Starting phenix.real_space_refine on Mon Sep 23 13:02:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3a_11055/09_2024/6z3a_11055_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3a_11055/09_2024/6z3a_11055.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/6z3a_11055/09_2024/6z3a_11055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3a_11055/09_2024/6z3a_11055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3a_11055/09_2024/6z3a_11055_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3a_11055/09_2024/6z3a_11055_neut.cif" } 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= 0.019 sd= 0.323 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 S 194 5.16 5 C 29704 2.51 5 N 7680 2.21 5 O 8556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 46142 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 18496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2311, 18496 Classifications: {'peptide': 2311} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 2242} Chain breaks: 9 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 155 Chain: "C" Number of atoms: 4541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 4530 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 554, 4530 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 4606 Chain: "D" Number of atoms: 4545 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 4534 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 554, 4534 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 4610 Chain: "E" Number of atoms: 18496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2311, 18496 Classifications: {'peptide': 2311} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 2242} Chain breaks: 9 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 155 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3770 SG CYS F 490 36.075 153.497 110.956 1.00207.44 S ATOM 3794 SG CYS F 493 35.634 157.327 111.749 1.00173.90 S ATOM 31201 SG CYS E 467 100.788 69.602 110.218 1.00214.30 S ATOM 31352 SG CYS E 490 97.402 68.950 110.769 1.00206.97 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG C 228 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 228 " occ=0.50 residue: pdb=" N AARG D 228 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 228 " occ=0.50 Time building chain proxies: 22.00, per 1000 atoms: 0.48 Number of scatterers: 46142 At special positions: 0 Unit cell: (134.62, 223.66, 177.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 194 16.00 P 6 15.00 O 8556 8.00 N 7680 7.00 C 29704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.50 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E2402 " pdb="ZN ZN E2402 " - pdb=" NE2 HIS E 553 " pdb="ZN ZN E2402 " - pdb=" SG CYS E 490 " pdb="ZN ZN E2402 " - pdb=" SG CYS E 467 " pdb=" ZN F2402 " pdb="ZN ZN F2402 " - pdb=" NE2 HIS F 553 " pdb="ZN ZN F2402 " - pdb=" SG CYS F 490 " pdb="ZN ZN F2402 " - pdb=" SG CYS F 493 " 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11076 Finding SS restraints... Secondary structure from input PDB file: 306 helices and 6 sheets defined 68.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'F' and resid 4 through 18 removed outlier: 3.661A pdb=" N LEU F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 57 removed outlier: 3.993A pdb=" N LEU F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 84 removed outlier: 3.749A pdb=" N LEU F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 removed outlier: 3.854A pdb=" N LEU F 88 " --> pdb=" O PRO F 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 88' Processing helix chain 'F' and resid 98 through 113 removed outlier: 3.711A pdb=" N ASP F 104 " --> pdb=" O GLN F 100 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 133 removed outlier: 3.662A pdb=" N MET F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS F 126 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 removed outlier: 3.698A pdb=" N PHE F 137 " --> pdb=" O CYS F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 161 removed outlier: 3.991A pdb=" N PHE F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLN F 145 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N HIS F 149 " --> pdb=" O GLN F 145 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU F 151 " --> pdb=" O THR F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 165 Processing helix chain 'F' and resid 171 through 189 removed outlier: 3.781A pdb=" N PHE F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 229 removed outlier: 4.362A pdb=" N PHE F 213 " --> pdb=" O THR F 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG F 220 " --> pdb=" O GLN F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 253 removed outlier: 3.559A pdb=" N LYS F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR F 243 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE F 244 " --> pdb=" O GLN F 240 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL F 251 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 284 removed outlier: 3.609A pdb=" N ASN F 284 " --> pdb=" O HIS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 306 Processing helix chain 'F' and resid 311 through 319 Processing helix chain 'F' and resid 321 through 325 removed outlier: 4.276A pdb=" N ALA F 325 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 355 Processing helix chain 'F' and resid 390 through 403 Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 411 through 421 Processing helix chain 'F' and resid 431 through 445 removed outlier: 4.357A pdb=" N ILE F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 436 " --> pdb=" O PHE F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 471 removed outlier: 3.597A pdb=" N CYS F 467 " --> pdb=" O GLY F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 504 removed outlier: 3.535A pdb=" N VAL F 503 " --> pdb=" O ASN F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 516 Processing helix chain 'F' and resid 516 through 526 Processing helix chain 'F' and resid 527 through 529 No H-bonds generated for 'chain 'F' and resid 527 through 529' Processing helix chain 'F' and resid 536 through 554 Processing helix chain 'F' and resid 569 through 578 removed outlier: 3.657A pdb=" N MET F 578 " --> pdb=" O GLN F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 589 removed outlier: 3.539A pdb=" N ARG F 585 " --> pdb=" O ASN F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 596 removed outlier: 3.770A pdb=" N PHE F 595 " --> pdb=" O ILE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 616 Processing helix chain 'F' and resid 620 through 622 No H-bonds generated for 'chain 'F' and resid 620 through 622' Processing helix chain 'F' and resid 623 through 636 Processing helix chain 'F' and resid 639 through 655 removed outlier: 3.838A pdb=" N ILE F 653 " --> pdb=" O LYS F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 658 through 676 Processing helix chain 'F' and resid 679 through 685 Processing helix chain 'F' and resid 687 through 696 removed outlier: 3.954A pdb=" N ARG F 693 " --> pdb=" O PRO F 689 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN F 694 " --> pdb=" O VAL F 690 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU F 695 " --> pdb=" O LEU F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 714 Processing helix chain 'F' and resid 716 through 722 removed outlier: 3.791A pdb=" N ILE F 720 " --> pdb=" O SER F 716 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 728 removed outlier: 3.642A pdb=" N TYR F 727 " --> pdb=" O PHE F 724 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE F 728 " --> pdb=" O GLN F 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 724 through 728' Processing helix chain 'F' and resid 729 through 734 removed outlier: 3.907A pdb=" N ILE F 734 " --> pdb=" O PRO F 730 " (cutoff:3.500A) Processing helix chain 'F' and resid 740 through 749 Processing helix chain 'F' and resid 755 through 767 Processing helix chain 'F' and resid 768 through 777 removed outlier: 3.627A pdb=" N PHE F 772 " --> pdb=" O SER F 768 " (cutoff:3.500A) Processing helix chain 'F' and resid 783 through 793 Processing helix chain 'F' and resid 809 through 817 Processing helix chain 'F' and resid 827 through 843 Processing helix chain 'F' and resid 844 through 848 removed outlier: 3.505A pdb=" N PHE F 848 " --> pdb=" O ILE F 845 " (cutoff:3.500A) Processing helix chain 'F' and resid 860 through 864 removed outlier: 3.977A pdb=" N ASN F 863 " --> pdb=" O ASN F 860 " (cutoff:3.500A) Processing helix chain 'F' and resid 868 through 892 removed outlier: 4.444A pdb=" N LEU F 881 " --> pdb=" O GLN F 877 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY F 882 " --> pdb=" O ASP F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 900 through 916 Processing helix chain 'F' and resid 918 through 925 Processing helix chain 'F' and resid 927 through 939 removed outlier: 3.851A pdb=" N ILE F 931 " --> pdb=" O ALA F 927 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 939 " --> pdb=" O THR F 935 " (cutoff:3.500A) Processing helix chain 'F' and resid 942 through 956 removed outlier: 3.705A pdb=" N ALA F 946 " --> pdb=" O VAL F 942 " (cutoff:3.500A) Processing helix chain 'F' and resid 962 through 965 removed outlier: 3.638A pdb=" N VAL F 965 " --> pdb=" O LEU F 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 962 through 965' Processing helix chain 'F' and resid 966 through 977 removed outlier: 3.790A pdb=" N ILE F 970 " --> pdb=" O ILE F 966 " (cutoff:3.500A) Processing helix chain 'F' and resid 978 through 980 No H-bonds generated for 'chain 'F' and resid 978 through 980' Processing helix chain 'F' and resid 981 through 999 Processing helix chain 'F' and resid 999 through 1004 Processing helix chain 'F' and resid 1007 through 1017 removed outlier: 3.836A pdb=" N THR F1011 " --> pdb=" O LYS F1007 " (cutoff:3.500A) Processing helix chain 'F' and resid 1021 through 1026 Processing helix chain 'F' and resid 1029 through 1039 removed outlier: 3.601A pdb=" N SER F1038 " --> pdb=" O ASN F1034 " (cutoff:3.500A) Processing helix chain 'F' and resid 1041 through 1050 removed outlier: 4.382A pdb=" N ILE F1045 " --> pdb=" O ASP F1041 " (cutoff:3.500A) Processing helix chain 'F' and resid 1054 through 1075 removed outlier: 3.918A pdb=" N ILE F1058 " --> pdb=" O ASN F1054 " (cutoff:3.500A) Processing helix chain 'F' and resid 1091 through 1105 Processing helix chain 'F' and resid 1109 through 1124 Processing helix chain 'F' and resid 1148 through 1164 Processing helix chain 'F' and resid 1173 through 1191 Processing helix chain 'F' and resid 1206 through 1215 removed outlier: 4.143A pdb=" N ALA F1210 " --> pdb=" O TYR F1206 " (cutoff:3.500A) Processing helix chain 'F' and resid 1217 through 1225 removed outlier: 3.699A pdb=" N TYR F1225 " --> pdb=" O LYS F1221 " (cutoff:3.500A) Processing helix chain 'F' and resid 1226 through 1228 No H-bonds generated for 'chain 'F' and resid 1226 through 1228' Processing helix chain 'F' and resid 1246 through 1252 Processing helix chain 'F' and resid 1256 through 1270 Processing helix chain 'F' and resid 1274 through 1282 removed outlier: 3.760A pdb=" N PHE F1279 " --> pdb=" O LEU F1276 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER F1280 " --> pdb=" O HIS F1277 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER F1281 " --> pdb=" O VAL F1278 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU F1282 " --> pdb=" O PHE F1279 " (cutoff:3.500A) Processing helix chain 'F' and resid 1293 through 1299 removed outlier: 4.284A pdb=" N SER F1299 " --> pdb=" O LEU F1295 " (cutoff:3.500A) Processing helix chain 'F' and resid 1311 through 1329 removed outlier: 4.006A pdb=" N CYS F1329 " --> pdb=" O SER F1325 " (cutoff:3.500A) Processing helix chain 'F' and resid 1335 through 1340 Processing helix chain 'F' and resid 1340 through 1366 Processing helix chain 'F' and resid 1367 through 1369 No H-bonds generated for 'chain 'F' and resid 1367 through 1369' Processing helix chain 'F' and resid 1379 through 1394 Processing helix chain 'F' and resid 1396 through 1407 Processing helix chain 'F' and resid 1409 through 1423 removed outlier: 4.023A pdb=" N CYS F1420 " --> pdb=" O TYR F1416 " (cutoff:3.500A) Processing helix chain 'F' and resid 1428 through 1431 removed outlier: 3.576A pdb=" N ASN F1431 " --> pdb=" O LYS F1428 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1428 through 1431' Processing helix chain 'F' and resid 1432 through 1446 removed outlier: 4.125A pdb=" N LEU F1438 " --> pdb=" O LEU F1434 " (cutoff:3.500A) Processing helix chain 'F' and resid 1447 through 1457 Processing helix chain 'F' and resid 1462 through 1467 Processing helix chain 'F' and resid 1475 through 1487 removed outlier: 3.998A pdb=" N ALA F1479 " --> pdb=" O ASN F1475 " (cutoff:3.500A) Processing helix chain 'F' and resid 1488 through 1490 No H-bonds generated for 'chain 'F' and resid 1488 through 1490' Processing helix chain 'F' and resid 1492 through 1505 removed outlier: 3.729A pdb=" N THR F1496 " --> pdb=" O ASP F1492 " (cutoff:3.500A) Processing helix chain 'F' and resid 1508 through 1515 Processing helix chain 'F' and resid 1532 through 1545 removed outlier: 4.844A pdb=" N GLU F1540 " --> pdb=" O SER F1536 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA F1541 " --> pdb=" O ILE F1537 " (cutoff:3.500A) Processing helix chain 'F' and resid 1548 through 1559 Processing helix chain 'F' and resid 1566 through 1584 removed outlier: 3.684A pdb=" N LEU F1570 " --> pdb=" O ASP F1566 " (cutoff:3.500A) Processing helix chain 'F' and resid 1586 through 1605 Processing helix chain 'F' and resid 1617 through 1635 removed outlier: 4.193A pdb=" N LYS F1623 " --> pdb=" O ASN F1619 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU F1633 " --> pdb=" O ASP F1629 " (cutoff:3.500A) Processing helix chain 'F' and resid 1638 through 1656 Processing helix chain 'F' and resid 1659 through 1677 Processing helix chain 'F' and resid 1679 through 1700 Processing helix chain 'F' and resid 1704 through 1715 removed outlier: 5.021A pdb=" N HIS F1712 " --> pdb=" O GLU F1708 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS F1713 " --> pdb=" O SER F1709 " (cutoff:3.500A) Processing helix chain 'F' and resid 1718 through 1733 removed outlier: 3.680A pdb=" N GLY F1733 " --> pdb=" O LEU F1729 " (cutoff:3.500A) Processing helix chain 'F' and resid 1734 through 1749 removed outlier: 3.536A pdb=" N ALA F1738 " --> pdb=" O GLU F1734 " (cutoff:3.500A) Processing helix chain 'F' and resid 1758 through 1775 Processing helix chain 'F' and resid 1779 through 1793 removed outlier: 3.891A pdb=" N GLN F1785 " --> pdb=" O GLN F1781 " (cutoff:3.500A) Processing helix chain 'F' and resid 1797 through 1816 Processing helix chain 'F' and resid 1823 through 1838 removed outlier: 3.645A pdb=" N TYR F1827 " --> pdb=" O GLY F1823 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU F1838 " --> pdb=" O LEU F1834 " (cutoff:3.500A) Processing helix chain 'F' and resid 1843 through 1865 Proline residue: F1849 - end of helix removed outlier: 5.040A pdb=" N PHE F1854 " --> pdb=" O LYS F1850 " (cutoff:3.500A) Processing helix chain 'F' and resid 1874 through 1892 removed outlier: 3.790A pdb=" N HIS F1891 " --> pdb=" O GLU F1887 " (cutoff:3.500A) Processing helix chain 'F' and resid 1896 through 1899 removed outlier: 3.798A pdb=" N PHE F1899 " --> pdb=" O ILE F1896 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1896 through 1899' Processing helix chain 'F' and resid 1900 through 1906 Processing helix chain 'F' and resid 1913 through 1929 Processing helix chain 'F' and resid 1931 through 1933 No H-bonds generated for 'chain 'F' and resid 1931 through 1933' Processing helix chain 'F' and resid 1934 through 1942 removed outlier: 4.436A pdb=" N VAL F1942 " --> pdb=" O ILE F1938 " (cutoff:3.500A) Processing helix chain 'F' and resid 1948 through 1963 removed outlier: 4.505A pdb=" N ARG F1952 " --> pdb=" O LYS F1948 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE F1956 " --> pdb=" O ARG F1952 " (cutoff:3.500A) Processing helix chain 'F' and resid 1969 through 1984 removed outlier: 4.070A pdb=" N SER F1973 " --> pdb=" O ASP F1969 " (cutoff:3.500A) Processing helix chain 'F' and resid 2085 through 2104 removed outlier: 4.391A pdb=" N PHE F2099 " --> pdb=" O THR F2095 " (cutoff:3.500A) Processing helix chain 'F' and resid 2137 through 2149 Processing helix chain 'F' and resid 2157 through 2164 Processing helix chain 'F' and resid 2167 through 2181 removed outlier: 4.443A pdb=" N LEU F2171 " --> pdb=" O VAL F2167 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU F2172 " --> pdb=" O ASP F2168 " (cutoff:3.500A) Processing helix chain 'F' and resid 2185 through 2193 removed outlier: 3.900A pdb=" N GLU F2191 " --> pdb=" O GLN F2187 " (cutoff:3.500A) Processing helix chain 'F' and resid 2195 through 2221 removed outlier: 4.128A pdb=" N MET F2213 " --> pdb=" O SER F2209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS F2218 " --> pdb=" O ALA F2214 " (cutoff:3.500A) Processing helix chain 'F' and resid 2265 through 2267 No H-bonds generated for 'chain 'F' and resid 2265 through 2267' Processing helix chain 'F' and resid 2268 through 2273 removed outlier: 3.627A pdb=" N GLY F2273 " --> pdb=" O LEU F2269 " (cutoff:3.500A) Processing helix chain 'F' and resid 2279 through 2293 Processing helix chain 'F' and resid 2295 through 2305 removed outlier: 4.038A pdb=" N THR F2305 " --> pdb=" O ASN F2301 " (cutoff:3.500A) Processing helix chain 'F' and resid 2316 through 2329 Processing helix chain 'F' and resid 2340 