cc_final: 0.7864 (mmp) REVERT: A 74 VAL cc_start: 0.8344 (m) cc_final: 0.7978 (p) REVERT: A 104 LYS cc_start: 0.8023 (tptp) cc_final: 0.7437 (tptp) REVERT: A 114 ASP cc_start: 0.7990 (t0) cc_final: 0.7507 (t0) REVERT: A 125 LYS cc_start: 0.8234 (ptpp) cc_final: 0.8002 (ttpp) REVERT: A 142 MET cc_start: 0.7913 (mtm) cc_final: 0.7689 (mtm) REVERT: A 170 ARG cc_start: 0.8321 (ttp-110) cc_final: 0.7534 (ttm-80) REVERT: A 171 LEU cc_start: 0.8365 (pp) cc_final: 0.8121 (pp) REVERT: A 188 GLU cc_start: 0.7566 (pm20) cc_final: 0.7089 (pm20) REVERT: A 204 GLU cc_start: 0.7681 (pt0) cc_final: 0.7431 (pt0) REVERT: A 206 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7157 (tm-30) REVERT: A 212 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6915 (m-30) REVERT: A 226 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6532 (tm-30) REVERT: B 16 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7717 (mt) REVERT: B 32 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6640 (tm-30) REVERT: B 51 MET cc_start: 0.7516 (mmm) cc_final: 0.7281 (mmm) REVERT: B 64 VAL cc_start: 0.7319 (t) cc_final: 0.7077 (p) REVERT: B 97 GLU cc_start: 0.7116 (pm20) cc_final: 0.6499 (pm20) REVERT: B 100 LEU cc_start: 0.8591 (mm) cc_final: 0.8025 (tp) REVERT: B 142 MET cc_start: 0.7565 (mmm) cc_final: 0.7362 (mmm) REVERT: B 205 MET cc_start: 0.7482 (ppp) cc_final: 0.6840 (ppp) REVERT: B 214 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5738 (tm-30) REVERT: B 219 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7638 (mtm-85) REVERT: C 8 LYS cc_start: 0.8318 (mttt) cc_final: 0.7829 (mtpt) REVERT: C 87 ILE cc_start: 0.8170 (tp) cc_final: 0.7667 (pt) REVERT: C 99 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7956 (mtmm) REVERT: C 151 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7666 (ptp-110) REVERT: C 180 ARG cc_start: 0.7288 (ttp80) cc_final: 0.6898 (ttp80) REVERT: C 185 ASP cc_start: 0.6074 (p0) cc_final: 0.5301 (p0) REVERT: C 186 PHE cc_start: 0.7757 (m-80) cc_final: 0.7218 (m-10) REVERT: C 187 GLU cc_start: 0.7110 (mp0) cc_final: 0.6167 (mp0) REVERT: C 195 PHE cc_start: 0.7861 (m-80) cc_final: 0.7484 (m-80) REVERT: C 203 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7357 (ttmm) REVERT: C 214 ASN cc_start: 0.8786 (t0) cc_final: 0.8416 (t0) REVERT: C 218 GLU cc_start: 0.8214 (pm20) cc_final: 0.7991 (pm20) REVERT: C 330 HIS cc_start: 0.8180 (m90) cc_final: 0.7770 (m-70) REVERT: C 349 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: C 368 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7921 (mtm-85) REVERT: C 371 ARG cc_start: 0.6596 (mtp-110) cc_final: 0.6151 (ptm160) REVERT: C 374 GLU cc_start: 0.5885 (pt0) cc_final: 0.4841 (pt0) REVERT: C 389 PHE cc_start: 0.7831 (m-10) cc_final: 0.7480 (m-10) REVERT: C 392 GLU cc_start: 0.7405 (mp0) cc_final: 0.6985 (mp0) REVERT: C 394 ARG cc_start: 0.7108 (ttm110) cc_final: 0.6853 (ttm110) REVERT: C 427 ASP cc_start: 0.7282 (m-30) cc_final: 0.7008 (m-30) REVERT: C 430 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7519 (mttp) REVERT: C 434 ASP cc_start: 0.7930 (m-30) cc_final: 0.7532 (m-30) REVERT: C 499 SER cc_start: 0.7332 (p) cc_final: 0.7023 (p) REVERT: C 517 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6809 (pm20) REVERT: C 523 GLU cc_start: 0.7615 (tp30) cc_final: 0.7290 (tp30) REVERT: C 538 LEU cc_start: 0.8300 (tp) cc_final: 0.8060 (tp) REVERT: C 549 ASP cc_start: 0.7340 (t0) cc_final: 0.7030 (t0) REVERT: C 593 LYS cc_start: 0.8055 (tptt) cc_final: 0.7421 (tppt) REVERT: C 611 GLU cc_start: 0.7433 (tt0) cc_final: 0.6681 (mt-10) REVERT: C 651 ASP cc_start: 0.7904 (m-30) cc_final: 0.6938 (p0) REVERT: C 653 MET cc_start: 0.7354 (ttm) cc_final: 0.6956 (ttp) REVERT: C 656 SER cc_start: 0.8594 (t) cc_final: 0.8016 (m) REVERT: C 714 VAL cc_start: 0.8450 (p) cc_final: 0.8226 (t) REVERT: C 719 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7737 (mtmm) REVERT: C 730 SER cc_start: 0.8725 (m) cc_final: 0.8304 (t) REVERT: C 731 ARG cc_start: 0.7838 (ptp-110) cc_final: 0.7482 (ptm160) REVERT: C 734 ILE cc_start: 0.7738 (mt) cc_final: 0.7476 (pt) REVERT: C 778 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7518 (mm-30) REVERT: C 788 SER cc_start: 0.8412 (m) cc_final: 0.7663 (p) REVERT: C 790 ASP cc_start: 0.7430 (t70) cc_final: 0.7190 (t70) REVERT: C 800 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6971 (mtp) REVERT: C 811 ASN cc_start: 0.7666 (p0) cc_final: 0.6991 (p0) REVERT: C 814 ASP cc_start: 0.7401 (m-30) cc_final: 0.6871 (m-30) REVERT: C 825 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6763 (tm-30) REVERT: C 914 LYS cc_start: 0.8099 (tppt) cc_final: 0.7749 (tppt) REVERT: C 930 ASP cc_start: 0.7745 (t0) cc_final: 0.7207 (m-30) REVERT: C 947 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7723 (tm-30) REVERT: C 948 ILE cc_start: 0.8796 (mm) cc_final: 0.8436 (mm) REVERT: C 950 GLU cc_start: 0.8517 (pt0) cc_final: 0.8262 (pt0) REVERT: C 954 LYS cc_start: 0.8836 (tttp) cc_final: 0.8563 (ttpp) REVERT: C 960 LEU cc_start: 0.8238 (mp) cc_final: 0.7876 (pp) REVERT: C 1028 LYS cc_start: 0.8602 (ptpp) cc_final: 0.8294 (pttt) REVERT: C 1032 LYS cc_start: 0.9224 (tptt) cc_final: 0.8428 (mttt) REVERT: C 1035 LYS cc_start: 0.8680 (tppt) cc_final: 0.8435 (mttt) REVERT: C 1095 ASP cc_start: 0.7391 (m-30) cc_final: 0.6999 (m-30) REVERT: C 1119 MET cc_start: 0.8147 (tpp) cc_final: 0.7728 (tpt) REVERT: C 1122 LYS cc_start: 0.8278 (tptm) cc_final: 0.7588 (tptp) REVERT: C 1126 ASP cc_start: 0.7321 (m-30) cc_final: 0.6659 (m-30) REVERT: C 1131 MET cc_start: 0.8194 (ttt) cc_final: 0.7900 (ttt) REVERT: C 1133 LYS cc_start: 0.8005 (tppt) cc_final: 0.7708 (tppt) REVERT: C 1140 LYS cc_start: 0.8045 (ptpt) cc_final: 0.7762 (ptpt) REVERT: C 1141 LEU cc_start: 0.8143 (tp) cc_final: 0.7892 (tt) REVERT: C 1143 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7319 (tm-30) REVERT: C 1146 GLN cc_start: 0.7588 (tp40) cc_final: 0.7034 (tp-100) REVERT: C 1147 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8047 (mmm-85) REVERT: C 1197 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7222 (tm-30) REVERT: C 1200 LYS cc_start: 0.8389 (tttt) cc_final: 0.8043 (tttt) REVERT: C 1229 TYR cc_start: 0.8172 (m-80) cc_final: 0.7725 (m-10) REVERT: C 1264 GLN cc_start: 0.8172 (mp10) cc_final: 0.7500 (mp10) REVERT: C 1268 GLN cc_start: 0.7002 (pp30) cc_final: 0.6600 (pp30) REVERT: C 1274 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: D 21 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7303 (ptmm) REVERT: D 29 MET cc_start: 0.7997 (ttt) cc_final: 0.7462 (ttm) REVERT: D 33 TRP cc_start: 0.7634 (m-10) cc_final: 0.7231 (m-10) REVERT: D 39 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7802 (mtmm) REVERT: D 52 GLU cc_start: 0.7031 (tp30) cc_final: 0.6773 (tm-30) REVERT: D 53 ARG cc_start: 0.7473 (ttt90) cc_final: 0.6956 (ttt90) REVERT: D 96 LYS cc_start: 0.8373 (mtpp) cc_final: 0.8099 (mmtm) REVERT: D 115 TRP cc_start: 0.8536 (m-10) cc_final: 0.8271 (m-10) REVERT: D 118 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7910 (mmmt) REVERT: D 128 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7403 (mt) REVERT: D 138 VAL cc_start: 0.8514 (t) cc_final: 0.8218 (p) REVERT: D 148 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6461 (tm-30) REVERT: D 151 MET cc_start: 0.8040 (pmm) cc_final: 0.7508 (pmm) REVERT: D 157 GLN cc_start: 0.7746 (mt0) cc_final: 0.7131 (mp10) REVERT: D 158 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7744 (mp10) REVERT: D 177 ASP cc_start: 0.7513 (p0) cc_final: 0.7008 (p0) REVERT: D 180 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6591 (ppp) REVERT: D 192 MET cc_start: 0.7787 (tpp) cc_final: 0.7582 (tpp) REVERT: D 193 ASP cc_start: 0.6505 (t0) cc_final: 0.6205 (t0) REVERT: D 202 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.8028 (mtm-85) REVERT: D 215 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8488 (ptpt) REVERT: D 219 LYS cc_start: 0.8987 (ttmt) cc_final: 0.8538 (ptmm) REVERT: D 235 GLU cc_start: 0.7448 (pm20) cc_final: 0.7206 (pm20) REVERT: D 251 PRO cc_start: 0.7781 (Cg_endo) cc_final: 0.7513 (Cg_exo) REVERT: D 275 ARG cc_start: 0.7827 (tpp-160) cc_final: 0.7000 (tpp-160) REVERT: D 279 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7466 (tp) REVERT: D 282 LEU cc_start: 0.8548 (mt) cc_final: 0.8237 (tt) REVERT: D 295 GLU cc_start: 0.7679 (tm-30) cc_final: 0.6724 (tm-30) REVERT: D 298 MET cc_start: 0.7484 (ttp) cc_final: 0.6526 (ttp) REVERT: D 332 LYS cc_start: 0.7084 (mtmm) cc_final: 0.6762 (mtmm) REVERT: D 360 TYR cc_start: 0.8214 (p90) cc_final: 0.7579 (p90) REVERT: D 368 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7805 (tp) REVERT: D 399 LYS cc_start: 0.7709 (mtmt) cc_final: 0.7216 (mtmt) REVERT: D 402 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7076 (tm-30) REVERT: D 441 LEU cc_start: 0.8415 (mm) cc_final: 0.8104 (mp) REVERT: D 442 ILE cc_start: 0.8333 (tt) cc_final: 0.7932 (pt) REVERT: D 475 GLU cc_start: 0.7788 (mp0) cc_final: 0.7236 (mp0) REVERT: D 500 ILE cc_start: 0.8163 (mm) cc_final: 0.7872 (tt) REVERT: D 541 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8686 (tp) REVERT: D 554 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7102 (tm-30) REVERT: D 572 THR cc_start: 0.7865 (p) cc_final: 0.7403 (p) REVERT: D 579 LEU cc_start: 0.8383 (tp) cc_final: 0.8050 (tp) REVERT: D 589 TYR cc_start: 0.8148 (t80) cc_final: 0.7892 (t80) REVERT: D 622 ASP cc_start: 0.7079 (m-30) cc_final: 0.6818 (m-30) REVERT: D 649 LYS cc_start: 0.8572 (mmmt) cc_final: 0.7630 (mmmt) REVERT: D 652 GLU cc_start: 0.8581 (mp0) cc_final: 0.7313 (mp0) REVERT: D 665 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: D 684 ASP cc_start: 0.7739 (m-30) cc_final: 0.7339 (m-30) REVERT: D 691 ASP cc_start: 0.7929 (m-30) cc_final: 0.7612 (m-30) REVERT: D 695 LYS cc_start: 0.8534 (tmtt) cc_final: 0.8174 (tmtt) REVERT: D 703 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7877 (t) REVERT: D 714 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6622 (tm-30) REVERT: D 770 LEU cc_start: 0.7673 (mm) cc_final: 0.7345 (mt) REVERT: D 772 TYR cc_start: 0.8350 (t80) cc_final: 0.7996 (t80) REVERT: D 781 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8131 (tptm) REVERT: D 789 