through 2352 Processing helix chain 'F' and resid 2353 through 2359 Processing helix chain 'F' and resid 2361 through 2365 Processing helix chain 'C' and resid 201 through 212 Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 249 through 265 removed outlier: 3.666A pdb=" N LYS C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 287 Processing helix chain 'C' and resid 294 through 309 removed outlier: 4.520A pdb=" N PHE C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 Processing helix chain 'C' and resid 355 through 382 Processing helix chain 'C' and resid 392 through 407 removed outlier: 3.820A pdb=" N LEU C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 435 removed outlier: 3.524A pdb=" N VAL C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 445 removed outlier: 4.117A pdb=" N LEU C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 462 removed outlier: 3.799A pdb=" N TRP C 450 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR C 455 " --> pdb=" O ARG C 451 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 470 Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.521A pdb=" N SER C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 525 removed outlier: 3.750A pdb=" N ASP C 524 " --> pdb=" O SER C 521 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE C 525 " --> pdb=" O LYS C 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 521 through 525' Processing helix chain 'C' and resid 535 through 563 Processing helix chain 'C' and resid 572 through 593 removed outlier: 4.272A pdb=" N SER C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 622 removed outlier: 3.915A pdb=" N ILE C 608 " --> pdb=" O ARG C 604 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C 609 " --> pdb=" O CYS C 605 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR C 613 " --> pdb=" O GLU C 609 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 618 " --> pdb=" O ILE C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 634 removed outlier: 3.686A pdb=" N LYS C 632 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 647 removed outlier: 3.605A pdb=" N ILE C 639 " --> pdb=" O GLU C 635 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 645 " --> pdb=" O SER C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 657 through 667 removed outlier: 3.510A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP C 662 " --> pdb=" O ARG C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 681 Processing helix chain 'C' and resid 692 through 709 removed outlier: 3.517A pdb=" N GLU C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ASN C 702 " --> pdb=" O LYS C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 726 removed outlier: 3.782A pdb=" N ILE C 724 " --> pdb=" O MET C 720 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 725 " --> pdb=" O ALA C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 743 removed outlier: 3.504A pdb=" N ASP C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER C 740 " --> pdb=" O GLU C 736 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 212 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 249 through 265 removed outlier: 3.616A pdb=" N LYS D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 287 Processing helix chain 'D' and resid 294 through 309 removed outlier: 4.516A pdb=" N PHE D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE D 309 " --> pdb=" O GLN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 333 Processing helix chain 'D' and resid 355 through 382 Processing helix chain 'D' and resid 392 through 407 removed outlier: 3.807A pdb=" N LEU D 396 " --> pdb=" O ASP D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 435 removed outlier: 3.505A pdb=" N ILE D 418 " --> pdb=" O MET D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 445 removed outlier: 4.108A pdb=" N LEU D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 462 removed outlier: 3.789A pdb=" N TRP D 450 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR D 455 " --> pdb=" O ARG D 451 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG D 456 " --> pdb=" O ASP D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 removed outlier: 3.521A pdb=" N ASP D 469 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 535 through 563 Processing helix chain 'D' and resid 572 through 593 removed outlier: 3.504A pdb=" N ILE D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET D 589 " --> pdb=" O GLU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 622 removed outlier: 3.947A pdb=" N ILE D 608 " --> pdb=" O ARG D 604 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 609 " --> pdb=" O CYS D 605 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 618 " --> pdb=" O ILE D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 626 Processing helix chain 'D' and resid 627 through 634 removed outlier: 3.712A pdb=" N LYS D 632 " --> pdb=" O GLU D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 647 removed outlier: 3.659A pdb=" N ILE D 639 " --> pdb=" O GLU D 635 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D 645 " --> pdb=" O SER D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 657 through 667 removed outlier: 3.532A pdb=" N ARG D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP D 662 " --> pdb=" O ARG D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 681 Processing helix chain 'D' and resid 693 through 709 removed outlier: 3.556A pdb=" N MET D 699 " --> pdb=" O GLU D 695 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN D 702 " --> pdb=" O LYS D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 726 removed outlier: 3.700A pdb=" N ILE D 724 " --> pdb=" O MET D 720 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 725 " --> pdb=" O ALA D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 743 removed outlier: 3.568A pdb=" N ASP D 739 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER D 740 " --> pdb=" O GLU D 736 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 18 removed outlier: 3.660A pdb=" N LEU E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 57 removed outlier: 3.993A pdb=" N LEU E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 84 removed outlier: 3.748A pdb=" N LEU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 88 removed outlier: 3.854A pdb=" N LEU E 88 " --> pdb=" O PRO E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 88' Processing helix chain 'E' and resid 98 through 113 removed outlier: 3.711A pdb=" N ASP E 104 " --> pdb=" O GLN E 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 133 removed outlier: 3.662A pdb=" N MET E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 138 removed outlier: 3.697A pdb=" N PHE E 137 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 161 removed outlier: 3.991A pdb=" N PHE E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN E 145 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N HIS E 149 " --> pdb=" O GLN E 145 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 165 Processing helix chain 'E' and resid 171 through 189 removed outlier: 3.782A pdb=" N PHE E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 229 removed outlier: 4.362A pdb=" N PHE E 213 " --> pdb=" O THR E 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG E 220 " --> pdb=" O GLN E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 253 removed outlier: 3.559A pdb=" N LYS E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE E 244 " --> pdb=" O GLN E 240 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL E 251 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.609A pdb=" N ASN E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 306 Processing helix chain 'E' and resid 311 through 319 Processing helix chain 'E' and resid 321 through 325 removed outlier: 4.276A pdb=" N ALA E 325 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 355 Processing helix chain 'E' and resid 390 through 403 Processing helix chain 'E' and resid 404 through 406 No H-bonds generated for 'chain 'E' and resid 404 through 406' Processing helix chain 'E' and resid 411 through 421 Processing helix chain 'E' and resid 431 through 445 removed outlier: 4.357A pdb=" N ILE E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 436 " --> pdb=" O PHE E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 471 removed outlier: 3.597A pdb=" N CYS E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 504 removed outlier: 3.534A pdb=" N VAL E 503 " --> pdb=" O ASN E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 516 Processing helix chain 'E' and resid 516 through 526 Processing helix chain 'E' and resid 527 through 529 No H-bonds generated for 'chain 'E' and resid 527 through 529' Processing helix chain 'E' and resid 536 through 554 Processing helix chain 'E' and resid 569 through 578 removed outlier: 3.658A pdb=" N MET E 578 " --> pdb=" O GLN E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 589 removed outlier: 3.539A pdb=" N ARG E 585 " --> pdb=" O ASN E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 596 removed outlier: 3.770A pdb=" N PHE E 595 " --> pdb=" O ILE E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 616 Processing helix chain 'E' and resid 620 through 622 No H-bonds generated for 'chain 'E' and resid 620 through 622' Processing helix chain 'E' and resid 623 through 636 Processing helix chain 'E' and resid 639 through 655 removed outlier: 3.839A pdb=" N ILE E 653 " --> pdb=" O LYS E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 658 through 676 Processing helix chain 'E' and resid 679 through 685 Processing helix chain 'E' and resid 687 through 696 removed outlier: 3.954A pdb=" N ARG E 693 " --> pdb=" O PRO E 689 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN E 694 " --> pdb=" O VAL E 690 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU E 695 " --> pdb=" O LEU E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 714 Processing helix chain 'E' and resid 716 through 722 removed outlier: 3.791A pdb=" N ILE E 720 " --> pdb=" O SER E 716 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 728 removed outlier: 3.642A pdb=" N TYR E 727 " --> pdb=" O PHE E 724 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE E 728 " --> pdb=" O GLN E 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 724 through 728' Processing helix chain 'E' and resid 729 through 734 removed outlier: 3.907A pdb=" N ILE E 734 " --> pdb=" O PRO E 730 " (cutoff:3.500A) Processing helix chain 'E' and resid 740 through 749 Processing helix chain 'E' and resid 755 through 767 Processing helix chain 'E' and resid 768 through 777 removed outlier: 3.626A pdb=" N PHE E 772 " --> pdb=" O SER E 768 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 793 Processing helix chain 'E' and resid 809 through 817 Processing helix chain 'E' and resid 827 through 843 Processing helix chain 'E' and resid 844 through 848 removed outlier: 3.506A pdb=" N PHE E 848 " --> pdb=" O ILE E 845 " (cutoff:3.500A) Processing helix chain 'E' and resid 860 through 864 removed outlier: 3.977A pdb=" N ASN E 863 " --> pdb=" O ASN E 860 " (cutoff:3.500A) Processing helix chain 'E' and resid 868 through 892 removed outlier: 4.443A pdb=" N LEU E 881 " --> pdb=" O GLN E 877 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY E 882 " --> pdb=" O ASP E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 900 through 916 Processing helix chain 'E' and resid 918 through 925 Processing helix chain 'E' and resid 927 through 939 removed outlier: 3.850A pdb=" N ILE E 931 " --> pdb=" O ALA E 927 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU E 939 " --> pdb=" O THR E 935 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 956 removed outlier: 3.705A pdb=" N ALA E 946 " --> pdb=" O VAL E 942 " (cutoff:3.500A) Processing helix chain 'E' and resid 962 through 965 removed outlier: 3.639A pdb=" N VAL E 965 " --> pdb=" O LEU E 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 962 through 965' Processing helix chain 'E' and resid 966 through 977 removed outlier: 3.790A pdb=" N ILE E 970 " --> pdb=" O ILE E 966 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 980 No H-bonds generated for 'chain 'E' and resid 978 through 980' Processing helix chain 'E' and resid 981 through 999 Processing helix chain 'E' and resid 999 through 1004 Processing helix chain 'E' and resid 1007 through 1017 removed outlier: 3.837A pdb=" N THR E1011 " --> pdb=" O LYS E1007 " (cutoff:3.500A) Processing helix chain 'E' and resid 1021 through 1026 Processing helix chain 'E' and resid 1029 through 1039 removed outlier: 3.601A pdb=" N SER E1038 " --> pdb=" O ASN E1034 " (cutoff:3.500A) Processing helix chain 'E' and resid 1041 through 1050 removed outlier: 4.382A pdb=" N ILE E1045 " --> pdb=" O ASP E1041 " (cutoff:3.500A) Processing helix chain 'E' and resid 1054 through 1075 removed outlier: 3.918A pdb=" N ILE E1058 " --> pdb=" O ASN E1054 " (cutoff:3.500A) Processing helix chain 'E' and resid 1091 through 1105 Processing helix chain 'E' and resid 1109 through 1124 Processing helix chain 'E' and resid 1148 through 1164 Processing helix chain 'E' and resid 1173 through 1191 Processing helix chain 'E' and resid 1206 through 1215 removed outlier: 4.143A pdb=" N ALA E1210 " --> pdb=" O TYR E1206 " (cutoff:3.500A) Processing helix chain 'E' and resid 1217 through 1225 removed outlier: 3.699A pdb=" N TYR E1225 " --> pdb=" O LYS E1221 " (cutoff:3.500A) Processing helix chain 'E' and resid 1226 through 1228 No H-bonds generated for 'chain 'E' and resid 1226 through 1228' Processing helix chain 'E' and resid 1246 through 1252 Processing helix chain 'E' and resid 1256 through 1270 Processing helix chain 'E' and resid 1274 through 1282 removed outlier: 3.761A pdb=" N PHE E1279 " --> pdb=" O LEU E1276 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER E1280 " --> pdb=" O HIS E1277 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER E1281 " --> pdb=" O VAL E1278 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU E1282 " --> pdb=" O PHE E1279 " (cutoff:3.500A) Processing helix chain 'E' and resid 1293 through 1299 removed outlier: 4.284A pdb=" N SER E1299 " --> pdb=" O LEU E1295 " (cutoff:3.500A) Processing helix chain 'E' and resid 1311 through 1329 removed outlier: 4.006A pdb=" N CYS E1329 " --> pdb=" O SER E1325 " (cutoff:3.500A) Processing helix chain 'E' and resid 1335 through 1340 Processing helix chain 'E' and resid 1340 through 1366 Processing helix chain 'E' and resid 1367 through 1369 No H-bonds generated for 'chain 'E' and resid 1367 through 1369' Processing helix chain 'E' and resid 1379 through 1394 Processing helix chain 'E' and resid 1396 through 1407 Processing helix chain 'E' and resid 1409 through 1423 removed outlier: 4.023A pdb=" N CYS E1420 " --> pdb=" O TYR E1416 " (cutoff:3.500A) Processing helix chain 'E' and resid 1428 through 1431 removed outlier: 3.576A pdb=" N ASN E1431 " --> pdb=" O LYS E1428 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1428 through 1431' Processing helix chain 'E' and resid 1432 through 1446 removed outlier: 4.125A pdb=" N LEU E1438 " --> pdb=" O LEU E1434 " (cutoff:3.500A) Processing helix chain 'E' and resid 1447 through 1457 Processing helix chain 'E' and resid 1462 through 1467 Processing helix chain 'E' and resid 1475 through 1487 removed outlier: 3.998A pdb=" N ALA E1479 " --> pdb=" O ASN E1475 " (cutoff:3.500A) Processing helix chain 'E' and resid 1488 through 1490 No H-bonds generated for 'chain 'E' and resid 1488 through 1490' Processing helix chain 'E' and resid 1492 through 1505 removed outlier: 3.730A pdb=" N THR E1496 " --> pdb=" O ASP E1492 " (cutoff:3.500A) Processing helix chain 'E' and resid 1508 through 1515 Processing helix chain 'E' and resid 1532 through 1545 removed outlier: 4.844A pdb=" N GLU E1540 " --> pdb=" O SER E1536 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA E1541 " --> pdb=" O ILE E1537 " (cutoff:3.500A) Processing helix chain 'E' and resid 1548 through 1559 Processing helix chain 'E' and resid 1566 through 1584 removed outlier: 3.684A pdb=" N LEU E1570 " --> pdb=" O ASP E1566 " (cutoff:3.500A) Processing helix chain 'E' and resid 1586 through 1605 Processing helix chain 'E' and resid 1617 through 1635 removed outlier: 4.193A pdb=" N LYS E1623 " --> pdb=" O ASN E1619 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU E1633 " --> pdb=" O ASP E1629 " (cutoff:3.500A) Processing helix chain 'E' and resid 1638 through 1656 Processing helix chain 'E' and resid 1659 through 1677 Processing helix chain 'E' and resid 1679 through 1700 Processing helix chain 'E' and resid 1704 through 1715 removed outlier: 5.021A pdb=" N HIS E1712 " --> pdb=" O GLU E1708 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS E1713 " --> pdb=" O SER E1709 " (cutoff:3.500A) Processing helix chain 'E' and resid 1718 through 1733 removed outlier: 3.680A pdb=" N GLY E1733 " --> pdb=" O LEU E1729 " (cutoff:3.500A) Processing helix chain 'E' and resid 1734 through 1749 removed outlier: 3.535A pdb=" N ALA E1738 " --> pdb=" O GLU E1734 " (cutoff:3.500A) Processing helix chain 'E' and resid 1758 through 1775 Processing helix chain 'E' and resid 1779 through 1793 removed outlier: 3.892A pdb=" N GLN E1785 " --> pdb=" O GLN E1781 " (cutoff:3.500A) Processing helix chain 'E' and resid 1797 through 1816 Processing helix chain 'E' and resid 1823 through 1838 removed outlier: 3.645A pdb=" N TYR E1827 " --> pdb=" O GLY E1823 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU E1838 " --> pdb=" O LEU E1834 " (cutoff:3.500A) Processing helix chain 'E' and resid 1843 through 1865 Proline residue: E1849 - end of helix removed outlier: 5.040A pdb=" N PHE E1854 " --> pdb=" O LYS E1850 " (cutoff:3.500A) Processing helix chain 'E' and resid 1874 through 1892 removed outlier: 3.789A pdb=" N HIS E1891 " --> pdb=" O GLU E1887 " (cutoff:3.500A) Processing helix chain 'E' and resid 1894 through 1899 removed outlier: 3.839A pdb=" N TYR E1898 " --> pdb=" O TYR E1895 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE E1899 " --> pdb=" O ILE E1896 " (cutoff:3.500A) Processing helix chain 'E' and resid 1900 through 1906 Processing helix chain 'E' and resid 1913 through 1929 Processing helix chain 'E' and resid 1931 through 1933 No H-bonds generated for 'chain 'E' and resid 1931 through 1933' Processing helix chain 'E' and resid 1934 through 1942 removed outlier: 4.435A pdb=" N VAL E1942 " --> pdb=" O ILE E1938 " (cutoff:3.500A) Processing helix chain 'E' and resid 1948 through 1963 removed outlier: 4.506A pdb=" N ARG E1952 " --> pdb=" O LYS E1948 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE E1956 " --> pdb=" O ARG E1952 " (cutoff:3.500A) Processing helix chain 'E' and resid 1969 through 1984 removed outlier: 4.069A pdb=" N SER E1973 " --> pdb=" O ASP E1969 " (cutoff:3.500A) Processing helix chain 'E' and resid 2085 through 2104 removed outlier: 4.391A pdb=" N PHE E2099 " --> pdb=" O THR E2095 " (cutoff:3.500A) Processing helix chain 'E' and resid 2137 through 2149 Processing helix chain 'E' and resid 2157 through 2164 Processing helix chain 'E' and resid 2167 through 2181 removed outlier: 4.444A pdb=" N LEU E2171 " --> pdb=" O VAL E2167 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU E2172 " --> pdb=" O ASP E2168 " (cutoff:3.500A) Processing helix chain 'E' and resid 2185 through 2193 removed outlier: 3.901A pdb=" N GLU E2191 " --> pdb=" O GLN E2187 " (cutoff:3.500A) Processing helix chain 'E' and resid 2195 through 2221 removed outlier: 4.128A pdb=" N MET E2213 " --> pdb=" O SER E2209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS E2218 " --> pdb=" O ALA E2214 " (cutoff:3.500A) Processing helix chain 'E' and resid 2265 through 2267 No H-bonds generated for 'chain 'E' and resid 2265 through 2267' Processing helix chain 'E' and resid 2268 through 2273 removed outlier: 3.628A pdb=" N GLY E2273 " --> pdb=" O LEU E2269 " (cutoff:3.500A) Processing helix chain 'E' and resid 2279 through 2293 Processing helix chain 'E' and resid 2295 through 2305 removed outlier: 4.038A pdb=" N THR E2305 " --> pdb=" O ASN E2301 " (cutoff:3.500A) Processing helix chain 'E' and resid 2316 through 2329 Processing helix chain 'E' and resid 2340 through 2352 Processing helix chain 'E' and resid 2353 through 2359 Processing helix chain 'E' and resid 2361 through 2365 Processing sheet with id=AA1, first strand: chain 'F' and resid 361 through 362 Processing sheet with id=AA2, first strand: chain 'F' and resid 2065 through 2068 removed outlier: 4.245A pdb=" N GLY F2076 " --> pdb=" O MET F2131 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE F2128 " --> pdb=" O SER F2121 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER F2121 " --> pdb=" O ILE F2128 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLU F2130 " --> pdb=" O VAL F2119 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL F2119 " --> pdb=" O GLU F2130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 2230 through 2232 Processing sheet with id=AA4, first strand: chain 'E' and resid 361 through 362 Processing sheet with id=AA5, first strand: chain 'E' and resid 2065 through 2068 removed outlier: 4.245A pdb=" N GLY E2076 " --> pdb=" O MET E2131 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE E2128 " --> pdb=" O SER E2121 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER E2121 " --> pdb=" O ILE E2128 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLU E2130 " --> pdb=" O VAL E2119 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL E2119 " --> pdb=" O GLU E2130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 2230 through 2232 2501 hydrogen bonds defined for protein. 7410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.76 Time building geometry restraints manager: 10.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10367 1.33 - 1.45: 10060 1.45 - 1.57: 26335 1.57 - 1.69: 12 1.69 - 1.81: 308 Bond restraints: 47082 Sorted by residual: bond pdb=" O3A ANP E2401 " pdb=" PB ANP E2401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" O3A ANP F2401 " pdb=" PB ANP F2401 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.22e+01 bond pdb=" N3B ANP E2401 " pdb=" PG ANP E2401 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" N3B ANP F2401 " pdb=" PG ANP F2401 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" N PHE F1293 " pdb=" CA PHE F1293 " ideal model delta sigma weight residual 1.459 1.402 0.057 1.20e-02 6.94e+03 2.28e+01 ... (remaining 47077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 62786 4.06 - 8.12: 875 8.12 - 12.18: 110 12.18 - 16.24: 11 16.24 - 20.30: 5 Bond angle restraints: 63787 Sorted by residual: angle pdb=" N PHE E1293 " pdb=" CA PHE E1293 " pdb=" C PHE E1293 " ideal model delta sigma weight residual 111.14 100.52 10.62 1.08e+00 8.57e-01 9.68e+01 angle pdb=" N PHE F1293 " pdb=" CA PHE F1293 " pdb=" C PHE F1293 " ideal model delta sigma weight residual 111.14 100.53 10.61 1.08e+00 8.57e-01 9.65e+01 angle pdb=" C PHE F1293 " pdb=" N LEU F1294 " pdb=" CA LEU F1294 " ideal model delta sigma weight residual 120.28 109.24 11.04 1.34e+00 5.57e-01 6.78e+01 angle pdb=" C PHE E1293 " pdb=" N LEU E1294 " pdb=" CA LEU E1294 " ideal model delta sigma weight residual 120.28 109.25 11.03 1.34e+00 5.57e-01 6.78e+01 angle pdb=" PB ANP E2401 " pdb=" N3B ANP E2401 " pdb=" PG ANP E2401 " ideal model delta sigma weight residual 126.95 106.65 20.30 3.00e+00 1.11e-01 4.58e+01 ... (remaining 63782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 28111 35.96 - 71.91: 312 71.91 - 107.87: 12 107.87 - 143.82: 0 143.82 - 179.78: 2 Dihedral angle restraints: 28437 sinusoidal: 11421 harmonic: 17016 Sorted by residual: dihedral pdb=" CD BARG D 228 " pdb=" NE BARG D 228 " pdb=" CZ BARG D 228 " pdb=" NH1BARG D 228 " ideal model delta sinusoidal sigma weight residual 0.00 179.78 -179.78 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG C 228 " pdb=" NE BARG C 228 " pdb=" CZ BARG C 228 " pdb=" NH1BARG C 228 " ideal model delta sinusoidal sigma weight residual 0.00 179.76 -179.76 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA SER F1754 " pdb=" C SER F1754 " pdb=" N VAL F1755 " pdb=" CA VAL F1755 " ideal model delta harmonic sigma weight residual -180.00 -124.48 -55.52 0 5.00e+00 4.00e-02 1.23e+02 ... (remaining 28434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 6555 0.099 - 0.199: 732 0.199 - 0.298: 49 0.298 - 0.398: 4 0.398 - 0.497: 2 Chirality restraints: 7342 Sorted by residual: chirality pdb=" CG LEU F1739 " pdb=" CB LEU F1739 " pdb=" CD1 LEU F1739 " pdb=" CD2 LEU F1739 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CG LEU E1739 " pdb=" CB LEU E1739 " pdb=" CD1 LEU E1739 " pdb=" CD2 LEU E1739 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CG LEU E2268 " pdb=" CB LEU E2268 " pdb=" CD1 LEU E2268 " pdb=" CD2 LEU E2268 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 7339 not shown) Planarity restraints: 8019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 470 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C VAL C 470 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL C 470 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR C 471 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 470 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C VAL D 470 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL D 470 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR D 471 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 770 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" CD GLN F 770 " -0.057 2.00e-02 2.50e+03 pdb=" OE1 GLN F 770 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 GLN F 770 " 0.019 2.00e-02 2.50e+03 ... (remaining 8016 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 91 2.32 - 2.97: 20997 2.97 - 3.61: 76887 3.61 - 4.26: 112742 4.26 - 4.90: 178095 Nonbonded interactions: 388812 Sorted by model distance: nonbonded pdb=" O ASN F1292 " pdb=" CD PRO F1296 " model vdw 1.678 3.440 nonbonded pdb=" O ASN E1292 " pdb=" CD PRO E1296 " model vdw 1.678 3.440 nonbonded pdb=" NZ LYS F1259 " pdb=" OG SER F1291 " model vdw 1.785 3.120 nonbonded pdb=" NZ LYS E1259 " pdb=" OG SER E1291 " model vdw 1.786 3.120 nonbonded pdb=" O SER F1291 " pdb=" N LEU F1295 " model vdw 2.094 3.120 ... (remaining 388807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 189 through 227 or resid 229 through 747)) selection = (chain 'D' and (resid 189 through 227 or resid 229 through 550 or (resid 551 and \ (name N or name CA or name C or name O or name CB )) or resid 552 through 747)) \ } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.410 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 88.670 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.170 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.007 0.145 47082 Z= 0.450 Angle : 1.246 20.295 63787 Z= 0.651 Chirality : 0.063 0.497 7342 Planarity : 0.008 0.076 8019 Dihedral : 12.663 179.776 17361 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.07 % Favored : 88.84 % Rotamer: Outliers : 1.08 % Allowed : 8.12 % Favored : 90.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.32 % 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: -4.47 (0.09), residues: 5688 helix: -2.55 (0.07), residues: 3606 sheet: -2.64 (0.44), residues: 74 loop : -3.54 (0.12), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP D 643 HIS 0.025 0.003 HIS D 665 PHE 0.052 0.004 PHE F1046 TYR 0.031 0.003 TYR E1786 ARG 0.031 0.001 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1604 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1552 time to evaluate : 4.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 55 LEU cc_start: 0.8657 (pt) cc_final: 0.8440 (pt) REVERT: F 120 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8584 (tp) REVERT: F 123 MET cc_start: 0.9130 (mtp) cc_final: 0.8909 (mtp) REVERT: F 154 MET cc_start: 0.8301 (ttp) cc_final: 0.7986 (tmm) REVERT: F 186 TYR cc_start: 0.9039 (t80) cc_final: 0.8728 (t80) REVERT: F 194 THR cc_start: 0.8391 (m) cc_final: 0.7997 (m) REVERT: F 295 MET cc_start: 0.9029 (tpt) cc_final: 0.8349 (ptt) REVERT: F 318 HIS cc_start: 0.8893 (m-70) cc_final: 0.8620 (m-70) REVERT: F 345 ILE cc_start: 0.9042 (mt) cc_final: 0.8837 (mm) REVERT: F 347 TYR cc_start: 0.8975 (t80) cc_final: 0.8654 (t80) REVERT: F 392 GLN cc_start: 0.7655 (mt0) cc_final: 0.7217 (mm-40) REVERT: F 441 VAL cc_start: 0.9501 (p) cc_final: 0.9281 (m) REVERT: F 540 LEU cc_start: 0.9537 (mt) cc_final: 0.9249 (mt) REVERT: F 549 ARG cc_start: 0.9274 (mtt-85) cc_final: 0.8762 (tpp80) REVERT: F 579 ASN cc_start: 0.8202 (t0) cc_final: 0.7837 (t0) REVERT: F 587 LEU cc_start: 0.9125 (tt) cc_final: 0.8665 (mm) REVERT: F 636 LEU cc_start: 0.9600 (mt) cc_final: 0.9367 (mt) REVERT: F 667 LEU cc_start: 0.8621 (tm) cc_final: 0.8413 (tm) REVERT: F 668 GLN cc_start: 0.8685 (mm110) cc_final: 0.8417 (mm110) REVERT: F 671 ASN cc_start: 0.8912 (m110) cc_final: 0.8512 (m-40) REVERT: F 691 LEU cc_start: 0.9060 (tp) cc_final: 0.8741 (mt) REVERT: F 907 ILE cc_start: 0.9455 (mt) cc_final: 0.9168 (mt) REVERT: F 928 GLN cc_start: 0.9025 (pm20) cc_final: 0.8529 (pt0) REVERT: F 950 TRP cc_start: 0.7811 (m100) cc_final: 0.6810 (m100) REVERT: F 1108 LEU cc_start: 0.8104 (tm) cc_final: 0.7774 (tm) REVERT: F 1118 LYS cc_start: 0.9345 (ptpt) cc_final: 0.8833 (ptpp) REVERT: F 1126 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7341 (tm) REVERT: F 1314 ASP cc_start: 0.9462 (t0) cc_final: 0.9098 (m-30) REVERT: F 1353 PHE cc_start: 0.9062 (m-10) cc_final: 0.8794 (m-80) REVERT: F 1503 MET cc_start: 0.8805 (ttp) cc_final: 0.8423 (tpp) REVERT: F 1510 SER cc_start: 0.9407 (m) cc_final: 0.9193 (p) REVERT: F 1512 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8190 (mp) REVERT: F 1550 THR cc_start: 0.9183 (m) cc_final: 0.8820 (m) REVERT: F 1628 TYR cc_start: 0.8649 (t80) cc_final: 0.8420 (t80) REVERT: F 1651 TYR cc_start: 0.8539 (t80) cc_final: 0.8209 (t80) REVERT: F 1666 ILE cc_start: 0.9050 (pp) cc_final: 0.8793 (pp) REVERT: F 1691 PHE cc_start: 0.9252 (t80) cc_final: 0.8920 (t80) REVERT: F 1696 LEU cc_start: 0.9469 (pp) cc_final: 0.9252 (pp) REVERT: F 1720 GLN cc_start: 0.8098 (pm20) cc_final: 0.7847 (pm20) REVERT: F 1837 PHE cc_start: 0.8704 (m-10) cc_final: 0.8495 (m-80) REVERT: F 1920 MET cc_start: 0.9253 (mtm) cc_final: 0.9047 (ppp) REVERT: F 1937 TYR cc_start: 0.8989 (m-80) cc_final: 0.8789 (m-80) REVERT: F 1955 HIS cc_start: 0.8824 (t70) cc_final: 0.8621 (t-170) REVERT: F 2110 ARG cc_start: 0.8588 (ttm110) cc_final: 0.7597 (tpt170) REVERT: F 2161 ARG cc_start: 0.9176 (ptm160) cc_final: 0.8338 (ptp90) REVERT: F 2282 LYS cc_start: 0.9146 (tttm) cc_final: 0.8928 (mtpt) REVERT: F 2295 ASN cc_start: 0.9166 (p0) cc_final: 0.8955 (t0) REVERT: F 2301 ASN cc_start: 0.8660 (m-40) cc_final: 0.8408 (m110) REVERT: F 2364 TRP cc_start: 0.8569 (t60) cc_final: 0.8180 (t60) REVERT: C 201 ASP cc_start: 0.8313 (t0) cc_final: 0.8064 (t0) REVERT: C 210 ILE cc_start: 0.9282 (mt) cc_final: 0.9051 (mt) REVERT: C 220 LEU cc_start: 0.7917 (mt) cc_final: 0.7609 (mp) REVERT: C 257 LEU cc_start: 0.9374 (tp) cc_final: 0.8564 (tp) REVERT: C 269 ARG cc_start: 0.9033 (mtp180) cc_final: 0.8824 (mtp85) REVERT: C 278 ILE cc_start: 0.9647 (mt) cc_final: 0.9289 (tp) REVERT: C 303 MET cc_start: 0.8742 (ttm) cc_final: 0.8509 (ttm) REVERT: C 328 ASP cc_start: 0.8731 (p0) cc_final: 0.8526 (m-30) REVERT: C 377 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.8107 (mtp85) REVERT: C 417 VAL cc_start: 0.8905 (m) cc_final: 0.8435 (m) REVERT: C 431 ILE cc_start: 0.9208 (pt) cc_final: 0.8869 (pt) REVERT: C 435 MET cc_start: 0.6736 (ptp) cc_final: 0.6499 (ptt) REVERT: C 437 ASN cc_start: 0.8169 (t0) cc_final: 0.7966 (p0) REVERT: C 518 ARG cc_start: 0.8647 (ttt180) cc_final: 0.8232 (ttt180) REVERT: C 540 LYS cc_start: 0.9389 (ptpp) cc_final: 0.9163 (ptpp) REVERT: C 547 LYS cc_start: 0.9188 (mttt) cc_final: 0.8833 (mttp) REVERT: C 558 ASN cc_start: 0.8959 (m-40) cc_final: 0.8545 (t0) REVERT: C 562 ILE cc_start: 0.8081 (mt) cc_final: 0.7661 (mt) REVERT: C 591 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8421 (mt-10) REVERT: C 654 THR cc_start: 0.6384 (p) cc_final: 0.5807 (p) REVERT: C 660 MET cc_start: 0.9097 (mtp) cc_final: 0.8648 (mmm) REVERT: C 664 ARG cc_start: 0.8992 (ptt180) cc_final: 0.8737 (ppt170) REVERT: C 700 GLN cc_start: 0.8635 (pp30) cc_final: 0.8118 (pp30) REVERT: C 707 ARG cc_start: 0.8216 (tmm-80) cc_final: 0.7898 (tmm160) REVERT: D 220 LEU cc_start: 0.7740 (mt) cc_final: 0.7531 (mt) REVERT: D 231 LEU cc_start: 0.7359 (pt) cc_final: 0.7084 (mt) REVERT: D 256 SER cc_start: 0.9201 (t) cc_final: 0.7355 (p) REVERT: D 257 LEU cc_start: 0.9390 (tp) cc_final: 0.8414 (tp) REVERT: D 269 ARG cc_start: 0.8996 (mtp180) cc_final: 0.8728 (mtp85) REVERT: D 278 ILE cc_start: 0.9641 (mt) cc_final: 0.9213 (tp) REVERT: D 303 MET cc_start: 0.8760 (ttm) cc_final: 0.8512 (ttm) REVERT: D 328 ASP cc_start: 0.8720 (p0) cc_final: 0.8512 (m-30) REVERT: D 431 ILE cc_start: 0.9171 (pt) cc_final: 0.8903 (pt) REVERT: D 462 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8055 (mt-10) REVERT: D 540 LYS cc_start: 0.9409 (ptpp) cc_final: 0.9099 (ptpp) REVERT: D 547 LYS cc_start: 0.9226 (mttt) cc_final: 0.8681 (mttp) REVERT: D 558 ASN cc_start: 0.8875 (m-40) cc_final: 0.8415 (t0) REVERT: D 562 ILE cc_start: 0.8045 (mt) cc_final: 0.7655 (mt) REVERT: D 654 THR cc_start: 0.5696 (p) cc_final: 0.5292 (p) REVERT: D 662 ASP cc_start: 0.8208 (m-30) cc_final: 0.7985 (m-30) REVERT: D 664 ARG cc_start: 0.9039 (ptt180) cc_final: 0.8510 (ppt170) REVERT: D 720 MET cc_start: 0.7896 (mtm) cc_final: 0.7136 (ptp) REVERT: E 55 LEU cc_start: 0.8721 (pt) cc_final: 0.8426 (pt) REVERT: E 120 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8147 (pp) REVERT: E 123 MET cc_start: 0.9147 (mtp) cc_final: 0.8592 (ptt) REVERT: E 126 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7598 (tppt) REVERT: E 154 MET cc_start: 0.8369 (ttp) cc_final: 0.8125 (tmm) REVERT: E 186 TYR cc_start: 0.9061 (t80) cc_final: 0.8361 (t80) REVERT: E 295 MET cc_start: 0.9126 (tpt) cc_final: 0.8728 (ptt) REVERT: E 318 HIS cc_start: 0.8720 (m-70) cc_final: 0.7857 (m90) REVERT: E 458 TRP cc_start: 0.8516 (m100) cc_final: 0.8088 (m100) REVERT: E 545 PHE cc_start: 0.9142 (m-80) cc_final: 0.8917 (m-80) REVERT: E 549 ARG cc_start: 0.9368 (mtt-85) cc_final: 0.8833 (tpp80) REVERT: E 551 PHE cc_start: 0.9004 (m-10) cc_final: 0.8588 (m-80) REVERT: E 579 ASN cc_start: 0.8308 (t0) cc_final: 0.7734 (t0) REVERT: E 587 LEU cc_start: 0.9194 (tt) cc_final: 0.8745 (mm) REVERT: E 592 ILE cc_start: 0.9696 (mt) cc_final: 0.9460 (mt) REVERT: E 631 TRP cc_start: 0.8879 (m100) cc_final: 0.8658 (m100) REVERT: E 668 GLN cc_start: 0.8741 (mm110) cc_final: 0.8420 (mm-40) REVERT: E 691 LEU cc_start: 0.9290 (tp) cc_final: 0.9050 (mt) REVERT: E 727 TYR cc_start: 0.8015 (m-80) cc_final: 0.7521 (m-80) REVERT: E 747 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8903 (pt) REVERT: E 835 ASN cc_start: 0.9336 (m110) cc_final: 0.9136 (p0) REVERT: E 902 GLU cc_start: 0.8391 (mp0) cc_final: 0.8035 (pt0) REVERT: E 907 ILE cc_start: 0.9497 (mt) cc_final: 0.9286 (mt) REVERT: E 928 GLN cc_start: 0.8868 (pm20) cc_final: 0.8562 (pt0) REVERT: E 955 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7850 (mtt-85) REVERT: E 1056 TYR cc_start: 0.8008 (m-80) cc_final: 0.7762 (m-80) REVERT: E 1100 ASP cc_start: 0.9370 (p0) cc_final: 0.8906 (t0) REVERT: E 1109 ASP cc_start: 0.8161 (t0) cc_final: 0.7899 (p0) REVERT: E 1118 LYS cc_start: 0.9394 (ptpt) cc_final: 0.8879 (ptpp) REVERT: E 1126 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7053 (tm) REVERT: E 1178 LEU cc_start: 0.8492 (mm) cc_final: 0.8291 (mm) REVERT: E 1212 LEU cc_start: 0.8441 (mt) cc_final: 0.8224 (mp) REVERT: E 1314 ASP cc_start: 0.9403 (t0) cc_final: 0.8957 (m-30) REVERT: E 1476 TRP cc_start: 0.8559 (p90) cc_final: 0.7445 (p90) REVERT: E 1503 MET cc_start: 0.8871 (ttp) cc_final: 0.8353 (tpp) REVERT: E 1510 SER cc_start: 0.9283 (m) cc_final: 0.9063 (p) REVERT: E 1512 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8024 (mp) REVERT: E 1543 ASN cc_start: 0.9028 (m110) cc_final: 0.8678 (m110) REVERT: E 1550 THR cc_start: 0.9265 (m) cc_final: 0.8789 (m) REVERT: E 1564 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8263 (tp) REVERT: E 1573 TYR cc_start: 0.7345 (t80) cc_final: 0.7119 (t80) REVERT: E 1651 TYR cc_start: 0.8620 (t80) cc_final: 0.8180 (t80) REVERT: E 1666 ILE cc_start: 0.9039 (pp) cc_final: 0.8810 (pp) REVERT: E 1669 MET cc_start: 0.8831 (tpt) cc_final: 0.8628 (tpt) REVERT: E 1691 PHE cc_start: 0.9197 (t80) cc_final: 0.8900 (t80) REVERT: E 1696 LEU cc_start: 0.9458 (pp) cc_final: 0.9253 (pp) REVERT: E 1711 MET cc_start: 0.7606 (ttm) cc_final: 0.7315 (ppp) REVERT: E 1720 GLN cc_start: 0.8087 (pm20) cc_final: 0.7853 (pm20) REVERT: E 1937 TYR cc_start: 0.9002 (m-80) cc_final: 0.8787 (m-80) REVERT: E 2110 ARG cc_start: 0.8469 (ttm110) cc_final: 0.7479 (tpt170) REVERT: E 2282 LYS cc_start: 0.9113 (tttm) cc_final: 0.8878 (mtpp) REVERT: E 2301 ASN cc_start: 0.8736 (m-40) cc_final: 0.8488 (m110) REVERT: E 2364 TRP cc_start: 0.8786 (t60) cc_final: 0.8195 (t60) outliers start: 52 outliers final: 3 residues processed: 1581 average time/residue: 0.4899 time to fit residues: 1243.7310 Evaluate side-chains 956 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 945 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1292 ASN Chi-restraints excluded: chain F residue 1512 ILE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1292 ASN Chi-restraints excluded: chain E residue 1512 ILE Chi-restraints excluded: chain E residue 1564 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 483 optimal weight: 3.9990 chunk 433 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 448 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 272 optimal weight: 6.9990 chunk 333 optimal weight: 8.9990 chunk 519 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 ASN F 372 GLN F 548 HIS ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 633 GLN ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 892 HIS F 908 ASN F 975 GLN F1073 GLN F1161 ASN ** F1177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1235 GLN F1335 ASN F1431 ASN F1462 ASN ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1543 ASN F1557 GLN F1574 ASN F1591 GLN F1596 ASN F1619 ASN ** F1625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1699 ASN F1756 ASN ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1943 ASN ** F1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 347 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN C 554 ASN C 558 ASN C 596 GLN C 606 HIS ** C 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN D 347 ASN D 437 ASN D 494 ASN ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN D 665 HIS ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN E 367 ASN E 548 HIS ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 633 GLN E 671 ASN ** E 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 892 HIS E 951 HIS E 975 GLN E1073 GLN E1161 ASN E1235 GLN E1335 ASN E1431 ASN E1462 ASN ** E1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1543 ASN E1557 GLN E1574 ASN E1591 GLN E1596 ASN E1618 GLN E1619 ASN E1625 HIS ** E1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1699 ASN E1756 ASN ** E1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1891 HIS ** E1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1943 ASN ** E1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2092 GLN E2301 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 47082 Z= 0.236 Angle : 0.858 14.065 63787 Z= 0.435 Chirality : 0.047 0.247 7342 Planarity : 0.006 0.074 8019 Dihedral : 8.371 177.945 6262 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 3.59 % Allowed : 15.86 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.02 (0.10), residues: 5688 helix: -1.27 (0.08), residues: 3600 sheet: -2.23 (0.47), residues: 64 loop : -3.27 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E1897 HIS 0.014 0.001 HIS E1891 PHE 0.035 0.002 PHE C 399 TYR 0.033 0.002 TYR F1786 ARG 0.017 0.001 ARG E2110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1089 time to evaluate : 4.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 45 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6863 (mm) REVERT: F 90 MET cc_start: 0.7775 (mmt) cc_final: 0.7503 (mmm) REVERT: F 154 MET cc_start: 0.8451 (ttp) cc_final: 0.7990 (tmm) REVERT: F 186 TYR cc_start: 0.9110 (t80) cc_final: 0.8779 (t80) REVERT: F 392 GLN cc_start: 0.7224 (mt0) cc_final: 0.7003 (tt0) REVERT: F 487 TRP cc_start: 0.5536 (t60) cc_final: 0.4897 (t60) REVERT: F 576 CYS cc_start: 0.9095 (m) cc_final: 0.8802 (m) REVERT: F 579 ASN cc_start: 0.8321 (t0) cc_final: 0.8100 (t0) REVERT: F 636 LEU cc_start: 0.9614 (mt) cc_final: 0.9385 (mt) REVERT: F 671 ASN cc_start: 0.8845 (m110) cc_final: 0.8458 (m110) REVERT: F 691 LEU cc_start: 0.9090 (tp) cc_final: 0.8707 (mt) REVERT: F 759 MET cc_start: 0.9158 (tpp) cc_final: 0.8885 (ppp) REVERT: F 767 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7305 (p0) REVERT: F 947 PHE cc_start: 0.8770 (m-80) cc_final: 0.8466 (m-10) REVERT: F 1032 MET cc_start: 0.8507 (mmt) cc_final: 0.7943 (mpp) REVERT: F 1060 GLN cc_start: 0.8797 (tp40) cc_final: 0.8093 (tp40) REVERT: F 1106 ARG cc_start: 0.9178 (ptp-110) cc_final: 0.8547 (mmt180) REVERT: F 1107 ASN cc_start: 0.8886 (m-40) cc_final: 0.8154 (t0) REVERT: F 1118 LYS cc_start: 0.9376 (ptpt) cc_final: 0.9062 (ptpp) REVERT: F 1126 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7142 (tm) REVERT: F 1245 TYR cc_start: 0.9066 (m-80) cc_final: 0.8801 (m-80) REVERT: F 1314 ASP cc_start: 0.9399 (t0) cc_final: 0.9088 (m-30) REVERT: F 1447 ASP cc_start: 0.7462 (m-30) cc_final: 0.7261 (t0) REVERT: F 1510 SER cc_start: 0.9411 (m) cc_final: 0.9203 (p) REVERT: F 1536 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8570 (t) REVERT: F 1651 TYR cc_start: 0.8621 (t80) cc_final: 0.8007 (t80) REVERT: F 1704 ASP cc_start: 0.8971 (p0) cc_final: 0.8665 (p0) REVERT: F 1720 GLN cc_start: 0.8110 (pm20) cc_final: 0.7663 (mp10) REVERT: F 1837 PHE cc_start: 0.8571 (m-10) cc_final: 0.8362 (m-80) REVERT: F 1937 TYR cc_start: 0.9005 (m-80) cc_final: 0.8702 (m-80) REVERT: F 2110 ARG cc_start: 0.8583 (ttm110) cc_final: 0.8043 (tpt170) REVERT: F 2225 ARG cc_start: 0.6168 (OUTLIER) cc_final: 0.5842 (mmm-85) REVERT: F 2247 LEU cc_start: 0.8643 (mt) cc_final: 0.7972 (mp) REVERT: F 2282 LYS cc_start: 0.9167 (tttm) cc_final: 0.8768 (mtpp) REVERT: F 2292 MET cc_start: 0.8832 (ptp) cc_final: 0.8343 (ptp) REVERT: F 2304 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8044 (tm-30) REVERT: F 2350 GLU cc_start: 0.8803 (pt0) cc_final: 0.8559 (pt0) REVERT: F 2364 TRP cc_start: 0.8566 (t60) cc_final: 0.8160 (t60) REVERT: C 190 MET cc_start: 0.7295 (mpp) cc_final: 0.7082 (mmm) REVERT: C 257 LEU cc_start: 0.9374 (tp) cc_final: 0.9020 (tp) REVERT: C 278 ILE cc_start: 0.9619 (mt) cc_final: 0.9285 (tp) REVERT: C 303 MET cc_start: 0.8846 (ttm) cc_final: 0.8538 (ttm) REVERT: C 328 ASP cc_start: 0.8847 (p0) cc_final: 0.8478 (m-30) REVERT: C 373 GLU cc_start: 0.8363 (tt0) cc_final: 0.7858 (tt0) REVERT: C 377 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.7936 (mtp85) REVERT: C 437 ASN cc_start: 0.8399 (t0) cc_final: 0.8088 (p0) REVERT: C 463 LYS cc_start: 0.8746 (mttt) cc_final: 0.8488 (mtpt) REVERT: C 518 ARG cc_start: 0.8564 (ttt180) cc_final: 0.8301 (ttp-170) REVERT: C 540 LYS cc_start: 0.9422 (ptpp) cc_final: 0.9156 (ptpp) REVERT: C 547 LYS cc_start: 0.9085 (mttt) cc_final: 0.8817 (mttm) REVERT: C 558 ASN cc_start: 0.8805 (m110) cc_final: 0.8599 (t0) REVERT: C 562 ILE cc_start: 0.7899 (mt) cc_final: 0.7314 (mt) REVERT: C 575 LEU cc_start: 0.9171 (mt) cc_final: 0.8890 (mp) REVERT: C 593 TYR cc_start: 0.7864 (m-80) cc_final: 0.7416 (m-80) REVERT: C 609 GLU cc_start: 0.9243 (mm-30) cc_final: 0.9024 (mm-30) REVERT: C 610 HIS cc_start: 0.8892 (t-90) cc_final: 0.8377 (t-90) REVERT: C 654 THR cc_start: 0.6010 (p) cc_final: 0.5468 (p) REVERT: C 660 MET cc_start: 0.9049 (mtp) cc_final: 0.8709 (mmm) REVERT: C 664 ARG cc_start: 0.9035 (ptt180) cc_final: 0.8744 (ppt170) REVERT: D 257 LEU cc_start: 0.9373 (tp) cc_final: 0.9144 (tp) REVERT: D 269 ARG cc_start: 0.9092 (mtp180) cc_final: 0.8862 (mtp85) REVERT: D 278 ILE cc_start: 0.9587 (mt) cc_final: 0.9233 (tp) REVERT: D 303 MET cc_start: 0.8811 (ttm) cc_final: 0.8464 (ttm) REVERT: D 328 ASP cc_start: 0.8855 (p0) cc_final: 0.8444 (m-30) REVERT: D 373 GLU cc_start: 0.8380 (tt0) cc_final: 0.7785 (tt0) REVERT: D 462 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7996 (mt-10) REVERT: D 540 LYS cc_start: 0.9458 (ptpp) cc_final: 0.9163 (ptpp) REVERT: D 544 TRP cc_start: 0.8622 (m100) cc_final: 0.8422 (m100) REVERT: D 547 LYS cc_start: 0.8993 (mttt) cc_final: 0.8646 (mttm) REVERT: D 559 LEU cc_start: 0.9406 (pp) cc_final: 0.9133 (pp) REVERT: D 562 ILE cc_start: 0.8189 (mt) cc_final: 0.7615 (mt) REVERT: D 573 GLU cc_start: 0.8812 (mp0) cc_final: 0.8589 (mp0) REVERT: D 575 LEU cc_start: 0.9195 (mt) cc_final: 0.8848 (mp) REVERT: D 593 TYR cc_start: 0.7725 (m-80) cc_final: 0.7171 (m-80) REVERT: D 609 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8560 (tp30) REVERT: D 610 HIS cc_start: 0.8934 (t-170) cc_final: 0.8617 (t-90) REVERT: D 612 LEU cc_start: 0.9254 (tp) cc_final: 0.8875 (tt) REVERT: D 661 ARG cc_start: 0.9018 (ptp-170) cc_final: 0.8754 (ptp90) REVERT: D 664 ARG cc_start: 0.9052 (ptt180) cc_final: 0.8576 (ppt170) REVERT: D 702 ASN cc_start: 0.9136 (m110) cc_final: 0.8712 (p0) REVERT: D 707 ARG cc_start: 0.8748 (mmt90) cc_final: 0.8521 (mmt-90) REVERT: D 720 MET cc_start: 0.7973 (mtm) cc_final: 0.7437 (ptm) REVERT: E 154 MET cc_start: 0.8397 (ttp) cc_final: 0.7989 (ppp) REVERT: E 166 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8826 (pp) REVERT: E 186 TYR cc_start: 0.9093 (t80) cc_final: 0.8877 (t80) REVERT: E 295 MET cc_start: 0.9218 (tpt) cc_final: 0.8576 (ptt) REVERT: E 297 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7576 (ttmm) REVERT: E 318 HIS cc_start: 0.8468 (m-70) cc_final: 0.7606 (m90) REVERT: E 395 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9214 (tptp) REVERT: E 458 TRP cc_start: 0.8398 (m100) cc_final: 0.7920 (m100) REVERT: E 469 GLU cc_start: 0.8616 (tp30) cc_final: 0.8329 (tp30) REVERT: E 545 PHE cc_start: 0.9132 (m-80) cc_final: 0.8872 (m-80) REVERT: E 549 ARG cc_start: 0.9272 (mtt-85) cc_final: 0.8533 (tpp80) REVERT: E 579 ASN cc_start: 0.8518 (t0) cc_final: 0.8279 (t0) REVERT: E 587 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8649 (mt) REVERT: E 668 GLN cc_start: 0.8768 (mm110) cc_final: 0.8240 (mm-40) REVERT: E 691 LEU cc_start: 0.9266 (tp) cc_final: 0.9005 (mt) REVERT: E 697 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8698 (mmtm) REVERT: E 947 PHE cc_start: 0.8986 (m-80) cc_final: 0.8540 (m-80) REVERT: E 951 HIS cc_start: 0.8299 (t-90) cc_final: 0.8042 (t-90) REVERT: E 955 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7991 (mtt-85) REVERT: E 983 LYS cc_start: 0.8947 (mtpp) cc_final: 0.8595 (mptt) REVERT: E 1106 ARG cc_start: 0.9309 (ptp-110) cc_final: 0.8743 (mmm160) REVERT: E 1118 LYS cc_start: 0.9391 (ptpt) cc_final: 0.9107 (ptpp) REVERT: E 1122 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8662 (mtm) REVERT: E 1126 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6907 (tm) REVERT: E 1178 LEU cc_start: 0.8668 (mm) cc_final: 0.8434 (mm) REVERT: E 1190 TYR cc_start: 0.7796 (t80) cc_final: 0.7571 (t80) REVERT: E 1245 TYR cc_start: 0.9033 (m-80) cc_final: 0.8725 (m-80) REVERT: E 1314 ASP cc_start: 0.9291 (t0) cc_final: 0.8989 (m-30) REVERT: E 1353 PHE cc_start: 0.8871 (m-80) cc_final: 0.8608 (m-80) REVERT: E 1421 TYR cc_start: 0.6989 (m-80) cc_final: 0.6718 (m-80) REVERT: E 1451 LEU cc_start: 0.9111 (tp) cc_final: 0.8801 (mm) REVERT: E 1476 TRP cc_start: 0.8586 (p90) cc_final: 0.7556 (p90) REVERT: E 1510 SER cc_start: 0.9346 (m) cc_final: 0.9141 (p) REVERT: E 1536 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8331 (t) REVERT: E 1651 TYR cc_start: 0.8541 (t80) cc_final: 0.8092 (t80) REVERT: E 1666 ILE cc_start: 0.8975 (pp) cc_final: 0.8767 (pp) REVERT: E 1711 MET cc_start: 0.7532 (ttm) cc_final: 0.7235 (ppp) REVERT: E 1720 GLN cc_start: 0.8063 (pm20) cc_final: 0.7564 (mp10) REVERT: E 1897 TRP cc_start: 0.7152 (m100) cc_final: 0.6921 (m-10) REVERT: E 2040 PHE cc_start: 0.6770 (m-80) cc_final: 0.6527 (m-80) REVERT: E 2210 TYR cc_start: 0.8845 (t80) cc_final: 0.8634 (t80) REVERT: E 2247 LEU cc_start: 0.8735 (mt) cc_final: 0.8066 (mp) REVERT: E 2282 LYS cc_start: 0.9207 (tttm) cc_final: 0.8763 (mtpp) REVERT: E 2304 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8164 (tm-30) REVERT: E 2349 GLN cc_start: 0.8985 (mp10) cc_final: 0.8679 (mp10) REVERT: E 2357 LEU cc_start: 0.8918 (mt) cc_final: 0.8616 (mt) REVERT: E 2364 TRP cc_start: 0.8893 (t60) cc_final: 0.8086 (t60) outliers start: 180 outliers final: 86 residues processed: 1189 average time/residue: 0.4717 time to fit residues: 924.1107 Evaluate side-chains 987 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 890 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 250 TYR Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 548 HIS Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 797 THR Chi-restraints excluded: chain F residue 841 LEU Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1165 VAL Chi-restraints excluded: chain F residue 1294 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1434 LEU Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1536 SER Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1714 LEU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1771 LEU Chi-restraints excluded: chain F residue 1942 VAL Chi-restraints excluded: chain F residue 2084 VAL Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2206 TYR Chi-restraints excluded: chain F residue 2225 ARG Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain F residue 2344 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 606 HIS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 149 HIS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 841 LEU Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1114 GLU Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1122 MET Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1165 VAL Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1434 LEU Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1714 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1771 LEU Chi-restraints excluded: chain E residue 1905 LEU Chi-restraints excluded: chain E residue 1942 VAL Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2206 TYR Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2344 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 288 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 432 optimal weight: 9.9990 chunk 353 optimal weight: 6.9990 chunk 143 optimal weight: 0.5980 chunk 520 optimal weight: 8.9990 chunk 562 optimal weight: 5.9990 chunk 463 optimal weight: 7.9990 chunk 516 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 417 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN F 668 GLN F 671 ASN ** F 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 868 GLN F 885 GLN F 908 ASN ** F1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1235 GLN F1317 ASN ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1625 HIS ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1891 HIS ** F1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS C 665 HIS ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS D 437 ASN ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 GLN E 548 HIS E 574 GLN E 868 GLN E 885 GLN ** E1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1235 GLN E1317 ASN ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1507 GLN ** E1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1955 HIS ** E2187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2229 ASN E2343 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 47082 Z= 0.330 Angle : 0.878 12.797 63787 Z= 0.448 Chirality : 0.049 0.436 7342 Planarity : 0.006 0.063 8019 Dihedral : 7.938 174.710 6244 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 5.37 % Allowed : 17.94 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.56 (0.10), residues: 5688 helix: -0.87 (0.08), residues: 3628 sheet: -2.53 (0.43), residues: 76 loop : -3.14 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 487 HIS 0.025 0.002 HIS F 548 PHE 0.037 0.003 PHE D 206 TYR 0.025 0.002 TYR F1786 ARG 0.010 0.001 ARG C 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 909 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 123 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8738 (ttm) REVERT: F 186 TYR cc_start: 0.9094 (t80) cc_final: 0.8851 (t80) REVERT: F 289 LEU cc_start: 0.4590 (OUTLIER) cc_final: 0.3972 (tt) REVERT: F 295 MET cc_start: 0.9156 (tpt) cc_final: 0.8121 (ptt) REVERT: F 307 ILE cc_start: 0.9525 (pt) cc_final: 0.9037 (mm) REVERT: F 484 MET cc_start: 0.8810 (mtp) cc_final: 0.8576 (mtt) REVERT: F 549 ARG cc_start: 0.9150 (mtt-85) cc_final: 0.8637 (ttm170) REVERT: F 579 ASN cc_start: 0.8679 (t0) cc_final: 0.8370 (t0) REVERT: F 587 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8715 (mt) REVERT: F 671 ASN cc_start: 0.8960 (m-40) cc_final: 0.8577 (m110) REVERT: F 691 LEU cc_start: 0.9165 (tp) cc_final: 0.8707 (mt) REVERT: F 748 MET cc_start: 0.8988 (mmm) cc_final: 0.8787 (mmm) REVERT: F 759 MET cc_start: 0.9240 (tpp) cc_final: 0.8859 (tpp) REVERT: F 767 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7452 (p0) REVERT: F 937 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8543 (mm) REVERT: F 1006 LEU cc_start: 0.9044 (tt) cc_final: 0.8786 (mt) REVERT: F 1118 LYS cc_start: 0.9429 (ptpt) cc_final: 0.9059 (ptpp) REVERT: F 1126 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7005 (tm) REVERT: F 1155 PHE cc_start: 0.8975 (t80) cc_final: 0.8732 (m-80) REVERT: F 1245 TYR cc_start: 0.9123 (m-80) cc_final: 0.8837 (m-80) REVERT: F 1314 ASP cc_start: 0.9393 (t0) cc_final: 0.9165 (m-30) REVERT: F 1334 MET cc_start: 0.5356 (ptt) cc_final: 0.5103 (ptt) REVERT: F 1353 PHE cc_start: 0.9050 (m-80) cc_final: 0.8814 (m-80) REVERT: F 1390 GLU cc_start: 0.7703 (tm-30) cc_final: 0.6928 (mp0) REVERT: F 1444 GLU cc_start: 0.7348 (tt0) cc_final: 0.7074 (tt0) REVERT: F 1503 MET cc_start: 0.8816 (ttm) cc_final: 0.8425 (ttp) REVERT: F 1527 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7242 (mp) REVERT: F 1666 ILE cc_start: 0.9147 (pp) cc_final: 0.8922 (pp) REVERT: F 1670 ARG cc_start: 0.8967 (ttp-170) cc_final: 0.8658 (ttt180) REVERT: F 1837 PHE cc_start: 0.8628 (m-10) cc_final: 0.8423 (m-10) REVERT: F 1920 MET cc_start: 0.9164 (mmm) cc_final: 0.8546 (tmm) REVERT: F 1937 TYR cc_start: 0.8975 (m-80) cc_final: 0.8698 (m-80) REVERT: F 1959 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8533 (mtmm) REVERT: F 2213 MET cc_start: 0.8817 (mmm) cc_final: 0.8559 (mmm) REVERT: F 2225 ARG cc_start: 0.6248 (mmm-85) cc_final: 0.5641 (mmm-85) REVERT: F 2247 LEU cc_start: 0.8742 (mt) cc_final: 0.8312 (mp) REVERT: F 2263 ARG cc_start: 0.5533 (tmt-80) cc_final: 0.4499 (tpm170) REVERT: F 2282 LYS cc_start: 0.9234 (tttm) cc_final: 0.8805 (mtpp) REVERT: F 2292 MET cc_start: 0.8905 (ptp) cc_final: 0.8604 (ptm) REVERT: F 2344 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8088 (p) REVERT: F 2364 TRP cc_start: 0.8869 (t60) cc_final: 0.8520 (t60) REVERT: C 201 ASP cc_start: 0.8415 (t0) cc_final: 0.7836 (m-30) REVERT: C 275 LEU cc_start: 0.9237 (mt) cc_final: 0.8883 (mt) REVERT: C 278 ILE cc_start: 0.9597 (mt) cc_final: 0.9306 (tp) REVERT: C 303 MET cc_start: 0.8915 (ttm) cc_final: 0.8514 (tpt) REVERT: C 437 ASN cc_start: 0.8715 (t0) cc_final: 0.8064 (p0) REVERT: C 507 LEU cc_start: 0.9049 (tp) cc_final: 0.8837 (tp) REVERT: C 518 ARG cc_start: 0.8646 (ttt180) cc_final: 0.8405 (ttp-170) REVERT: C 540 LYS cc_start: 0.9447 (ptpp) cc_final: 0.9214 (ptpp) REVERT: C 547 LYS cc_start: 0.9047 (mttt) cc_final: 0.8749 (mttm) REVERT: C 558 ASN cc_start: 0.8902 (m110) cc_final: 0.8653 (t0) REVERT: C 562 ILE cc_start: 0.8027 (mt) cc_final: 0.7487 (mt) REVERT: C 575 LEU cc_start: 0.9245 (mt) cc_final: 0.8938 (mp) REVERT: C 593 TYR cc_start: 0.7820 (m-80) cc_final: 0.7192 (m-80) REVERT: C 617 ARG cc_start: 0.8896 (ptp-110) cc_final: 0.8397 (ptp-110) REVERT: C 654 THR cc_start: 0.6397 (p) cc_final: 0.5900 (p) REVERT: C 660 MET cc_start: 0.9155 (mtp) cc_final: 0.8785 (mmm) REVERT: C 664 ARG cc_start: 0.9126 (ptt180) cc_final: 0.8721 (ppt170) REVERT: C 745 MET cc_start: 0.6918 (ptp) cc_final: 0.6656 (ptp) REVERT: D 303 MET cc_start: 0.8895 (ttm) cc_final: 0.8461 (mtp) REVERT: D 437 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7567 (p0) REVERT: D 462 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8068 (mt-10) REVERT: D 544 TRP cc_start: 0.8757 (m100) cc_final: 0.8509 (m100) REVERT: D 547 LYS cc_start: 0.8936 (mttt) cc_final: 0.8628 (mttm) REVERT: D 573 GLU cc_start: 0.8773 (mp0) cc_final: 0.8514 (mp0) REVERT: D 575 LEU cc_start: 0.9290 (mt) cc_final: 0.8979 (mp) REVERT: D 609 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8476 (tp30) REVERT: D 610 HIS cc_start: 0.9157 (t-170) cc_final: 0.8913 (t-90) REVERT: D 664 ARG cc_start: 0.9109 (ptt180) cc_final: 0.8656 (ppt170) REVERT: D 720 MET cc_start: 0.8025 (mtm) cc_final: 0.7532 (ptm) REVERT: E 113 ASN cc_start: 0.7914 (p0) cc_final: 0.7155 (p0) REVERT: E 186 TYR cc_start: 0.9053 (t80) cc_final: 0.8816 (t80) REVERT: E 289 LEU cc_start: 0.4590 (OUTLIER) cc_final: 0.3885 (tt) REVERT: E 295 MET cc_start: 0.9108 (tpt) cc_final: 0.8656 (ptt) REVERT: E 297 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7562 (ttmm) REVERT: E 416 ARG cc_start: 0.9021 (mmm160) cc_final: 0.8390 (mmm160) REVERT: E 458 TRP cc_start: 0.8575 (m100) cc_final: 0.7960 (m100) REVERT: E 469 GLU cc_start: 0.8804 (tp30) cc_final: 0.8477 (tp30) REVERT: E 549 ARG cc_start: 0.9161 (mtt-85) cc_final: 0.8784 (ttm170) REVERT: E 574 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.9006 (mm-40) REVERT: E 579 ASN cc_start: 0.8902 (t0) cc_final: 0.8588 (t0) REVERT: E 587 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8736 (mt) REVERT: E 664 MET cc_start: 0.7585 (mtt) cc_final: 0.7353 (ttm) REVERT: E 691 LEU cc_start: 0.9248 (tp) cc_final: 0.8883 (mt) REVERT: E 747 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8581 (tp) REVERT: E 947 PHE cc_start: 0.9107 (m-80) cc_final: 0.8791 (m-80) REVERT: E 998 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8488 (pm20) REVERT: E 1118 LYS cc_start: 0.9500 (ptpt) cc_final: 0.9181 (ptpp) REVERT: E 1126 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6866 (tm) REVERT: E 1178 LEU cc_start: 0.8861 (mm) cc_final: 0.8599 (mm) REVERT: E 1245 TYR cc_start: 0.9141 (m-80) cc_final: 0.8825 (m-80) REVERT: E 1314 ASP cc_start: 0.9254 (t0) cc_final: 0.9028 (m-30) REVERT: E 1334 MET cc_start: 0.5819 (ptt) cc_final: 0.5609 (ptt) REVERT: E 1353 PHE cc_start: 0.8990 (m-10) cc_final: 0.8745 (m-80) REVERT: E 1503 MET cc_start: 0.8717 (ttp) cc_final: 0.8430 (ptm) REVERT: E 1527 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7633 (mp) REVERT: E 1543 ASN cc_start: 0.9227 (m-40) cc_final: 0.8996 (m110) REVERT: E 1786 TYR cc_start: 0.8377 (t80) cc_final: 0.8068 (t80) REVERT: E 1837 PHE cc_start: 0.8608 (m-80) cc_final: 0.8205 (m-80) REVERT: E 1897 TRP cc_start: 0.7560 (m100) cc_final: 0.7220 (m-10) REVERT: E 2040 PHE cc_start: 0.6746 (m-80) cc_final: 0.6423 (m-80) REVERT: E 2110 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7999 (tpt170) REVERT: E 2210 TYR cc_start: 0.8938 (t80) cc_final: 0.8675 (t80) REVERT: E 2213 MET cc_start: 0.8982 (mmm) cc_final: 0.8764 (mmm) REVERT: E 2247 LEU cc_start: 0.8742 (mt) cc_final: 0.8290 (mp) REVERT: E 2263 ARG cc_start: 0.5420 (tmt-80) cc_final: 0.5157 (tpm170) REVERT: E 2282 LYS cc_start: 0.9210 (tttm) cc_final: 0.8827 (mtpp) REVERT: E 2292 MET cc_start: 0.8759 (ptp) cc_final: 0.7930 (ptp) REVERT: E 2344 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8250 (p) REVERT: E 2350 GLU cc_start: 0.9025 (tt0) cc_final: 0.8602 (pt0) outliers start: 271 outliers final: 137 residues processed: 1088 average time/residue: 0.4590 time to fit residues: 836.3785 Evaluate side-chains 963 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 808 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 250 TYR Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 426 GLN Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 469 GLU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 666 THR Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 841 LEU Chi-restraints excluded: chain F residue 881 LEU Chi-restraints excluded: chain F residue 937 LEU Chi-restraints excluded: chain F residue 939 LEU Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1164 LEU Chi-restraints excluded: chain F residue 1265 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1294 LEU Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1389 ASP Chi-restraints excluded: chain F residue 1411 GLU Chi-restraints excluded: chain F residue 1434 LEU Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1771 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1902 THR Chi-restraints excluded: chain F residue 1905 LEU Chi-restraints excluded: chain F residue 1942 VAL Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2111 SER Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2164 HIS Chi-restraints excluded: chain F residue 2206 TYR Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain F residue 2344 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 149 HIS Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 624 LYS Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 841 LEU Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 978 SER Chi-restraints excluded: chain E residue 998 GLU Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1114 GLU Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1382 THR Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1399 LEU Chi-restraints excluded: chain E residue 1411 GLU Chi-restraints excluded: chain E residue 1434 LEU Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1506 HIS Chi-restraints excluded: chain E residue 1527 LEU Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1571 LEU Chi-restraints excluded: chain E residue 1614 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1714 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1771 LEU Chi-restraints excluded: chain E residue 1905 LEU Chi-restraints excluded: chain E residue 1906 SER Chi-restraints excluded: chain E residue 1942 VAL Chi-restraints excluded: chain E residue 1955 HIS Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2110 ARG Chi-restraints excluded: chain E residue 2111 SER Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2206 TYR Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2344 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 514 optimal weight: 0.9990 chunk 391 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 349 optimal weight: 10.0000 chunk 522 optimal weight: 10.0000 chunk 552 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 494 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 113 ASN ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN F 548 HIS F 668 GLN ** F 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1073 GLN ** F1177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1471 GLN ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2229 ASN F2356 ASN C 334 HIS D 334 HIS ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 574 GLN ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1073 GLN ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1511 GLN ** E1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1955 HIS E2343 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 47082 Z= 0.257 Angle : 0.846 14.517 63787 Z= 0.420 Chirality : 0.048 0.401 7342 Planarity : 0.005 0.068 8019 Dihedral : 7.655 177.709 6244 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 5.39 % Allowed : 19.47 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.20 (0.11), residues: 5688 helix: -0.59 (0.08), residues: 3646 sheet: -2.43 (0.43), residues: 80 loop : -3.02 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F1897 HIS 0.017 0.001 HIS E1955 PHE 0.035 0.002 PHE D 323 TYR 0.026 0.002 TYR F1786 ARG 0.008 0.001 ARG C 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 902 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 120 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8640 (pp) REVERT: F 154 MET cc_start: 0.8068 (tmm) cc_final: 0.7464 (ppp) REVERT: F 186 TYR cc_start: 0.9063 (t80) cc_final: 0.8273 (t80) REVERT: F 289 LEU cc_start: 0.4168 (OUTLIER) cc_final: 0.3604 (tt) REVERT: F 307 ILE cc_start: 0.9487 (pt) cc_final: 0.9027 (mm) REVERT: F 484 MET cc_start: 0.8817 (mtp) cc_final: 0.8540 (mtt) REVERT: F 575 LYS cc_start: 0.8569 (tptm) cc_final: 0.8340 (tttt) REVERT: F 579 ASN cc_start: 0.8724 (t0) cc_final: 0.8438 (t0) REVERT: F 587 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8771 (mt) REVERT: F 671 ASN cc_start: 0.8918 (m-40) cc_final: 0.8585 (m110) REVERT: F 691 LEU cc_start: 0.9265 (tp) cc_final: 0.8766 (mt) REVERT: F 759 MET cc_start: 0.9271 (tpp) cc_final: 0.8903 (tpp) REVERT: F 767 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7409 (p0) REVERT: F 998 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: F 1099 LEU cc_start: 0.9469 (mt) cc_final: 0.9161 (pp) REVERT: F 1118 LYS cc_start: 0.9414 (ptpt) cc_final: 0.9054 (ptpp) REVERT: F 1126 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6835 (tm) REVERT: F 1155 PHE cc_start: 0.9010 (t80) cc_final: 0.8766 (m-80) REVERT: F 1245 TYR cc_start: 0.9151 (m-80) cc_final: 0.8858 (m-80) REVERT: F 1334 MET cc_start: 0.5227 (ptt) cc_final: 0.4901 (ptt) REVERT: F 1353 PHE cc_start: 0.9228 (m-80) cc_final: 0.8878 (m-80) REVERT: F 1503 MET cc_start: 0.8766 (ttm) cc_final: 0.8318 (ttp) REVERT: F 1527 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7141 (mp) REVERT: F 1536 SER cc_start: 0.8865 (t) cc_final: 0.8564 (t) REVERT: F 1666 ILE cc_start: 0.9139 (pp) cc_final: 0.8924 (pp) REVERT: F 1711 MET cc_start: 0.7952 (ttm) cc_final: 0.7576 (ttm) REVERT: F 1837 PHE cc_start: 0.8601 (m-10) cc_final: 0.8368 (m-80) REVERT: F 1920 MET cc_start: 0.9146 (mmm) cc_final: 0.8491 (tmm) REVERT: F 1937 TYR cc_start: 0.8993 (m-80) cc_final: 0.8682 (m-80) REVERT: F 2213 MET cc_start: 0.8910 (mmm) cc_final: 0.8611 (mmm) REVERT: F 2225 ARG cc_start: 0.6225 (mmm-85) cc_final: 0.5958 (mmm-85) REVERT: F 2263 ARG cc_start: 0.5485 (tmt-80) cc_final: 0.4479 (tpm170) REVERT: F 2282 LYS cc_start: 0.9272 (tttm) cc_final: 0.8828 (mtpp) REVERT: F 2344 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8191 (p) REVERT: F 2356 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8580 (t0) REVERT: F 2360 MET cc_start: 0.7685 (mmm) cc_final: 0.7469 (mmm) REVERT: F 2364 TRP cc_start: 0.9177 (t60) cc_final: 0.8468 (t60) REVERT: C 278 ILE cc_start: 0.9515 (mt) cc_final: 0.8866 (mm) REVERT: C 303 MET cc_start: 0.8934 (ttm) cc_final: 0.8586 (mtp) REVERT: C 377 ARG cc_start: 0.8987 (mtp-110) cc_final: 0.7836 (mmm160) REVERT: C 400 GLU cc_start: 0.9351 (tt0) cc_final: 0.8861 (tt0) REVERT: C 437 ASN cc_start: 0.8795 (t0) cc_final: 0.8202 (p0) REVERT: C 449 TRP cc_start: 0.7795 (t60) cc_final: 0.6844 (t60) REVERT: C 547 LYS cc_start: 0.9029 (mttt) cc_final: 0.8759 (mttm) REVERT: C 562 ILE cc_start: 0.8103 (mt) cc_final: 0.7580 (mt) REVERT: C 610 HIS cc_start: 0.9158 (t-170) cc_final: 0.8664 (t-170) REVERT: C 617 ARG cc_start: 0.8569 (ptp-110) cc_final: 0.8367 (ptp-110) REVERT: C 654 THR cc_start: 0.6293 (p) cc_final: 0.5807 (p) REVERT: C 660 MET cc_start: 0.9041 (mtp) cc_final: 0.8815 (mmm) REVERT: C 664 ARG cc_start: 0.9147 (ptt180) cc_final: 0.8736 (ppt170) REVERT: C 707 ARG cc_start: 0.8681 (ttt180) cc_final: 0.8265 (ttt180) REVERT: C 745 MET cc_start: 0.6997 (ptp) cc_final: 0.6671 (ptp) REVERT: D 238 LYS cc_start: 0.8980 (tttm) cc_final: 0.8766 (tptp) REVERT: D 278 ILE cc_start: 0.9501 (mt) cc_final: 0.9066 (mm) REVERT: D 303 MET cc_start: 0.8898 (ttm) cc_final: 0.8610 (mtp) REVERT: D 449 TRP cc_start: 0.7817 (t60) cc_final: 0.7615 (t60) REVERT: D 540 LYS cc_start: 0.9444 (ptpp) cc_final: 0.9209 (ptpp) REVERT: D 547 LYS cc_start: 0.8956 (mttt) cc_final: 0.8648 (mttm) REVERT: D 573 GLU cc_start: 0.8694 (mp0) cc_final: 0.8404 (mp0) REVERT: D 575 LEU cc_start: 0.9245 (mt) cc_final: 0.8959 (mp) REVERT: D 609 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8680 (tp30) REVERT: D 610 HIS cc_start: 0.9116 (t-170) cc_final: 0.8822 (t-90) REVERT: D 661 ARG cc_start: 0.9006 (ptp-170) cc_final: 0.8475 (ptp90) REVERT: D 664 ARG cc_start: 0.9130 (ptt180) cc_final: 0.8605 (ppt170) REVERT: D 720 MET cc_start: 0.7970 (mtm) cc_final: 0.7656 (ptm) REVERT: E 126 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7501 (tppt) REVERT: E 154 MET cc_start: 0.8214 (tmm) cc_final: 0.7506 (ppp) REVERT: E 208 PHE cc_start: 0.7004 (t80) cc_final: 0.5854 (t80) REVERT: E 289 LEU cc_start: 0.4090 (OUTLIER) cc_final: 0.3400 (tt) REVERT: E 295 MET cc_start: 0.9015 (tpt) cc_final: 0.8636 (ptt) REVERT: E 297 LYS cc_start: 0.7761 (mtpp) cc_final: 0.7142 (ttpp) REVERT: E 418 ASN cc_start: 0.9080 (m-40) cc_final: 0.8873 (m-40) REVERT: E 458 TRP cc_start: 0.8687 (m100) cc_final: 0.7950 (m100) REVERT: E 469 GLU cc_start: 0.8830 (tp30) cc_final: 0.8540 (tp30) REVERT: E 549 ARG cc_start: 0.9120 (mtt-85) cc_final: 0.8720 (ttm170) REVERT: E 575 LYS cc_start: 0.9021 (tptm) cc_final: 0.8672 (tptm) REVERT: E 668 GLN cc_start: 0.8822 (mm110) cc_final: 0.8365 (mm110) REVERT: E 747 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8460 (tp) REVERT: E 947 PHE cc_start: 0.9162 (m-80) cc_final: 0.8729 (m-80) REVERT: E 998 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8401 (pm20) REVERT: E 1106 ARG cc_start: 0.9342 (ptp-110) cc_final: 0.8537 (mmt180) REVERT: E 1118 LYS cc_start: 0.9491 (ptpt) cc_final: 0.9154 (ptpp) REVERT: E 1126 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6792 (tm) REVERT: E 1178 LEU cc_start: 0.8853 (mm) cc_final: 0.8601 (mm) REVERT: E 1245 TYR cc_start: 0.9139 (m-80) cc_final: 0.8915 (m-80) REVERT: E 1334 MET cc_start: 0.5833 (ptt) cc_final: 0.5597 (ptt) REVERT: E 1351 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8507 (ttp-110) REVERT: E 1353 PHE cc_start: 0.9117 (m-10) cc_final: 0.8781 (m-80) REVERT: E 1527 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7503 (mp) REVERT: E 1536 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8399 (t) REVERT: E 1666 ILE cc_start: 0.9143 (pp) cc_final: 0.8928 (pp) REVERT: E 1731 LYS cc_start: 0.9137 (ptmt) cc_final: 0.8771 (mmtm) REVERT: E 1837 PHE cc_start: 0.8554 (m-10) cc_final: 0.8255 (m-80) REVERT: E 1883 SER cc_start: 0.8965 (t) cc_final: 0.8693 (p) REVERT: E 1897 TRP cc_start: 0.7798 (m100) cc_final: 0.7478 (m-10) REVERT: E 2038 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6931 (tm130) REVERT: E 2040 PHE cc_start: 0.6810 (m-80) cc_final: 0.5845 (m-80) REVERT: E 2110 ARG cc_start: 0.8672 (ttm110) cc_final: 0.7988 (tpt170) REVERT: E 2176 GLU cc_start: 0.9248 (tt0) cc_final: 0.8959 (tm-30) REVERT: E 2213 MET cc_start: 0.9038 (mmm) cc_final: 0.8795 (mmm) REVERT: E 2263 ARG cc_start: 0.5101 (tmt-80) cc_final: 0.4873 (tpt90) REVERT: E 2282 LYS cc_start: 0.9236 (tttm) cc_final: 0.8783 (mtpp) REVERT: E 2292 MET cc_start: 0.8693 (ptp) cc_final: 0.7992 (ptp) REVERT: E 2344 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8061 (p) outliers start: 272 outliers final: 144 residues processed: 1079 average time/residue: 0.4825 time to fit residues: 874.7982 Evaluate side-chains 961 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 799 time to evaluate : 4.