LYS cc_start: 0.7728 (ttpt) cc_final: 0.7205 (ptmm) REVERT: D 793 SER cc_start: 0.7853 (p) cc_final: 0.7616 (p) REVERT: D 822 MET cc_start: 0.6361 (tmm) cc_final: 0.6034 (tmm) REVERT: D 913 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7214 (mm-30) REVERT: D 915 ILE cc_start: 0.8204 (tt) cc_final: 0.7982 (pt) REVERT: D 922 SER cc_start: 0.8205 (m) cc_final: 0.7713 (p) REVERT: D 959 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7938 (mmtp) REVERT: D 979 ASN cc_start: 0.6928 (OUTLIER) cc_final: 0.6148 (p0) REVERT: D 1020 TRP cc_start: 0.8049 (p90) cc_final: 0.7734 (p90) REVERT: D 1025 MET cc_start: 0.8861 (mpp) cc_final: 0.8587 (mpp) REVERT: D 1099 TYR cc_start: 0.7769 (m-80) cc_final: 0.6731 (m-80) REVERT: D 1149 ARG cc_start: 0.8042 (tpp80) cc_final: 0.7494 (tpp80) REVERT: D 1218 HIS cc_start: 0.8034 (m-70) cc_final: 0.7661 (m-70) REVERT: D 1220 ILE cc_start: 0.8642 (tt) cc_final: 0.8301 (tp) REVERT: D 1224 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7450 (mtm180) REVERT: D 1250 ASP cc_start: 0.7209 (p0) cc_final: 0.6836 (p0) REVERT: D 1320 ILE cc_start: 0.7931 (mm) cc_final: 0.7699 (mm) REVERT: D 1327 GLU cc_start: 0.7173 (pm20) cc_final: 0.6049 (mp0) REVERT: D 1345 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7439 (mtp180) REVERT: E 53 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7709 (mm-30) REVERT: E 55 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: E 58 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8180 (pp) REVERT: E 62 GLN cc_start: 0.8286 (tp40) cc_final: 0.7785 (tp40) REVERT: G 27 ARG cc_start: 0.8279 (mtm180) cc_final: 0.7784 (mtm-85) REVERT: G 43 MET cc_start: 0.7388 (tmm) cc_final: 0.6566 (tmm) REVERT: G 73 MET cc_start: 0.6411 (ppp) cc_final: 0.5949 (ppp) REVERT: G 80 TRP cc_start: 0.7783 (t60) cc_final: 0.7304 (t60) REVERT: G 83 VAL cc_start: 0.8760 (t) cc_final: 0.8526 (p) REVERT: G 93 ILE cc_start: 0.7909 (mm) cc_final: 0.7443 (mm) outliers start: 104 outliers final: 65 residues processed: 844 average time/residue: 0.4607 time to fit residues: 574.4171 Evaluate side-chains 860 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 777 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 105 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 0.7980 chunk 309 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 300 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 236 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 284 optimal weight: 20.0000 chunk 299 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 23 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 686 GLN C1256 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 28008 Z= 0.200 Angle : 0.619 12.299 38141 Z= 0.318 Chirality : 0.043 0.356 4351 Planarity : 0.004 0.058 4731 Dihedral : 14.569 174.870 4488 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.26 % Allowed : 23.87 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3285 helix: 1.22 (0.16), residues: 1103 sheet: -0.16 (0.26), residues: 399 loop : -1.32 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D1193 HIS 0.008 0.001 HIS C 343 PHE 0.020 0.001 PHE D 892 TYR 0.022 0.001 TYR D 995 ARG 0.010 0.000 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 792 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.6816 (t0) cc_final: 0.6602 (t0) REVERT: A 16 ILE cc_start: 0.8408 (mt) cc_final: 0.8107 (tt) REVERT: A 33 ARG cc_start: 0.7557 (ptm160) cc_final: 0.7042 (ptm160) REVERT: A 51 MET cc_start: 0.8111 (mmm) cc_final: 0.7861 (mmp) REVERT: A 68 TYR cc_start: 0.8514 (m-80) cc_final: 0.8178 (m-80) REVERT: A 74 VAL cc_start: 0.8313 (m) cc_final: 0.7905 (p) REVERT: A 104 LYS cc_start: 0.8024 (tptp) cc_final: 0.7435 (tptp) REVERT: A 114 ASP cc_start: 0.8005 (t0) cc_final: 0.7517 (t0) REVERT: A 125 LYS cc_start: 0.8251 (ptpp) cc_final: 0.8008 (ttpp) REVERT: A 142 MET cc_start: 0.7903 (mtm) cc_final: 0.7629 (mtm) REVERT: A 170 ARG cc_start: 0.8352 (ttp-110) cc_final: 0.7590 (ttm-80) REVERT: A 171 LEU cc_start: 0.8379 (pp) cc_final: 0.8138 (pp) REVERT: A 188 GLU cc_start: 0.7562 (pm20) cc_final: 0.7121 (pm20) REVERT: A 212 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6887 (m-30) REVERT: A 226 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6553 (tm-30) REVERT: B 16 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7756 (mt) REVERT: B 32 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6629 (tm-30) REVERT: B 51 MET cc_start: 0.7565 (mmm) cc_final: 0.7322 (mmm) REVERT: B 64 VAL cc_start: 0.7285 (t) cc_final: 0.7038 (p) REVERT: B 67 GLU cc_start: 0.7822 (pm20) cc_final: 0.7615 (pm20) REVERT: B 97 GLU cc_start: 0.7079 (pm20) cc_final: 0.6510 (pm20) REVERT: B 100 LEU cc_start: 0.8621 (mm) cc_final: 0.8072 (tp) REVERT: B 142 MET cc_start: 0.7577 (mmm) cc_final: 0.7335 (mmm) REVERT: B 205 MET cc_start: 0.7533 (ppp) cc_final: 0.6861 (ppp) REVERT: B 214 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5806 (tm-30) REVERT: B 219 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7635 (mtm-85) REVERT: C 8 LYS cc_start: 0.8314 (mttt) cc_final: 0.7851 (mtpt) REVERT: C 40 GLU cc_start: 0.6277 (tp30) cc_final: 0.6006 (tp30) REVERT: C 41 GLN cc_start: 0.6891 (tm-30) cc_final: 0.6531 (tm-30) REVERT: C 99 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7747 (ttmm) REVERT: C 151 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7637 (ptp-110) REVERT: C 161 LYS cc_start: 0.8340 (ptmm) cc_final: 0.7704 (ptmm) REVERT: C 180 ARG cc_start: 0.7300 (ttp80) cc_final: 0.6894 (ttp80) REVERT: C 185 ASP cc_start: 0.6087 (p0) cc_final: 0.5314 (p0) REVERT: C 186 PHE cc_start: 0.7743 (m-80) cc_final: 0.7208 (m-10) REVERT: C 187 GLU cc_start: 0.7092 (mp0) cc_final: 0.6170 (mp0) REVERT: C 195 PHE cc_start: 0.7904 (m-80) cc_final: 0.7518 (m-80) REVERT: C 203 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7530 (ttpt) REVERT: C 214 ASN cc_start: 0.8764 (t0) cc_final: 0.8442 (t0) REVERT: C 218 GLU cc_start: 0.8231 (pm20) cc_final: 0.8002 (pm20) REVERT: C 330 HIS cc_start: 0.8250 (m90) cc_final: 0.7814 (m-70) REVERT: C 349 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: C 368 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7953 (mtm-85) REVERT: C 371 ARG cc_start: 0.6588 (mtp-110) cc_final: 0.6162 (ptm160) REVERT: C 374 GLU cc_start: 0.5914 (pt0) cc_final: 0.4811 (pt0) REVERT: C 392 GLU cc_start: 0.7491 (mp0) cc_final: 0.7150 (mp0) REVERT: C 394 ARG cc_start: 0.7117 (ttm110) cc_final: 0.6885 (ttm110) REVERT: C 427 ASP cc_start: 0.7266 (m-30) cc_final: 0.7002 (m-30) REVERT: C 448 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7088 (mp) REVERT: C 499 SER cc_start: 0.7307 (p) cc_final: 0.7039 (p) REVERT: C 517 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6836 (pm20) REVERT: C 523 GLU cc_start: 0.7614 (tp30) cc_final: 0.7265 (tp30) REVERT: C 538 LEU cc_start: 0.8287 (tp) cc_final: 0.8043 (tp) REVERT: C 549 ASP cc_start: 0.7407 (t0) cc_final: 0.7074 (t0) REVERT: C 593 LYS cc_start: 0.8048 (tptt) cc_final: 0.7437 (tppt) REVERT: C 611 GLU cc_start: 0.7435 (tt0) cc_final: 0.6732 (mt-10) REVERT: C 653 MET cc_start: 0.7377 (ttm) cc_final: 0.6967 (ttp) REVERT: C 656 SER cc_start: 0.8582 (t) cc_final: 0.7999 (m) REVERT: C 704 MET cc_start: 0.7003 (mmp) cc_final: 0.6506 (mmm) REVERT: C 706 ARG cc_start: 0.6634 (mmm-85) cc_final: 0.6266 (tpp80) REVERT: C 714 VAL cc_start: 0.8443 (p) cc_final: 0.8236 (t) REVERT: C 730 SER cc_start: 0.8714 (m) cc_final: 0.8291 (t) REVERT: C 731 ARG cc_start: 0.7874 (ptp-110) cc_final: 0.7517 (ptm160) REVERT: C 734 ILE cc_start: 0.7740 (mt) cc_final: 0.7504 (pt) REVERT: C 778 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7526 (mm-30) REVERT: C 788 SER cc_start: 0.8398 (m) cc_final: 0.7653 (p) REVERT: C 790 ASP cc_start: 0.7431 (t70) cc_final: 0.7168 (t70) REVERT: C 800 MET cc_start: 0.7348 (mmp) cc_final: 0.7134 (mmm) REVERT: C 811 ASN cc_start: 0.7614 (p0) cc_final: 0.6927 (p0) REVERT: C 814 ASP cc_start: 0.7429 (m-30) cc_final: 0.6924 (m-30) REVERT: C 825 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6777 (tm-30) REVERT: C 848 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6915 (pt0) REVERT: C 914 LYS cc_start: 0.8085 (tppt) cc_final: 0.7723 (tppt) REVERT: C 930 ASP cc_start: 0.7733 (t0) cc_final: 0.7209 (m-30) REVERT: C 943 LYS cc_start: 0.8442 (pttp) cc_final: 0.8194 (pttp) REVERT: C 947 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 948 ILE cc_start: 0.8793 (mm) cc_final: 0.8432 (mm) REVERT: C 950 GLU cc_start: 0.8506 (pt0) cc_final: 0.8266 (pt0) REVERT: C 960 LEU cc_start: 0.8227 (mp) cc_final: 0.7855 (pp) REVERT: C 1028 LYS cc_start: 0.8616 (ptpp) cc_final: 0.8392 (pttt) REVERT: C 1030 GLU cc_start: 0.8133 (pt0) cc_final: 0.7822 (pp20) REVERT: C 1032 LYS cc_start: 0.9198 (tptt) cc_final: 0.8816 (mttt) REVERT: C 1035 LYS cc_start: 0.8651 (tppt) cc_final: 0.8010 (tppt) REVERT: C 1095 ASP cc_start: 0.7381 (m-30) cc_final: 0.7105 (m-30) REVERT: C 1119 MET cc_start: 0.8141 (tpp) cc_final: 0.7721 (tpt) REVERT: C 1122 LYS cc_start: 0.8275 (tptm) cc_final: 0.7587 (tptp) REVERT: C 1126 ASP cc_start: 0.7322 (m-30) cc_final: 0.6660 (m-30) REVERT: C 1127 LYS cc_start: 0.8829 (tptp) cc_final: 0.8505 (tptp) REVERT: C 1131 MET cc_start: 0.8162 (ttt) cc_final: 0.7801 (ttt) REVERT: C 1141 LEU cc_start: 0.8124 (tp) cc_final: 0.7882 (tt) REVERT: C 1143 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7312 (tm-30) REVERT: C 1146 GLN cc_start: 0.7584 (tp40) cc_final: 0.7023 (tp-100) REVERT: C 1147 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.8010 (mmm-85) REVERT: C 1176 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7201 (tt) REVERT: C 1197 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7234 (tm-30) REVERT: C 1200 LYS cc_start: 0.8455 (tttt) cc_final: 0.8122 (tttt) REVERT: C 1229 TYR cc_start: 0.8158 (m-80) cc_final: 0.7683 (m-10) REVERT: C 1264 GLN cc_start: 0.8116 (mp10) cc_final: 0.7485 (mp10) REVERT: C 1268 GLN cc_start: 0.6883 (pp30) cc_final: 0.6636 (pp30) REVERT: C 1274 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: C 1329 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6670 (tt0) REVERT: D 21 LYS cc_start: 0.8113 (ptpt) cc_final: 0.7348 (ptmm) REVERT: D 29 MET cc_start: 0.8002 (ttt) cc_final: 0.7429 (ttm) REVERT: D 33 