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 250 TYR Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 813 LEU Chi-restraints excluded: chain F residue 841 LEU Chi-restraints excluded: chain F residue 881 LEU Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 956 HIS Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 978 SER Chi-restraints excluded: chain F residue 998 GLU Chi-restraints excluded: chain F residue 1011 THR Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1294 LEU Chi-restraints excluded: chain F residue 1317 ASN Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1389 ASP Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1411 GLU Chi-restraints excluded: chain F residue 1434 LEU Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1510 SER Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1771 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1905 LEU Chi-restraints excluded: chain F residue 1906 SER Chi-restraints excluded: chain F residue 1942 VAL Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2111 SER Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2206 TYR Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2291 LEU Chi-restraints excluded: chain F residue 2344 THR Chi-restraints excluded: chain F residue 2356 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 149 HIS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 665 MET Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 841 LEU Chi-restraints excluded: chain E residue 885 GLN Chi-restraints excluded: chain E residue 937 LEU Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 978 SER Chi-restraints excluded: chain E residue 998 GLU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1114 GLU Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1317 ASN Chi-restraints excluded: chain E residue 1351 ARG Chi-restraints excluded: chain E residue 1354 GLU Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1370 LEU Chi-restraints excluded: chain E residue 1382 THR Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1399 LEU Chi-restraints excluded: chain E residue 1411 GLU Chi-restraints excluded: chain E residue 1434 LEU Chi-restraints excluded: chain E residue 1527 LEU Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1771 LEU Chi-restraints excluded: chain E residue 1905 LEU Chi-restraints excluded: chain E residue 1906 SER Chi-restraints excluded: chain E residue 1942 VAL Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2111 SER Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2206 TYR Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2344 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 460 optimal weight: 10.0000 chunk 313 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 411 optimal weight: 0.5980 chunk 228 optimal weight: 5.9990 chunk 471 optimal weight: 0.0870 chunk 382 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 282 optimal weight: 10.0000 chunk 496 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 ASN ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 HIS F 668 GLN F 682 GLN F 735 GLN ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS D 334 HIS D 437 ASN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN E 197 ASN ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 574 GLN E 682 GLN ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 47082 Z= 0.225 Angle : 0.845 14.356 63787 Z= 0.412 Chirality : 0.048 0.351 7342 Planarity : 0.005 0.067 8019 Dihedral : 7.462 178.474 6244 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.69 % Allowed : 20.60 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.04 (0.11), residues: 5688 helix: -0.46 (0.08), residues: 3662 sheet: -2.04 (0.46), residues: 80 loop : -3.00 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F1897 HIS 0.012 0.001 HIS F 318 PHE 0.051 0.002 PHE D 206 TYR 0.028 0.002 TYR F1786 ARG 0.009 0.001 ARG F 943 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 891 time to evaluate : 4.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 63 ILE cc_start: 0.8159 (mm) cc_final: 0.7789 (mm) REVERT: F 135 VAL cc_start: 0.9136 (m) cc_final: 0.8910 (p) REVERT: F 154 MET cc_start: 0.8043 (tmm) cc_final: 0.7462 (ppp) REVERT: F 211 PHE cc_start: 0.8156 (t80) cc_final: 0.7801 (t80) REVERT: F 289 LEU cc_start: 0.4253 (OUTLIER) cc_final: 0.3691 (tt) REVERT: F 295 MET cc_start: 0.9164 (tpt) cc_final: 0.8075 (ptt) REVERT: F 471 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8301 (tp30) REVERT: F 484 MET cc_start: 0.8810 (mtp) cc_final: 0.8531 (mtt) REVERT: F 575 LYS cc_start: 0.8438 (tptm) cc_final: 0.8228 (tttt) REVERT: F 579 ASN cc_start: 0.8720 (t0) cc_final: 0.8497 (t0) REVERT: F 671 ASN cc_start: 0.8864 (m-40) cc_final: 0.8552 (m-40) REVERT: F 691 LEU cc_start: 0.9301 (tp) cc_final: 0.8785 (mt) REVERT: F 759 MET cc_start: 0.9295 (tpp) cc_final: 0.8988 (tpp) REVERT: F 943 ARG cc_start: 0.8581 (mpt-90) cc_final: 0.8070 (mmt90) REVERT: F 998 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: F 1020 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8168 (tt) REVERT: F 1118 LYS cc_start: 0.9382 (ptpt) cc_final: 0.9057 (ptpp) REVERT: F 1126 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6706 (tm) REVERT: F 1142 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6588 (tt0) REVERT: F 1245 TYR cc_start: 0.9111 (m-80) cc_final: 0.8785 (m-80) REVERT: F 1334 MET cc_start: 0.5103 (ptt) cc_final: 0.4850 (ptt) REVERT: F 1353 PHE cc_start: 0.9270 (m-80) cc_final: 0.8918 (m-80) REVERT: F 1451 LEU cc_start: 0.9186 (tp) cc_final: 0.8917 (mm) REVERT: F 1488 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8435 (pptt) REVERT: F 1503 MET cc_start: 0.8743 (ttm) cc_final: 0.8371 (ttp) REVERT: F 1527 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7113 (mp) REVERT: F 1536 SER cc_start: 0.8775 (t) cc_final: 0.8460 (t) REVERT: F 1622 MET cc_start: 0.8052 (ttt) cc_final: 0.7849 (ttt) REVERT: F 1666 ILE cc_start: 0.9065 (pp) cc_final: 0.8864 (pp) REVERT: F 1711 MET cc_start: 0.8097 (ttm) cc_final: 0.7733 (ttm) REVERT: F 1837 PHE cc_start: 0.8563 (m-10) cc_final: 0.8326 (m-80) REVERT: F 1937 TYR cc_start: 0.9030 (m-80) cc_final: 0.8699 (m-80) REVERT: F 2087 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8695 (p0) REVERT: F 2213 MET cc_start: 0.8899 (mmm) cc_final: 0.8631 (mmm) REVERT: F 2263 ARG cc_start: 0.5410 (tmt-80) cc_final: 0.4436 (tpm170) REVERT: F 2282 LYS cc_start: 0.9288 (tttm) cc_final: 0.8848 (mtpp) REVERT: F 2296 GLU cc_start: 0.8809 (pm20) cc_final: 0.8488 (mt-10) REVERT: F 2301 ASN cc_start: 0.8579 (m110) cc_final: 0.8234 (p0) REVERT: F 2357 LEU cc_start: 0.9169 (mt) cc_final: 0.8893 (pp) REVERT: F 2364 TRP cc_start: 0.9110 (t60) cc_final: 0.8593 (t60) REVERT: C 238 LYS cc_start: 0.8861 (tttm) cc_final: 0.8609 (tptp) REVERT: C 278 ILE cc_start: 0.9460 (mt) cc_final: 0.8853 (mm) REVERT: C 303 MET cc_start: 0.8944 (ttm) cc_final: 0.8644 (mtp) REVERT: C 377 ARG cc_start: 0.9063 (mtp180) cc_final: 0.8719 (mtp85) REVERT: C 437 ASN cc_start: 0.8759 (t0) cc_final: 0.8179 (p0) REVERT: C 449 TRP cc_start: 0.7839 (t60) cc_final: 0.7631 (t60) REVERT: C 518 ARG cc_start: 0.8595 (ttt180) cc_final: 0.8377 (ttp-170) REVERT: C 547 LYS cc_start: 0.9029 (mttt) cc_final: 0.8781 (mttm) REVERT: C 610 HIS cc_start: 0.9176 (t-170) cc_final: 0.8723 (t-170) REVERT: C 654 THR cc_start: 0.6513 (p) cc_final: 0.5956 (p) REVERT: C 664 ARG cc_start: 0.9001 (ptt180) cc_final: 0.8696 (ppt170) REVERT: C 707 ARG cc_start: 0.8604 (ttt180) cc_final: 0.8185 (ttt180) REVERT: C 745 MET cc_start: 0.6935 (ptp) cc_final: 0.6601 (ptp) REVERT: D 238 LYS cc_start: 0.8910 (tttm) cc_final: 0.8657 (tptp) REVERT: D 437 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7519 (p0) REVERT: D 449 TRP cc_start: 0.7840 (t60) cc_final: 0.7603 (t60) REVERT: D 540 LYS cc_start: 0.9473 (ptpp) cc_final: 0.9222 (ptpp) REVERT: D 547 LYS cc_start: 0.8889 (mttt) cc_final: 0.8609 (mttm) REVERT: D 575 LEU cc_start: 0.9227 (mt) cc_final: 0.8831 (mp) REVERT: D 609 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8441 (tp30) REVERT: D 610 HIS cc_start: 0.9116 (t-170) cc_final: 0.8791 (t-90) REVERT: D 660 MET cc_start: 0.8880 (mmp) cc_final: 0.8580 (mmt) REVERT: D 661 ARG cc_start: 0.8975 (ptp-170) cc_final: 0.8486 (ptp90) REVERT: D 664 ARG cc_start: 0.9065 (ptt180) cc_final: 0.8549 (ppt170) REVERT: D 720 MET cc_start: 0.8014 (mtm) cc_final: 0.7584 (ptm) REVERT: E 126 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7455 (tppt) REVERT: E 154 MET cc_start: 0.8189 (tmm) cc_final: 0.7521 (ppp) REVERT: E 210 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7993 (ptmm) REVERT: E 289 LEU cc_start: 0.4184 (OUTLIER) cc_final: 0.3454 (tt) REVERT: E 295 MET cc_start: 0.8986 (tpt) cc_final: 0.8660 (ptm) REVERT: E 297 LYS cc_start: 0.7705 (mtpp) cc_final: 0.7154 (ttmm) REVERT: E 418 ASN cc_start: 0.9095 (m-40) cc_final: 0.8827 (t0) REVERT: E 458 TRP cc_start: 0.8686 (m100) cc_final: 0.8035 (m100) REVERT: E 469 GLU cc_start: 0.8823 (tp30) cc_final: 0.8507 (tp30) REVERT: E 545 PHE cc_start: 0.9151 (m-80) cc_final: 0.8896 (m-80) REVERT: E 549 ARG cc_start: 0.9068 (mtt-85) cc_final: 0.8697 (ttm170) REVERT: E 574 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8740 (mm-40) REVERT: E 668 GLN cc_start: 0.8780 (mm110) cc_final: 0.8328 (mm-40) REVERT: E 691 LEU cc_start: 0.9349 (tp) cc_final: 0.8861 (mt) REVERT: E 747 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8535 (tp) REVERT: E 943 ARG cc_start: 0.8561 (mmt90) cc_final: 0.8347 (mmt90) REVERT: E 947 PHE cc_start: 0.9160 (m-80) cc_final: 0.8742 (m-80) REVERT: E 998 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8434 (pm20) REVERT: E 1020 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8079 (tt) REVERT: E 1099 LEU cc_start: 0.9212 (mm) cc_final: 0.8891 (pp) REVERT: E 1118 LYS cc_start: 0.9444 (ptpt) cc_final: 0.9121 (ptpp) REVERT: E 1178 LEU cc_start: 0.8808 (mm) cc_final: 0.8534 (mm) REVERT: E 1190 TYR cc_start: 0.7776 (t80) cc_final: 0.7430 (t80) REVERT: E 1334 MET cc_start: 0.5540 (ptt) cc_final: 0.5086 (ptt) REVERT: E 1351 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8545 (ttp-110) REVERT: E 1353 PHE cc_start: 0.9089 (m-10) cc_final: 0.8806 (m-80) REVERT: E 1485 VAL cc_start: 0.9282 (m) cc_final: 0.8901 (m) REVERT: E 1488 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8474 (pptt) REVERT: E 1527 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7472 (mp) REVERT: E 1536 SER cc_start: 0.8696 (t) cc_final: 0.8364 (t) REVERT: E 1615 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8622 (mt) REVERT: E 1666 ILE cc_start: 0.9184 (pp) cc_final: 0.8976 (pp) REVERT: E 1837 PHE cc_start: 0.8500 (m-10) cc_final: 0.8270 (m-80) REVERT: E 1897 TRP cc_start: 0.7911 (m100) cc_final: 0.7682 (m-10) REVERT: E 2038 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.6862 (tm130) REVERT: E 2040 PHE cc_start: 0.6760 (m-80) cc_final: 0.5806 (m-80) REVERT: E 2065 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8195 (tp) REVERT: E 2087 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8443 (p0) REVERT: E 2110 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7716 (tpp-160) REVERT: E 2176 GLU cc_start: 0.9260 (tt0) cc_final: 0.8933 (tm-30) REVERT: E 2213 MET cc_start: 0.9085 (mmm) cc_final: 0.8816 (mmm) REVERT: E 2263 ARG cc_start: 0.5066 (tmt-80) cc_final: 0.4378 (tpm170) REVERT: E 2282 LYS cc_start: 0.9261 (tttm) cc_final: 0.8853 (mtpp) REVERT: E 2296 GLU cc_start: 0.8853 (pm20) cc_final: 0.8380 (mt-10) REVERT: E 2301 ASN cc_start: 0.8552 (m110) cc_final: 0.8190 (p0) REVERT: E 2344 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.7968 (p) REVERT: E 2364 TRP cc_start: 0.8893 (t60) cc_final: 0.8661 (t60) outliers start: 236 outliers final: 134 residues processed: 1048 average time/residue: 0.4931 time to fit residues: 874.5932 Evaluate side-chains 976 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 818 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 956 HIS Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 978 SER Chi-restraints excluded: chain F residue 984 LEU Chi-restraints excluded: chain F residue 998 GLU Chi-restraints excluded: chain F residue 1020 LEU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1233 LEU Chi-restraints excluded: chain F residue 1294 LEU Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1411 GLU Chi-restraints excluded: chain F residue 1434 LEU Chi-restraints excluded: chain F residue 1435 LEU Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1901 LEU Chi-restraints excluded: chain F residue 1905 LEU Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2206 TYR Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2230 ILE Chi-restraints excluded: chain F residue 2291 LEU Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 149 HIS Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 654 PHE Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 841 LEU Chi-restraints excluded: chain E residue 885 GLN Chi-restraints excluded: chain E residue 937 LEU Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 998 GLU Chi-restraints excluded: chain E residue 1020 LEU Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1093 LEU Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1200 MET Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1317 ASN Chi-restraints excluded: chain E residue 1350 PHE Chi-restraints excluded: chain E residue 1351 ARG Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1382 THR Chi-restraints excluded: chain E residue 1411 GLU Chi-restraints excluded: chain E residue 1434 LEU Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1527 LEU Chi-restraints excluded: chain E residue 1615 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1874 LEU Chi-restraints excluded: chain E residue 1901 LEU Chi-restraints excluded: chain E residue 1905 LEU Chi-restraints excluded: chain E residue 1942 VAL Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2110 ARG Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2206 TYR Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2344 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 186 optimal weight: 20.0000 chunk 497 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 553 optimal weight: 4.9990 chunk 459 optimal weight: 6.9990 chunk 256 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 290 optimal weight: 0.6980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 152 ASN ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2241 HIS C 334 HIS D 437 ASN ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 HIS E 574 GLN ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 951 HIS E1383 ASN ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 47082 Z= 0.228 Angle : 0.849 15.174 63787 Z= 0.413 Chirality : 0.047 0.373 7342 Planarity : 0.004 0.063 8019 Dihedral : 7.333 178.720 6244 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 4.61 % Allowed : 21.88 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.11), residues: 5688 helix: -0.39 (0.08), residues: 3670 sheet: -1.80 (0.47), residues: 80 loop : -2.92 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F1897 HIS 0.012 0.001 HIS E 318 PHE 0.056 0.002 PHE F 884 TYR 0.038 0.002 TYR E1355 ARG 0.006 0.000 ARG E 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 866 time to evaluate : 4.