TRP cc_start: 0.7598 (m-10) cc_final: 0.7180 (m-10) REVERT: D 52 GLU cc_start: 0.7073 (tp30) cc_final: 0.6755 (tm-30) REVERT: D 53 ARG cc_start: 0.7487 (ttt90) cc_final: 0.6934 (ttt90) REVERT: D 96 LYS cc_start: 0.8387 (mtpp) cc_final: 0.8110 (mmtm) REVERT: D 115 TRP cc_start: 0.8538 (m-10) cc_final: 0.8273 (m-10) REVERT: D 118 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7913 (mmmt) REVERT: D 128 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7411 (mt) REVERT: D 138 VAL cc_start: 0.8523 (t) cc_final: 0.8220 (p) REVERT: D 148 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6440 (tm-30) REVERT: D 151 MET cc_start: 0.8027 (pmm) cc_final: 0.7424 (pmm) REVERT: D 157 GLN cc_start: 0.7744 (mt0) cc_final: 0.7159 (mp10) REVERT: D 158 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7687 (mp10) REVERT: D 177 ASP cc_start: 0.7508 (p0) cc_final: 0.7014 (p0) REVERT: D 180 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6589 (ppp) REVERT: D 192 MET cc_start: 0.7775 (tpp) cc_final: 0.7574 (tpp) REVERT: D 202 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.7791 (mtt-85) REVERT: D 215 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8582 (ptpt) REVERT: D 219 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8559 (ttpp) REVERT: D 235 GLU cc_start: 0.7462 (pm20) cc_final: 0.7215 (pm20) REVERT: D 251 PRO cc_start: 0.7806 (Cg_endo) cc_final: 0.7566 (Cg_exo) REVERT: D 275 ARG cc_start: 0.7815 (tpp-160) cc_final: 0.7043 (tpp-160) REVERT: D 279 LEU cc_start: 0.8205 (tp) cc_final: 0.7420 (tp) REVERT: D 280 LYS cc_start: 0.8577 (tptp) cc_final: 0.8360 (tppt) REVERT: D 282 LEU cc_start: 0.8552 (mt) cc_final: 0.8231 (tt) REVERT: D 295 GLU cc_start: 0.7667 (tm-30) cc_final: 0.6703 (tm-30) REVERT: D 298 MET cc_start: 0.7466 (ttp) cc_final: 0.6509 (ttp) REVERT: D 325 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7978 (mmtp) REVERT: D 332 LYS cc_start: 0.7055 (mtmm) cc_final: 0.6754 (mtmm) REVERT: D 345 LYS cc_start: 0.7793 (pttm) cc_final: 0.7500 (pttm) REVERT: D 360 TYR cc_start: 0.8199 (p90) cc_final: 0.7590 (p90) REVERT: D 368 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7789 (tp) REVERT: D 375 GLU cc_start: 0.7276 (tp30) cc_final: 0.6793 (tm-30) REVERT: D 399 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7214 (mtmt) REVERT: D 400 MET cc_start: 0.7109 (tmm) cc_final: 0.6607 (tmm) REVERT: D 402 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7053 (tm-30) REVERT: D 441 LEU cc_start: 0.8393 (mm) cc_final: 0.8112 (mp) REVERT: D 442 ILE cc_start: 0.8354 (tt) cc_final: 0.7966 (pt) REVERT: D 475 GLU cc_start: 0.7793 (mp0) cc_final: 0.7461 (mp0) REVERT: D 500 ILE cc_start: 0.8151 (mm) cc_final: 0.7854 (tt) REVERT: D 554 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7160 (tm-30) REVERT: D 572 THR cc_start: 0.7848 (p) cc_final: 0.7490 (p) REVERT: D 579 LEU cc_start: 0.8350 (tp) cc_final: 0.8024 (tp) REVERT: D 589 TYR cc_start: 0.8131 (t80) cc_final: 0.7881 (t80) REVERT: D 622 ASP cc_start: 0.7084 (m-30) cc_final: 0.6822 (m-30) REVERT: D 652 GLU cc_start: 0.8564 (mp0) cc_final: 0.7977 (mp0) REVERT: D 684 ASP cc_start: 0.7757 (m-30) cc_final: 0.7354 (m-30) REVERT: D 691 ASP cc_start: 0.7940 (m-30) cc_final: 0.7632 (m-30) REVERT: D 695 LYS cc_start: 0.8534 (tmtt) cc_final: 0.8173 (tmtt) REVERT: D 703 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.7868 (t) REVERT: D 714 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6582 (tm-30) REVERT: D 770 LEU cc_start: 0.7671 (mm) cc_final: 0.7343 (mt) REVERT: D 772 TYR cc_start: 0.8325 (t80) cc_final: 0.7875 (t80) REVERT: D 781 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8118 (tptm) REVERT: D 789 LYS cc_start: 0.7832 (ttpt) cc_final: 0.7298 (ptmm) REVERT: D 793 SER cc_start: 0.7851 (p) cc_final: 0.7637 (p) REVERT: D 810 THR cc_start: 0.8660 (p) cc_final: 0.8452 (m) REVERT: D 822 MET cc_start: 0.6664 (tmm) cc_final: 0.6075 (tmm) REVERT: D 865 HIS cc_start: 0.6857 (p-80) cc_final: 0.6654 (p-80) REVERT: D 913 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7217 (mm-30) REVERT: D 915 ILE cc_start: 0.8221 (tt) cc_final: 0.8019 (pt) REVERT: D 922 SER cc_start: 0.8205 (m) cc_final: 0.7704 (p) REVERT: D 959 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7918 (mmtp) REVERT: D 979 ASN cc_start: 0.6914 (OUTLIER) cc_final: 0.6136 (p0) REVERT: D 1020 TRP cc_start: 0.8017 (p90) cc_final: 0.7747 (p90) REVERT: D 1025 MET cc_start: 0.8863 (mpp) cc_final: 0.8580 (mpp) REVERT: D 1099 TYR cc_start: 0.7773 (m-80) cc_final: 0.6733 (m-80) REVERT: D 1120 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7475 (p) REVERT: D 1220 ILE cc_start: 0.8645 (tt) cc_final: 0.8300 (tp) REVERT: D 1224 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7495 (mtm180) REVERT: D 1250 ASP cc_start: 0.7187 (p0) cc_final: 0.6839 (p0) REVERT: D 1327 GLU cc_start: 0.7179 (pm20) cc_final: 0.6059 (mp0) REVERT: D 1345 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7780 (mtp85) REVERT: E 53 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7713 (mm-30) REVERT: E 55 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: E 58 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8178 (pp) REVERT: E 62 GLN cc_start: 0.8280 (tp40) cc_final: 0.7804 (tp40) REVERT: G 11 VAL cc_start: 0.8449 (m) cc_final: 0.8234 (p) REVERT: G 27 ARG cc_start: 0.8286 (mtm180) cc_final: 0.7791 (mtm-85) REVERT: G 43 MET cc_start: 0.7335 (tmm) cc_final: 0.6549 (tmm) REVERT: G 73 MET cc_start: 0.6200 (ppp) cc_final: 0.5703 (ppp) REVERT: G 80 TRP cc_start: 0.7768 (t60) cc_final: 0.7239 (t60) REVERT: G 83 VAL cc_start: 0.8750 (t) cc_final: 0.8515 (p) REVERT: G 93 ILE cc_start: 0.7885 (mm) cc_final: 0.7387 (mm) outliers start: 92 outliers final: 62 residues processed: 843 average time/residue: 0.4634 time to fit residues: 576.0907 Evaluate side-chains 853 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 774 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 4.9990 chunk 318 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 333 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN E 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 28008 Z= 0.250 Angle : 0.664 15.564 38141 Z= 0.339 Chirality : 0.044 0.371 4351 Planarity : 0.004 0.062 4731 Dihedral : 14.596 174.572 4488 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.30 % Allowed : 24.30 % Favored : 72.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % 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: -0.49 (0.14), residues: 3285 helix: 1.14 (0.16), residues: 1099 sheet: -0.30 (0.26), residues: 417 loop : -1.31 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D1193 HIS 0.008 0.001 HIS C 343 PHE 0.019 0.001 PHE D 892 TYR 0.023 0.002 TYR D 995 ARG 0.011 0.001 ARG C 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 785 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.6871 (t0) cc_final: 0.6660 (t0) REVERT: A 16 ILE cc_start: 0.8396 (mt) cc_final: 0.8102 (tt) REVERT: A 33 ARG cc_start: 0.7537 (ptm160) cc_final: 0.7016 (ptm160) REVERT: A 51 MET cc_start: 0.8149 (mmm) cc_final: 0.7894 (mmp) REVERT: A 74 VAL cc_start: 0.8421 (m) cc_final: 0.7950 (p) REVERT: A 101 THR cc_start: 0.8325 (m) cc_final: 0.7747 (p) REVERT: A 104 LYS cc_start: 0.8041 (tptp) cc_final: 0.7451 (tptp) REVERT: A 114 ASP cc_start: 0.8015 (t0) cc_final: 0.7521 (t0) REVERT: A 125 LYS cc_start: 0.8260 (ptpp) cc_final: 0.8007 (ttpp) REVERT: A 142 MET cc_start: 0.7961 (mtm) cc_final: 0.7636 (mtm) REVERT: A 145 LYS cc_start: 0.7644 (mtpp) cc_final: 0.7241 (mtpp) REVERT: A 170 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.7577 (ttm-80) REVERT: A 171 LEU cc_start: 0.8387 (pp) cc_final: 0.8150 (pp) REVERT: A 188 GLU cc_start: 0.7531 (pm20) cc_final: 0.7094 (pm20) REVERT: A 212 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6905 (m-30) REVERT: B 16 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7756 (mt) REVERT: B 32 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6614 (tm-30) REVERT: B 51 MET cc_start: 0.7509 (mmm) cc_final: 0.7285 (mmm) REVERT: B 64 VAL cc_start: 0.7302 (t) cc_final: 0.7063 (p) REVERT: B 97 GLU cc_start: 0.7067 (pm20) cc_final: 0.6478 (pm20) REVERT: B 100 LEU cc_start: 0.8606 (mm) cc_final: 0.8043 (tp) REVERT: B 142 MET cc_start: 0.7635 (mmm) cc_final: 0.7411 (mmm) REVERT: B 205 MET cc_start: 0.7525 (ppp) cc_final: 0.6878 (ppp) REVERT: B 214 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5827 (tm-30) REVERT: C 8 LYS cc_start: 0.8321 (mttt) cc_final: 0.7807 (mtpp) REVERT: C 41 GLN cc_start: 0.6957 (tm-30) cc_final: 0.6681 (tm-30) REVERT: C 99 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7713 (ttmm) REVERT: C 151 ARG cc_start: 0.7999 (ttm110) cc_final: 0.7659 (ptp-110) REVERT: C 177 ILE cc_start: 0.8379 (mm) cc_final: 0.8116 (tp) REVERT: C 180 ARG cc_start: 0.7314 (ttp80) cc_final: 0.6903 (ttp80) REVERT: C 185 ASP cc_start: 0.6154 (p0) cc_final: 0.5341 (p0) REVERT: C 186 PHE cc_start: 0.7752 (m-80) cc_final: 0.7239 (m-10) REVERT: C 187 GLU cc_start: 0.7112 (mp0) cc_final: 0.6180 (mp0) REVERT: C 195 PHE cc_start: 0.7911 (m-80) cc_final: 0.7564 (m-80) REVERT: C 202 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6728 (ttp80) REVERT: C 203 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7314 (ttmm) REVERT: C 214 ASN cc_start: 0.8748 (t0) cc_final: 0.8429 (t0) REVERT: C 218 GLU cc_start: 0.8236 (pm20) cc_final: 0.7903 (pm20) REVERT: C 330 HIS cc_start: 0.8272 (m90) cc_final: 0.7830 (m-70) REVERT: C 349 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7794 (pm20) REVERT: C 368 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7930 (mtm-85) REVERT: C 369 MET cc_start: 0.7738 (tpp) cc_final: 0.6363 (tpt) REVERT: C 371 ARG cc_start: 0.6688 (mtp-110) cc_final: 0.6263 (ptm160) REVERT: C 374 GLU cc_start: 0.5967 (pt0) cc_final: 0.4933 (pt0) REVERT: C 392 GLU cc_start: 0.7456 (mp0) cc_final: 0.7114 (mp0) REVERT: C 394 ARG cc_start: 0.7079 (ttm110) cc_final: 0.6851 (ttm110) REVERT: C 427 ASP cc_start: 0.7312 (m-30) cc_final: 0.7011 (m-30) REVERT: C 448 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7240 (mp) REVERT: C 499 SER cc_start: 0.7318 (p) cc_final: 0.7027 (p) REVERT: C 517 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6774 (pm20) REVERT: C 523 GLU cc_start: 0.7612 (tp30) cc_final: 0.7274 (tp30) REVERT: C 538 LEU cc_start: 0.8303 (tp) cc_final: 0.8032 (tp) REVERT: C 549 ASP cc_start: 0.7424 (t0) cc_final: 0.7105 (t0) REVERT: C 562 GLU cc_start: 0.7519 (tm-30) cc_final: 0.6509 (tm-30) REVERT: C 574 SER cc_start: 0.8928 (t) cc_final: 0.8361 (p) REVERT: C 593 LYS cc_start: 0.8060 (tptt) cc_final: 0.7372 (tppt) REVERT: C 611 GLU cc_start: 0.7411 (tt0) cc_final: 0.6714 (mt-10) REVERT: C 651 ASP cc_start: 0.7880 (m-30) cc_final: 0.7659 (m-30) REVERT: C 653 MET cc_start: 0.7400 (ttm) cc_final: 0.6992 (ttp) REVERT: C 656 SER cc_start: 0.8574 (t) cc_final: 0.7977 (m) REVERT: C 714 VAL cc_start: 0.8442 (p) cc_final: 0.8233 (t) REVERT: C 730 SER cc_start: 0.8714 (m) cc_final: 0.8300 (t) REVERT: C 731 ARG cc_start: 0.7913 (ptp-110) cc_final: 0.7561 (ptm160) REVERT: C 734 ILE cc_start: 0.7756 (mt) cc_final: 0.7507 (pt) REVERT: C 778 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7511 (mm-30) REVERT: C 788 SER cc_start: 0.8405 (m) cc_final: 0.7642 (p) REVERT: C 790 ASP cc_start: 0.7397 (t70) cc_final: 0.7074 (t70) REVERT: C 793 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6873 (mt-10) REVERT: C 800 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6942 (mtp) REVERT: C 811 ASN cc_start: 0.7623 (p0) cc_final: 0.6894 (p0) REVERT: C 814 ASP cc_start: 0.7392 (m-30) cc_final: 0.6949 (m-30) REVERT: C 825 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6801 (tm-30) REVERT: C 848 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6960 (pt0) REVERT: C 914 LYS cc_start: 0.8118 (tppt) cc_final: 0.7765 (tppt) REVERT: C 930 ASP cc_start: 0.7730 (t0) cc_final: 0.7187 (m-30) REVERT: C 947 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7742 (tm-30) REVERT: C 948 ILE cc_start: 0.8781 (mm) cc_final: 0.8412 (mm) REVERT: C 950 GLU cc_start: 0.8513 (pt0) cc_final: 0.8271 (pt0) REVERT: C 960 LEU cc_start: 0.8227 (mp) cc_final: 0.7860 (pp) REVERT: C 1028 LYS cc_start: 0.8599 (ptpp) cc_final: 0.8318 (pttt) REVERT: C 1030 GLU cc_start: 0.8145 (pt0) cc_final: 0.7820 (pp20) REVERT: C 1032 LYS cc_start: 0.9183 (tptt) cc_final: 0.8790 (mttt) REVERT: C 1035 LYS cc_start: 0.8700 (tppt) cc_final: 0.8040 (tppt) REVERT: C 1095 ASP cc_start: 0.7371 (m-30) cc_final: 0.7014 (m-30) REVERT: C 1119 MET cc_start: 0.8181 (tpp) cc_final: 0.7756 (tpt) REVERT: C 1122 LYS cc_start: 0.8275 (tptm) cc_final: 0.7224 (tppt) REVERT: C 1126 ASP cc_start: 0.7331 (m-30) cc_final: 0.6620 (m-30) REVERT: C 1127 LYS cc_start: 0.8798 (tptp) cc_final: 0.8454 (tptp) REVERT: C 1131 MET cc_start: 0.8155 (ttt) cc_final: 0.7786 (ttt) REVERT: C 1143 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7309 (tm-30) REVERT: C 1146 GLN cc_start: 0.7612 (tp40) cc_final: 0.7101 (tp-100) REVERT: C 1147 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.8037 (mmm-85) REVERT: C 1167 GLU cc_start: 0.7783 (pm20) cc_final: 0.7384 (pm20) REVERT: C 1176 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7185 (tt) REVERT: C 1197 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7282 (tm-30) REVERT: C 1200 LYS cc_start: 0.8422 (tttt) cc_final: 0.8146 (tttt) REVERT: C 1210 ILE cc_start: 0.7923 (tt) cc_final: 0.7697 (pt) REVERT: C 1229 TYR cc_start: 0.8168 (m-80) cc_final: 0.7790 (m-80) REVERT: C 1264 GLN cc_start: 0.8033 (mp10) cc_final: 0.7405 (mp10) REVERT: C 1268 GLN cc_start: 0.6925 (pp30) cc_final: 0.6721 (pp30) REVERT: C 1329 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6736 (tt0) REVERT: D 21 LYS cc_start: 0.8060 (ptpt) cc_final: 0.7335 (ptmm) REVERT: D 29 MET cc_start: 0.8025 (ttt) cc_final: 0.7435 (ttm) REVERT: D 33 TRP cc_start: 0.7650 (m-10) cc_final: 0.7222 (m-10) REVERT: D 52 GLU cc_start: 0.7066 (tp30) cc_final: 0.6797 (tm-30) REVERT: D 53 ARG cc_start: 0.7529 (ttt90) cc_final: 0.6919 (ttt90) REVERT: D 96 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8147 (mmtm) REVERT: D 115 TRP cc_start: 0.8556 (m-10) cc_final: 0.8265 (m-10) REVERT: D 118 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7938 (mmmt) REVERT: D 128 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7517 (mt) REVERT: D 138 VAL cc_start: 0.8550 (t) cc_final: 0.8253 (p) REVERT: D 148 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6422 (tm-30) REVERT: D 151 MET cc_start: 0.8015 (pmm) cc_final: 0.7423 (pmm) REVERT: D 157 GLN cc_start: 0.7760 (mt0) cc_final: 0.7177 (mp10) REVERT: D 158 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7667 (mp10) REVERT: D 177 ASP cc_start: 0.7484 (p0) cc_final: 0.6991 (p0) REVERT: D 180 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6567 (ppp) REVERT: D 202 ARG cc_start: 0.8426 (mtm-85) cc_final: 0.7813 (mtt-85) REVERT: D 214 ARG cc_start: 0.8349 (mmt180) cc_final: 0.8037 (mtt180) REVERT: D 216 LYS cc_start: 0.8966 (pttt) cc_final: 0.8601 (pttt) REVERT: D 219 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8533 (ttpp) REVERT: D 235 GLU cc_start: 0.7456 (pm20) cc_final: 0.7228 (pm20) REVERT: D 251 PRO cc_start: 0.7958 (Cg_endo) cc_final: 0.7728 (Cg_exo) REVERT: D 275 ARG cc_start: 0.7818 (tpp-160) cc_final: 0.6816 (tpp-160) REVERT: D 279 LEU cc_start: 0.8208 (tp) cc_final: 0.7419 (tp) REVERT: D 280 LYS cc_start: 0.8600 (tptp) cc_final: 0.8385 (tppt) REVERT: D 282 LEU cc_start: 0.8594 (mt) cc_final: 0.8256 (tt) REVERT: D 295 GLU cc_start: 0.7672 (tm-30) cc_final: 0.6658 (tm-30) REVERT: D 298 MET cc_start: 0.7431 (ttp) cc_final: 0.6436 (ttp) REVERT: D 325 LYS cc_start: 0.8282 (mmtt) cc_final: 0.8033 (mmtp) REVERT: D 332 LYS cc_start: 0.7110 (mtmm) cc_final: 0.6823 (mtmm) REVERT: D 345 LYS cc_start: 0.7813 (pttm) cc_final: 0.7508 (pttm) REVERT: D 368 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7803 (tp) REVERT: D 375 GLU cc_start: 0.7310 (tp30) cc_final: 0.6539 (tm-30) REVERT: D 399 LYS cc_start: 0.7796 (mtmt) cc_final: 0.7275 (mtmt) REVERT: D 400 MET cc_start: 0.7092 (tmm) cc_final: 0.6769 (tpp) REVERT: D 402 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7031 (tm-30) REVERT: D 441 LEU cc_start: 0.8366 (mm) cc_final: 0.8096 (mp) REVERT: D 442 ILE cc_start: 0.8360 (tt) cc_final: 0.7977 (pt) REVERT: D 475 GLU cc_start: 0.7804 (mp0) cc_final: 0.7491 (mp0) REVERT: D 500 ILE cc_start: 0.8135 (mm) cc_final: 0.7852 (tt) REVERT: D 554 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7079 (tm-30) REVERT: D 572 THR cc_start: 0.7885 (p) cc_final: 0.7512 (p) REVERT: D 579 LEU cc_start: 0.8376 (tp) cc_final: 0.8054 (tp) REVERT: D 589 TYR cc_start: 0.8171 (t80) cc_final: 0.7884 (t80) REVERT: D 603 LYS cc_start: 0.7470 (tmmt) cc_final: 0.7184 (mmpt) REVERT: D 622 ASP cc_start: 0.7100 (m-30) cc_final: 0.6873 (m-30) REVERT: D 652 GLU cc_start: 0.8561 (mp0) cc_final: 0.7977 (mp0) REVERT: D 684 ASP cc_start: 0.7783 (m-30) cc_final: 0.7368 (m-30) REVERT: D 691 ASP cc_start: 0.7938 (m-30) cc_final: 0.7644 (m-30) REVERT: D 695 LYS cc_start: 0.8549 (tmtt) cc_final: 0.8179 (tmtt) REVERT: D 703 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.7928 (t) REVERT: D 714 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6582 (tm-30) REVERT: D 772 TYR cc_start: 0.8326 (t80) cc_final: 0.8082 (t80) REVERT: D 781 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8111 (tptm) REVERT: D 789 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7485 (ptmm) REVERT: D 810 THR cc_start: 0.8650 (p) cc_final: 0.8446 (m) REVERT: D 822 MET cc_start: 0.6675 (tmm) cc_final: 0.6160 (tmm) REVERT: D 865 HIS cc_start: 0.6889 (p-80) cc_final: 0.6660 (p-80) REVERT: D 913 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7265 (mm-30) REVERT: D 922 SER cc_start: 0.8213 (m) cc_final: 0.7717 (p) REVERT: D 959 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7958 (mmtp) REVERT: D 979 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6204 (p0) REVERT: D 1025 MET cc_start: 0.8877 (mpp) cc_final: 0.8604 (mpp) REVERT: D 1099 TYR cc_start: 0.7741 (m-80) cc_final: 0.6721 (m-80) REVERT: D 1120 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7452 (p) REVERT: D 1146 GLU cc_start: 0.7218 (tp30) cc_final: 0.6989 (tp30) REVERT: D 1224 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7716 (mtm180) REVERT: D 1250 ASP cc_start: 0.7188 (p0) cc_final: 0.6837 (p0) REVERT: D 1327 GLU cc_start: 0.7210 (pm20) cc_final: 0.6078 (mp0) REVERT: E 53 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7772 (mm-30) REVERT: E 55 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7132 (tp30) REVERT: E 58 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8186 (pp) REVERT: E 62 GLN cc_start: 0.8296 (tp40) cc_final: 0.7828 (tp40) REVERT: G 27 ARG cc_start: 0.8291 (mtm180) cc_final: 0.7774 (mtm-85) REVERT: G 30 ILE cc_start: 0.8668 (mt) cc_final: 0.7928 (mt) REVERT: G 43 MET cc_start: 0.7307 (tmm) cc_final: 0.6597 (tmm) REVERT: G 73 MET cc_start: 0.6184 (ppp) cc_final: 0.5666 (ppp) REVERT: G 80 TRP cc_start: 0.7788 (t60) cc_final: 0.7284 (t60) REVERT: G 83 VAL cc_start: 0.8727 (t) cc_final: 0.8492 (p) REVERT: G 93 ILE cc_start: 0.7895 (mm) cc_final: 0.7434 (mm) outliers start: 93 outliers final: 66 residues processed: 834 average time/residue: 0.4510 time to fit residues: 553.4713 Evaluate side-chains 859 residues out of total 2819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 774 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 0.9990 chunk 283 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108729 restraints weight = 48824.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112365 restraints weight = 24556.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114683 restraints weight = 15130.983| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 28008 Z= 0.273 Angle : 0.672 12.891 38141 Z= 0.345 Chirality : 0.044 0.401 4351 Planarity : 0.004 0.059 4731 Dihedral : 14.607 174.290 4488 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.16 % Allowed : 24.90 % Favored : 71.94 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3285 helix: 1.07 (0.16), residues: 1095 sheet: -0.26 (0.26), residues: 412 loop : -1.35 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D1193 HIS 0.008 0.001 HIS C 343 PHE 0.020 0.002 PHE D 892 TYR 0.022 0.002 TYR B 185 ARG 0.010 0.001 ARG C 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8875.84 seconds wall clock time: 157 minutes 37.16 seconds (9457.16 seconds total)