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 135 VAL cc_start: 0.9142 (m) cc_final: 0.8925 (p) REVERT: F 154 MET cc_start: 0.8032 (tmm) cc_final: 0.7481 (ppp) REVERT: F 186 TYR cc_start: 0.9063 (t80) cc_final: 0.8740 (t80) REVERT: F 289 LEU cc_start: 0.4159 (OUTLIER) cc_final: 0.3538 (tt) REVERT: F 295 MET cc_start: 0.9081 (tpt) cc_final: 0.8232 (ptt) REVERT: F 484 MET cc_start: 0.8758 (mtp) cc_final: 0.8533 (mtt) REVERT: F 539 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8986 (mt) REVERT: F 549 ARG cc_start: 0.9001 (mtt-85) cc_final: 0.8711 (ttm170) REVERT: F 579 ASN cc_start: 0.8802 (t0) cc_final: 0.8577 (t0) REVERT: F 671 ASN cc_start: 0.8889 (m-40) cc_final: 0.8575 (m110) REVERT: F 759 MET cc_start: 0.9254 (tpp) cc_final: 0.8963 (tpp) REVERT: F 767 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7748 (p0) REVERT: F 943 ARG cc_start: 0.8550 (mpt-90) cc_final: 0.7951 (mmt180) REVERT: F 983 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8364 (ptmt) REVERT: F 998 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: F 1099 LEU cc_start: 0.9449 (mt) cc_final: 0.9119 (pp) REVERT: F 1118 LYS cc_start: 0.9391 (ptpt) cc_final: 0.9100 (ptpp) REVERT: F 1126 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6730 (tm) REVERT: F 1142 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6444 (tm-30) REVERT: F 1190 TYR cc_start: 0.7758 (t80) cc_final: 0.7412 (t80) REVERT: F 1245 TYR cc_start: 0.9130 (m-80) cc_final: 0.8799 (m-80) REVERT: F 1353 PHE cc_start: 0.9283 (m-10) cc_final: 0.8890 (m-80) REVERT: F 1488 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8416 (pptt) REVERT: F 1503 MET cc_start: 0.8785 (ttm) cc_final: 0.8420 (ttp) REVERT: F 1527 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7052 (mp) REVERT: F 1536 SER cc_start: 0.8798 (t) cc_final: 0.8481 (t) REVERT: F 1622 MET cc_start: 0.8189 (ttt) cc_final: 0.7924 (ttt) REVERT: F 1711 MET cc_start: 0.8169 (ttm) cc_final: 0.7797 (ttm) REVERT: F 1731 LYS cc_start: 0.8993 (ptmt) cc_final: 0.8762 (mmtm) REVERT: F 1837 PHE cc_start: 0.8631 (m-10) cc_final: 0.8271 (m-80) REVERT: F 1848 LEU cc_start: 0.9099 (mt) cc_final: 0.8898 (mt) REVERT: F 1937 TYR cc_start: 0.9052 (m-80) cc_final: 0.8706 (m-80) REVERT: F 1959 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8598 (mmmt) REVERT: F 2065 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8022 (tp) REVERT: F 2087 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8725 (p0) REVERT: F 2213 MET cc_start: 0.8909 (mmm) cc_final: 0.8636 (mmm) REVERT: F 2247 LEU cc_start: 0.8769 (mt) cc_final: 0.8305 (mp) REVERT: F 2263 ARG cc_start: 0.5377 (tmt-80) cc_final: 0.4688 (tpm170) REVERT: F 2282 LYS cc_start: 0.9261 (tttm) cc_final: 0.8853 (mtpt) REVERT: F 2296 GLU cc_start: 0.8817 (pm20) cc_final: 0.8564 (mm-30) REVERT: F 2360 MET cc_start: 0.7802 (mmm) cc_final: 0.7525 (mmm) REVERT: C 238 LYS cc_start: 0.8886 (tttm) cc_final: 0.8672 (tptp) REVERT: C 278 ILE cc_start: 0.9450 (mt) cc_final: 0.8851 (mm) REVERT: C 303 MET cc_start: 0.8949 (ttm) cc_final: 0.8597 (mtp) REVERT: C 377 ARG cc_start: 0.9034 (mtp180) cc_final: 0.8713 (mtp85) REVERT: C 437 ASN cc_start: 0.8786 (t0) cc_final: 0.8090 (p0) REVERT: C 449 TRP cc_start: 0.7763 (t60) cc_final: 0.7514 (t60) REVERT: C 547 LYS cc_start: 0.9003 (mttt) cc_final: 0.8752 (mttm) REVERT: C 561 MET cc_start: 0.8739 (mmm) cc_final: 0.8428 (mmm) REVERT: C 610 HIS cc_start: 0.9227 (t-170) cc_final: 0.8766 (t-90) REVERT: C 617 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8336 (ptp-110) REVERT: C 664 ARG cc_start: 0.9034 (ptt180) cc_final: 0.8715 (ppt170) REVERT: C 707 ARG cc_start: 0.8588 (ttt180) cc_final: 0.8172 (ttt180) REVERT: C 745 MET cc_start: 0.6878 (ptp) cc_final: 0.6522 (ptp) REVERT: D 238 LYS cc_start: 0.8936 (tttm) cc_final: 0.8699 (tptp) REVERT: D 303 MET cc_start: 0.8572 (mmm) cc_final: 0.8285 (mmm) REVERT: D 317 LEU cc_start: 0.9539 (tt) cc_final: 0.9218 (mp) REVERT: D 324 LEU cc_start: 0.9261 (mm) cc_final: 0.9034 (mm) REVERT: D 328 ASP cc_start: 0.8796 (p0) cc_final: 0.8486 (m-30) REVERT: D 449 TRP cc_start: 0.7871 (t60) cc_final: 0.7591 (t60) REVERT: D 547 LYS cc_start: 0.8900 (mttt) cc_final: 0.8636 (mttm) REVERT: D 575 LEU cc_start: 0.9227 (mt) cc_final: 0.8935 (mp) REVERT: D 609 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8280 (tp30) REVERT: D 610 HIS cc_start: 0.9141 (t-170) cc_final: 0.8825 (t-170) REVERT: D 660 MET cc_start: 0.8895 (mmp) cc_final: 0.8542 (mmt) REVERT: D 664 ARG cc_start: 0.9082 (ptt180) cc_final: 0.8507 (ppt170) REVERT: D 720 MET cc_start: 0.7990 (mtm) cc_final: 0.7587 (ptm) REVERT: E 114 TYR cc_start: 0.8902 (p90) cc_final: 0.8691 (p90) REVERT: E 126 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7773 (mtmt) REVERT: E 154 MET cc_start: 0.8213 (tmm) cc_final: 0.7392 (ppp) REVERT: E 210 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7728 (ptmm) REVERT: E 289 LEU cc_start: 0.4268 (OUTLIER) cc_final: 0.3624 (tt) REVERT: E 295 MET cc_start: 0.9102 (tpt) cc_final: 0.8699 (ptm) REVERT: E 297 LYS cc_start: 0.7741 (mtpp) cc_final: 0.7083 (ttmt) REVERT: E 318 HIS cc_start: 0.8360 (m-70) cc_final: 0.7998 (m-70) REVERT: E 416 ARG cc_start: 0.9222 (mmm160) cc_final: 0.8521 (mmm160) REVERT: E 418 ASN cc_start: 0.9081 (m-40) cc_final: 0.8807 (t0) REVERT: E 458 TRP cc_start: 0.8741 (m100) cc_final: 0.7986 (m100) REVERT: E 469 GLU cc_start: 0.8869 (tp30) cc_final: 0.8552 (tp30) REVERT: E 539 LEU cc_start: 0.9313 (tp) cc_final: 0.9030 (mt) REVERT: E 545 PHE cc_start: 0.9200 (m-80) cc_final: 0.8932 (m-80) REVERT: E 549 ARG cc_start: 0.8975 (mtt-85) cc_final: 0.8359 (mmm-85) REVERT: E 574 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8637 (mm-40) REVERT: E 575 LYS cc_start: 0.9058 (tptm) cc_final: 0.8827 (tptm) REVERT: E 587 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8541 (tt) REVERT: E 668 GLN cc_start: 0.8742 (mm110) cc_final: 0.8383 (mm-40) REVERT: E 691 LEU cc_start: 0.9336 (tp) cc_final: 0.8859 (mt) REVERT: E 768 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7456 (p) REVERT: E 943 ARG cc_start: 0.8475 (mmt90) cc_final: 0.8267 (mmt90) REVERT: E 947 PHE cc_start: 0.9150 (m-80) cc_final: 0.8679 (m-80) REVERT: E 998 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: E 1020 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8123 (tt) REVERT: E 1106 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.8582 (mmt180) REVERT: E 1118 LYS cc_start: 0.9440 (ptpt) cc_final: 0.9148 (ptpp) REVERT: E 1134 LYS cc_start: 0.8257 (tttp) cc_final: 0.7934 (tptt) REVERT: E 1178 LEU cc_start: 0.8747 (mm) cc_final: 0.8454 (mm) REVERT: E 1190 TYR cc_start: 0.7842 (t80) cc_final: 0.7546 (t80) REVERT: E 1297 TYR cc_start: 0.8057 (m-80) cc_final: 0.7438 (m-80) REVERT: E 1351 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8599 (ttp-110) REVERT: E 1353 PHE cc_start: 0.9220 (m-10) cc_final: 0.8974 (m-80) REVERT: E 1485 VAL cc_start: 0.9266 (m) cc_final: 0.8845 (m) REVERT: E 1488 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8418 (pptt) REVERT: E 1527 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7437 (mp) REVERT: E 1536 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8361 (t) REVERT: E 1615 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8704 (mt) REVERT: E 1666 ILE cc_start: 0.9060 (pp) cc_final: 0.8850 (pp) REVERT: E 1731 LYS cc_start: 0.9040 (ptmt) cc_final: 0.8723 (mmtm) REVERT: E 1837 PHE cc_start: 0.8424 (m-10) cc_final: 0.8223 (m-80) REVERT: E 1897 TRP cc_start: 0.8067 (m100) cc_final: 0.7824 (m-10) REVERT: E 2038 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6838 (tm130) REVERT: E 2040 PHE cc_start: 0.6691 (m-80) cc_final: 0.5753 (m-80) REVERT: E 2087 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8485 (p0) REVERT: E 2093 PHE cc_start: 0.9306 (t80) cc_final: 0.9025 (t80) REVERT: E 2174 TYR cc_start: 0.8329 (t80) cc_final: 0.8125 (t80) REVERT: E 2176 GLU cc_start: 0.9219 (tt0) cc_final: 0.8927 (tm-30) REVERT: E 2210 TYR cc_start: 0.8817 (t80) cc_final: 0.8395 (t80) REVERT: E 2213 MET cc_start: 0.9114 (mmm) cc_final: 0.8849 (mmm) REVERT: E 2247 LEU cc_start: 0.8762 (mt) cc_final: 0.8264 (mp) REVERT: E 2263 ARG cc_start: 0.5014 (tmt-80) cc_final: 0.4205 (tpm170) REVERT: E 2282 LYS cc_start: 0.9280 (tttm) cc_final: 0.8812 (mtpp) REVERT: E 2357 LEU cc_start: 0.9054 (mt) cc_final: 0.8800 (pp) REVERT: E 2364 TRP cc_start: 0.8852 (t60) cc_final: 0.8615 (t60) outliers start: 231 outliers final: 139 residues processed: 1019 average time/residue: 0.4848 time to fit residues: 827.0375 Evaluate side-chains 957 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 791 time to evaluate : 4.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 956 HIS Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 978 SER Chi-restraints excluded: chain F residue 983 LYS Chi-restraints excluded: chain F residue 998 GLU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1106 ARG Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1200 MET Chi-restraints excluded: chain F residue 1233 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1382 THR Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1411 GLU Chi-restraints excluded: chain F residue 1434 LEU Chi-restraints excluded: chain F residue 1435 LEU Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1890 GLN Chi-restraints excluded: chain F residue 1901 LEU Chi-restraints excluded: chain F residue 1942 VAL Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2230 ILE Chi-restraints excluded: chain F residue 2291 LEU Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 149 HIS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 654 PHE Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 885 GLN Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 978 SER Chi-restraints excluded: chain E residue 998 GLU Chi-restraints excluded: chain E residue 1020 LEU Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1093 LEU Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1114 GLU Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1351 ARG Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1382 THR Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1399 LEU Chi-restraints excluded: chain E residue 1411 GLU Chi-restraints excluded: chain E residue 1434 LEU Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1527 LEU Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1614 LEU Chi-restraints excluded: chain E residue 1615 LEU Chi-restraints excluded: chain E residue 1633 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1676 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1769 GLU Chi-restraints excluded: chain E residue 1901 LEU Chi-restraints excluded: chain E residue 1905 LEU Chi-restraints excluded: chain E residue 1942 VAL Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2206 TYR Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2291 LEU Chi-restraints excluded: chain E residue 2323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 533 optimal weight: 0.0980 chunk 62 optimal weight: 9.9990 chunk 315 optimal weight: 20.0000 chunk 404 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 465 optimal weight: 0.7980 chunk 309 optimal weight: 3.9990 chunk 551 optimal weight: 6.9990 chunk 345 optimal weight: 7.9990 chunk 336 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 GLN ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS D 334 HIS ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 HIS E 574 GLN ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1217 ASN ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 47082 Z= 0.221 Angle : 0.864 15.347 63787 Z= 0.415 Chirality : 0.048 0.386 7342 Planarity : 0.004 0.063 8019 Dihedral : 7.213 178.787 6244 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 4.21 % Allowed : 23.09 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.11), residues: 5688 helix: -0.31 (0.08), residues: 3672 sheet: -1.76 (0.48), residues: 80 loop : -2.89 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F1897 HIS 0.027 0.001 HIS E 548 PHE 0.047 0.002 PHE E1350 TYR 0.031 0.002 TYR E1786 ARG 0.007 0.000 ARG F1387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 852 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 154 MET cc_start: 0.7927 (tmm) cc_final: 0.7343 (ppp) REVERT: F 186 TYR cc_start: 0.9078 (t80) cc_final: 0.8794 (t80) REVERT: F 211 PHE cc_start: 0.8204 (t80) cc_final: 0.7983 (t80) REVERT: F 289 LEU cc_start: 0.4134 (OUTLIER) cc_final: 0.3486 (tt) REVERT: F 484 MET cc_start: 0.8727 (mtp) cc_final: 0.8497 (mtt) REVERT: F 539 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8981 (mt) REVERT: F 549 ARG cc_start: 0.8890 (mtt-85) cc_final: 0.8672 (ttm170) REVERT: F 579 ASN cc_start: 0.8779 (t0) cc_final: 0.8518 (t0) REVERT: F 668 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8876 (mm110) REVERT: F 671 ASN cc_start: 0.8750 (m-40) cc_final: 0.8424 (m110) REVERT: F 759 MET cc_start: 0.9247 (tpp) cc_final: 0.8975 (tpp) REVERT: F 767 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7745 (p0) REVERT: F 937 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8417 (mm) REVERT: F 952 LEU cc_start: 0.9221 (pp) cc_final: 0.8957 (mm) REVERT: F 983 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8423 (ptmt) REVERT: F 998 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: F 1099 LEU cc_start: 0.9457 (mt) cc_final: 0.9122 (pp) REVERT: F 1118 LYS cc_start: 0.9349 (ptpt) cc_final: 0.9075 (ptpp) REVERT: F 1126 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6746 (tm) REVERT: F 1142 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6417 (tm-30) REVERT: F 1190 TYR cc_start: 0.7658 (t80) cc_final: 0.7309 (t80) REVERT: F 1334 MET cc_start: 0.3923 (ptt) cc_final: 0.3597 (ptt) REVERT: F 1351 ARG cc_start: 0.9190 (ptm-80) cc_final: 0.8717 (ttp80) REVERT: F 1353 PHE cc_start: 0.9301 (m-10) cc_final: 0.8897 (m-80) REVERT: F 1488 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8374 (pptt) REVERT: F 1503 MET cc_start: 0.8782 (ttm) cc_final: 0.8418 (ttp) REVERT: F 1527 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7057 (mp) REVERT: F 1536 SER cc_start: 0.8759 (t) cc_final: 0.8452 (t) REVERT: F 1711 MET cc_start: 0.8271 (ttm) cc_final: 0.8035 (ttm) REVERT: F 1837 PHE cc_start: 0.8625 (m-10) cc_final: 0.8270 (m-80) REVERT: F 1937 TYR cc_start: 0.9067 (m-80) cc_final: 0.8734 (m-80) REVERT: F 2008 MET cc_start: 0.7723 (tmm) cc_final: 0.7153 (mtt) REVERT: F 2040 PHE cc_start: 0.6571 (m-80) cc_final: 0.6282 (m-80) REVERT: F 2065 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8042 (tp) REVERT: F 2087 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8712 (p0) REVERT: F 2093 PHE cc_start: 0.9292 (t80) cc_final: 0.9030 (t80) REVERT: F 2213 MET cc_start: 0.8844 (mmm) cc_final: 0.8590 (mmm) REVERT: F 2222 LEU cc_start: 0.9102 (pt) cc_final: 0.8764 (tt) REVERT: F 2247 LEU cc_start: 0.8811 (mt) cc_final: 0.8392 (mp) REVERT: F 2282 LYS cc_start: 0.9237 (tttm) cc_final: 0.8824 (mtpt) REVERT: F 2296 GLU cc_start: 0.8761 (pm20) cc_final: 0.8536 (mm-30) REVERT: F 2301 ASN cc_start: 0.8630 (m110) cc_final: 0.8263 (p0) REVERT: F 2350 GLU cc_start: 0.8891 (pt0) cc_final: 0.8625 (tt0) REVERT: C 238 LYS cc_start: 0.8867 (tttm) cc_final: 0.8624 (tptp) REVERT: C 278 ILE cc_start: 0.9429 (mt) cc_final: 0.8941 (mm) REVERT: C 303 MET cc_start: 0.8898 (ttm) cc_final: 0.8546 (mmm) REVERT: C 377 ARG cc_start: 0.8985 (mtp180) cc_final: 0.7826 (mmm160) REVERT: C 437 ASN cc_start: 0.8813 (t0) cc_final: 0.8205 (p0) REVERT: C 449 TRP cc_start: 0.7802 (t60) cc_final: 0.7491 (t60) REVERT: C 547 LYS cc_start: 0.9010 (mttt) cc_final: 0.8761 (mttm) REVERT: C 610 HIS cc_start: 0.9209 (t-170) cc_final: 0.8728 (t-170) REVERT: C 660 MET cc_start: 0.9059 (mmm) cc_final: 0.8854 (mmm) REVERT: C 664 ARG cc_start: 0.9051 (ptt180) cc_final: 0.8728 (ppt170) REVERT: C 707 ARG cc_start: 0.8582 (ttt180) cc_final: 0.8075 (ttt180) REVERT: C 745 MET cc_start: 0.6829 (ptp) cc_final: 0.6421 (ptp) REVERT: D 238 LYS cc_start: 0.8934 (tttm) cc_final: 0.8672 (tptp) REVERT: D 317 LEU cc_start: 0.9540 (tt) cc_final: 0.9192 (mp) REVERT: D 449 TRP cc_start: 0.7874 (t60) cc_final: 0.7583 (t60) REVERT: D 547 LYS cc_start: 0.8887 (mttt) cc_final: 0.8627 (mttm) REVERT: D 560 LEU cc_start: 0.9410 (mm) cc_final: 0.9041 (mm) REVERT: D 575 LEU cc_start: 0.9211 (mt) cc_final: 0.8668 (mp) REVERT: D 609 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8276 (tp30) REVERT: D 610 HIS cc_start: 0.9146 (t-170) cc_final: 0.8816 (t-170) REVERT: D 660 MET cc_start: 0.8856 (mmp) cc_final: 0.8478 (mmt) REVERT: D 661 ARG cc_start: 0.8874 (ptp-170) cc_final: 0.8589 (ptp90) REVERT: D 664 ARG cc_start: 0.8983 (ptt180) cc_final: 0.8369 (ptt90) REVERT: D 720 MET cc_start: 0.8004 (mtm) cc_final: 0.7566 (ptm) REVERT: E 126 LYS cc_start: 0.7997 (mtmt) cc_final: 0.7717 (mtmt) REVERT: E 135 VAL cc_start: 0.9090 (m) cc_final: 0.8857 (p) REVERT: E 154 MET cc_start: 0.8180 (tmm) cc_final: 0.7667 (ppp) REVERT: E 208 PHE cc_start: 0.7400 (t80) cc_final: 0.6211 (t80) REVERT: E 210 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7774 (ptmm) REVERT: E 289 LEU cc_start: 0.4176 (OUTLIER) cc_final: 0.3443 (tt) REVERT: E 295 MET cc_start: 0.9070 (tpt) cc_final: 0.8668 (ptm) REVERT: E 297 LYS cc_start: 0.7716 (mtpp) cc_final: 0.7048 (ttmt) REVERT: E 418 ASN cc_start: 0.9076 (m-40) cc_final: 0.8842 (t0) REVERT: E 458 TRP cc_start: 0.8752 (m100) cc_final: 0.7977 (m100) REVERT: E 469 GLU cc_start: 0.8834 (tp30) cc_final: 0.8490 (tp30) REVERT: E 539 LEU cc_start: 0.9322 (tp) cc_final: 0.9061 (mt) REVERT: E 545 PHE cc_start: 0.9100 (m-80) cc_final: 0.8795 (m-80) REVERT: E 549 ARG cc_start: 0.8938 (mtt-85) cc_final: 0.8256 (mmm-85) REVERT: E 574 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8769 (mm-40) REVERT: E 575 LYS cc_start: 0.8989 (tptm) cc_final: 0.8734 (tptm) REVERT: E 587 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8462 (tt) REVERT: E 668 GLN cc_start: 0.8784 (mm110) cc_final: 0.8357 (mm-40) REVERT: E 691 LEU cc_start: 0.9338 (tp) cc_final: 0.8934 (mt) REVERT: E 718 LYS cc_start: 0.8966 (tttt) cc_final: 0.8723 (mtpt) REVERT: E 768 SER cc_start: 0.8122 (OUTLIER) cc_final: 0.7721 (p) REVERT: E 947 PHE cc_start: 0.9139 (m-80) cc_final: 0.8697 (m-80) REVERT: E 998 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8508 (pm20) REVERT: E 1020 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8162 (tt) REVERT: E 1099 LEU cc_start: 0.9247 (mm) cc_final: 0.8924 (pp) REVERT: E 1106 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.8642 (mmt180) REVERT: E 1118 LYS cc_start: 0.9446 (ptpt) cc_final: 0.9121 (ptpp) REVERT: E 1134 LYS cc_start: 0.8238 (tttp) cc_final: 0.7920 (tptt) REVERT: E 1178 LEU cc_start: 0.8815 (mm) cc_final: 0.8524 (mm) REVERT: E 1190 TYR cc_start: 0.7881 (t80) cc_final: 0.7591 (t80) REVERT: E 1297 TYR cc_start: 0.8093 (m-80) cc_final: 0.7431 (m-80) REVERT: E 1334 MET cc_start: 0.4037 (ptt) cc_final: 0.3821 (ptt) REVERT: E 1351 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8781 (ptm-80) REVERT: E 1488 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8382 (pptt) REVERT: E 1527 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7369 (mp) REVERT: E 1536 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8352 (t) REVERT: E 1615 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8776 (mt) REVERT: E 1666 ILE cc_start: 0.8926 (pp) cc_final: 0.8716 (pp) REVERT: E 1724 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: E 1727 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8404 (pt0) REVERT: E 1897 TRP cc_start: 0.8071 (m100) cc_final: 0.7822 (m-10) REVERT: E 2020 ARG cc_start: 0.8793 (ptt180) cc_final: 0.8492 (ttp-170) REVERT: E 2038 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6720 (tm130) REVERT: E 2040 PHE cc_start: 0.6783 (m-80) cc_final: 0.5856 (m-80) REVERT: E 2087 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8451 (p0) REVERT: E 2093 PHE cc_start: 0.9314 (t80) cc_final: 0.9078 (t80) REVERT: E 2174 TYR cc_start: 0.8420 (t80) cc_final: 0.8218 (t80) REVERT: E 2176 GLU cc_start: 0.9209 (tt0) cc_final: 0.8922 (tm-30) REVERT: E 2213 MET cc_start: 0.9081 (mmm) cc_final: 0.8793 (mmm) REVERT: E 2247 LEU cc_start: 0.8739 (mt) cc_final: 0.8261 (mp) REVERT: E 2263 ARG cc_start: 0.5029 (tmt-80) cc_final: 0.4178 (tpm170) REVERT: E 2282 LYS cc_start: 0.9276 (tttm) cc_final: 0.8830 (mtpp) REVERT: E 2296 GLU cc_start: 0.8817 (pm20) cc_final: 0.8435 (mt-10) REVERT: E 2301 ASN cc_start: 0.8604 (m110) cc_final: 0.8201 (p0) REVERT: E 2350 GLU cc_start: 0.8891 (tt0) cc_final: 0.8487 (pt0) REVERT: E 2357 LEU cc_start: 0.9079 (mt) cc_final: 0.8832 (pp) REVERT: E 2364 TRP cc_start: 0.8875 (t60) cc_final: 0.8581 (t60) outliers start: 211 outliers final: 139 residues processed: 995 average time/residue: 0.4648 time to fit residues: 773.6914 Evaluate side-chains 962 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 794 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 687 ILE Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 937 LEU Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 956 HIS Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 978 SER Chi-restraints excluded: chain F residue 983 LYS Chi-restraints excluded: chain F residue 998 GLU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1106 ARG Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1200 MET Chi-restraints excluded: chain F residue 1233 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1382 THR Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1411 GLU Chi-restraints excluded: chain F residue 1434 LEU Chi-restraints excluded: chain F residue 1435 LEU Chi-restraints excluded: chain F residue 1452 ASP Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1614 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1901 LEU Chi-restraints excluded: chain F residue 1905 LEU Chi-restraints excluded: chain F residue 1942 VAL Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2077 ILE Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2172 GLU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2230 ILE Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 654 PHE Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 885 GLN Chi-restraints excluded: chain E residue 939 LEU Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 978 SER Chi-restraints excluded: chain E residue 998 GLU Chi-restraints excluded: chain E residue 1020 LEU Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1093 LEU Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1114 GLU Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1200 MET Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1351 ARG Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1382 THR Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1399 LEU Chi-restraints excluded: chain E residue 1411 GLU Chi-restraints excluded: chain E residue 1434 LEU Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1527 LEU Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1614 LEU Chi-restraints excluded: chain E residue 1615 LEU Chi-restraints excluded: chain E residue 1633 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1724 GLU Chi-restraints excluded: chain E residue 1727 GLU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1769 GLU Chi-restraints excluded: chain E residue 1874 LEU Chi-restraints excluded: chain E residue 1901 LEU Chi-restraints excluded: chain E residue 1905 LEU Chi-restraints excluded: chain E residue 1942 VAL Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2358 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 341 optimal weight: 30.0000 chunk 220 optimal weight: 2.9990 chunk 329 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 350 optimal weight: 10.0000 chunk 375 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 433 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1618 GLN ** F1732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS D 334 HIS D 437 ASN ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 HIS E 574 GLN E 928 GLN ** E1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 47082 Z= 0.251 Angle : 0.883 19.044 63787 Z= 0.427 Chirality : 0.049 0.387 7342 Planarity : 0.005 0.062 8019 Dihedral : 7.184 176.917 6244 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 23.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 4.51 % Allowed : 23.60 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.11), residues: 5688 helix: -0.32 (0.08), residues: 3678 sheet: -1.72 (0.49), residues: 80 loop : -2.79 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F1897 HIS 0.029 0.001 HIS C 334 PHE 0.046 0.002 PHE E1350 TYR 0.031 0.002 TYR E1786 ARG 0.012 0.001 ARG F1387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 818 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 154 MET cc_start: 0.7905 (tmm) cc_final: 0.7700 (tmm) REVERT: F 289 LEU cc_start: 0.4319 (OUTLIER) cc_final: 0.3694 (tt) REVERT: F 295 MET cc_start: 0.9268 (tpp) cc_final: 0.8474 (ptm) REVERT: F 416 ARG cc_start: 0.9429 (mmm160) cc_final: 0.8736 (mmm160) REVERT: F 484 MET cc_start: 0.8759 (mtp) cc_final: 0.8512 (mtt) REVERT: F 539 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9019 (mt) REVERT: F 549 ARG cc_start: 0.8763 (mtt-85) cc_final: 0.8538 (ttm170) REVERT: F 551 PHE cc_start: 0.8794 (m-80) cc_final: 0.8428 (m-80) REVERT: F 575 LYS cc_start: 0.8578 (tptt) cc_final: 0.8252 (tttt) REVERT: F 579 ASN cc_start: 0.8802 (t0) cc_final: 0.8520 (t0) REVERT: F 590 ARG cc_start: 0.9012 (mmm-85) cc_final: 0.8801 (mtm-85) REVERT: F 671 ASN cc_start: 0.8764 (m-40) cc_final: 0.8478 (m110) REVERT: F 759 MET cc_start: 0.9263 (tpp) cc_final: 0.8966 (tpp) REVERT: F 767 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7873 (p0) REVERT: F 937 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8454 (mm) REVERT: F 952 LEU cc_start: 0.9239 (pp) cc_final: 0.8999 (mm) REVERT: F 983 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8451 (ptmt) REVERT: F 998 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: F 1118 LYS cc_start: 0.9393 (ptpt) cc_final: 0.9104 (ptpp) REVERT: F 1126 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6821 (tm) REVERT: F 1142 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6470 (tm-30) REVERT: F 1190 TYR cc_start: 0.7692 (t80) cc_final: 0.7272 (t80) REVERT: F 1334 MET cc_start: 0.4131 (ptt) cc_final: 0.3814 (ptt) REVERT: F 1351 ARG cc_start: 0.9220 (ptm-80) cc_final: 0.8995 (ptm160) REVERT: F 1353 PHE cc_start: 0.9281 (m-10) cc_final: 0.8870 (m-80) REVERT: F 1485 VAL cc_start: 0.9237 (m) cc_final: 0.9017 (m) REVERT: F 1488 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8412 (pptt) REVERT: F 1503 MET cc_start: 0.8756 (ttm) cc_final: 0.8441 (ttp) REVERT: F 1527 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7064 (mp) REVERT: F 1536 SER cc_start: 0.8786 (t) cc_final: 0.8470 (t) REVERT: F 1837 PHE cc_start: 0.8573 (m-10) cc_final: 0.8243 (m-80) REVERT: F 1937 TYR cc_start: 0.9132 (m-80) cc_final: 0.8839 (m-80) REVERT: F 1959 LYS cc_start: 0.8837 (mtmt) cc_final: 0.8513 (mmmt) REVERT: F 2040 PHE cc_start: 0.6597 (m-80) cc_final: 0.6282 (m-80) REVERT: F 2065 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8001 (tp) REVERT: F 2087 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8769 (p0) REVERT: F 2093 PHE cc_start: 0.9321 (t80) cc_final: 0.9003 (t80) REVERT: F 2213 MET cc_start: 0.8955 (mmm) cc_final: 0.8694 (mmm) REVERT: F 2222 LEU cc_start: 0.8993 (pt) cc_final: 0.8705 (tt) REVERT: F 2263 ARG cc_start: 0.5650 (tpm170) cc_final: 0.4942 (tpm170) REVERT: F 2282 LYS cc_start: 0.9241 (tttm) cc_final: 0.8781 (mtpt) REVERT: F 2349 GLN cc_start: 0.8914 (mp10) cc_final: 0.8665 (mm-40) REVERT: C 238 LYS cc_start: 0.8888 (tttm) cc_final: 0.8616 (tptp) REVERT: C 317 LEU cc_start: 0.9542 (tt) cc_final: 0.9191 (mp) REVERT: C 377 ARG cc_start: 0.9034 (mtp180) cc_final: 0.8729 (mmm-85) REVERT: C 437 ASN cc_start: 0.8786 (t0) cc_final: 0.8152 (p0) REVERT: C 449 TRP cc_start: 0.7801 (t60) cc_final: 0.7447 (t60) REVERT: C 610 HIS cc_start: 0.9235 (t-170) cc_final: 0.8788 (t-90) REVERT: C 664 ARG cc_start: 0.9054 (ptt180) cc_final: 0.8724 (ppt170) REVERT: C 707 ARG cc_start: 0.8547 (ttt180) cc_final: 0.8141 (ttt180) REVERT: C 720 MET cc_start: 0.7868 (mtp) cc_final: 0.7400 (mtm) REVERT: C 745 MET cc_start: 0.6983 (ptp) cc_final: 0.6527 (ptp) REVERT: D 238 LYS cc_start: 0.8964 (tttm) cc_final: 0.8721 (tptp) REVERT: D 303 MET cc_start: 0.8614 (mmm) cc_final: 0.8395 (mmm) REVERT: D 317 LEU cc_start: 0.9537 (tt) cc_final: 0.9197 (mp) REVERT: D 449 TRP cc_start: 0.7840 (t60) cc_final: 0.7518 (t60) REVERT: D 547 LYS cc_start: 0.8904 (mttt) cc_final: 0.8657 (mttm) REVERT: D 575 LEU cc_start: 0.9297 (mt) cc_final: 0.8907 (mp) REVERT: D 609 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8253 (tp30) REVERT: D 610 HIS cc_start: 0.9186 (t-170) cc_final: 0.8859 (t-170) REVERT: D 660 MET cc_start: 0.8856 (mmp) cc_final: 0.8476 (mmt) REVERT: D 661 ARG cc_start: 0.8928 (ptp-170) cc_final: 0.8625 (ptp90) REVERT: D 664 ARG cc_start: 0.9022 (ptt180) cc_final: 0.8418 (ptt90) REVERT: D 720 MET cc_start: 0.8039 (mtm) cc_final: 0.7585 (ptm) REVERT: E 126 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7708 (mtmt) REVERT: E 135 VAL cc_start: 0.9159 (m) cc_final: 0.8943 (p) REVERT: E 154 MET cc_start: 0.8154 (tmm) cc_final: 0.7546 (ppp) REVERT: E 210 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7817 (ptmm) REVERT: E 242 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8209 (mmtt) REVERT: E 295 MET cc_start: 0.9134 (tpt) cc_final: 0.8699 (ptm) REVERT: E 297 LYS cc_start: 0.7673 (mtpp) cc_final: 0.6976 (ttpp) REVERT: E 416 ARG cc_start: 0.9285 (mmm160) cc_final: 0.8611 (mmm160) REVERT: E 458 TRP cc_start: 0.8756 (m100) cc_final: 0.7977 (m100) REVERT: E 469 GLU cc_start: 0.8939 (tp30) cc_final: 0.8620 (tp30) REVERT: E 539 LEU cc_start: 0.9323 (tp) cc_final: 0.9079 (mt) REVERT: E 549 ARG cc_start: 0.8936 (mtt-85) cc_final: 0.8357 (mmm-85) REVERT: E 570 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.9155 (t80) REVERT: E 574 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8733 (mm-40) REVERT: E 668 GLN cc_start: 0.8843 (mm110) cc_final: 0.8474 (mm-40) REVERT: E 691 LEU cc_start: 0.9338 (tp) cc_final: 0.8913 (mt) REVERT: E 718 LYS cc_start: 0.8961 (tttt) cc_final: 0.8709 (mtpt) REVERT: E 947 PHE cc_start: 0.9163 (m-80) cc_final: 0.8700 (m-80) REVERT: E 998 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8420 (pm20) REVERT: E 1020 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8183 (tt) REVERT: E 1099 LEU cc_start: 0.9262 (mm) cc_final: 0.8911 (pp) REVERT: E 1106 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8541 (mmt-90) REVERT: E 1118 LYS cc_start: 0.9471 (ptpt) cc_final: 0.9178 (ptpt) REVERT: E 1134 LYS cc_start: 0.8211 (tttp) cc_final: 0.7933 (tptt) REVERT: E 1178 LEU cc_start: 0.8860 (mm) cc_final: 0.8628 (mm) REVERT: E 1190 TYR cc_start: 0.7916 (t80) cc_final: 0.7643 (t80) REVERT: E 1297 TYR cc_start: 0.8118 (m-80) cc_final: 0.7457 (m-80) REVERT: E 1334 MET cc_start: 0.4294 (ptt) cc_final: 0.4083 (ptt) REVERT: E 1351 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8652 (ttp-110) REVERT: E 1488 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8373 (pptt) REVERT: E 1527 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7373 (mp) REVERT: E 1666 ILE cc_start: 0.8955 (pp) cc_final: 0.8749 (pp) REVERT: E 1711 MET cc_start: 0.7781 (ttm) cc_final: 0.6940 (ppp) REVERT: E 1724 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: E 1727 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8525 (pt0) REVERT: E 1769 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: E 1837 PHE cc_start: 0.8412 (m-10) cc_final: 0.8194 (m-80) REVERT: E 2020 ARG cc_start: 0.8813 (ptt180) cc_final: 0.8531 (ttp-170) REVERT: E 2038 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6789 (tm130) REVERT: E 2040 PHE cc_start: 0.6709 (m-80) cc_final: 0.5767 (m-80) REVERT: E 2087 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8492 (p0) REVERT: E 2093 PHE cc_start: 0.9325 (t80) cc_final: 0.8735 (t80) REVERT: E 2176 GLU cc_start: 0.9223 (tt0) cc_final: 0.8940 (tm-30) REVERT: E 2213 MET cc_start: 0.9112 (mmm) cc_final: 0.8818 (mmm) REVERT: E 2226 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8586 (t-90) REVERT: E 2263 ARG cc_start: 0.5034 (tmt-80) cc_final: 0.4122 (tpm170) REVERT: E 2282 LYS cc_start: 0.9306 (tttm) cc_final: 0.8869 (mtpp) REVERT: E 2292 MET cc_start: 0.8509 (ptp) cc_final: 0.8271 (ptp) REVERT: E 2296 GLU cc_start: 0.8927 (pm20) cc_final: 0.8366 (mt-10) REVERT: E 2301 ASN cc_start: 0.8618 (m110) cc_final: 0.8239 (p0) REVERT: E 2350 GLU cc_start: 0.8883 (tt0) cc_final: 0.8435 (pt0) REVERT: E 2364 TRP cc_start: 0.8969 (t60) cc_final: 0.8688 (t60) outliers start: 226 outliers final: 149 residues processed: 982 average time/residue: 0.4803 time to fit residues: 791.0253 Evaluate side-chains 949 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 773 time to evaluate : 4.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 250 TYR Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 687 ILE Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 937 LEU Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 956 HIS Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 978 SER Chi-restraints excluded: chain F residue 983 LYS Chi-restraints excluded: chain F residue 998 GLU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1094 VAL Chi-restraints excluded: chain F residue 1106 ARG Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1200 MET Chi-restraints excluded: chain F residue 1233 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1370 LEU Chi-restraints excluded: chain F residue 1382 THR Chi-restraints excluded: chain F residue 1390 GLU Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1411 GLU Chi-restraints excluded: chain F residue 1434 LEU Chi-restraints excluded: chain F residue 1435 LEU Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1571 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1727 GLU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1769 GLU Chi-restraints excluded: chain F residue 1901 LEU Chi-restraints excluded: chain F residue 1905 LEU Chi-restraints excluded: chain F residue 1942 VAL Chi-restraints excluded: chain F residue 2065 LEU Chi-restraints excluded: chain F residue 2077 ILE Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2172 GLU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2230 ILE Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 654 PHE Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 884 PHE Chi-restraints excluded: chain E residue 928 GLN Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 978 SER Chi-restraints excluded: chain E residue 998 GLU Chi-restraints excluded: chain E residue 1020 LEU Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1093 LEU Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1200 MET Chi-restraints excluded: chain E residue 1217 ASN Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1350 PHE Chi-restraints excluded: chain E residue 1351 ARG Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1370 LEU Chi-restraints excluded: chain E residue 1382 THR Chi-restraints excluded: chain E residue 1389 ASP Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1405 LEU Chi-restraints excluded: chain E residue 1411 GLU Chi-restraints excluded: chain E residue 1434 LEU Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1527 LEU Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1614 LEU Chi-restraints excluded: chain E residue 1633 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1724 GLU Chi-restraints excluded: chain E residue 1727 GLU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1769 GLU Chi-restraints excluded: chain E residue 1874 LEU Chi-restraints excluded: chain E residue 1901 LEU Chi-restraints excluded: chain E residue 1905 LEU Chi-restraints excluded: chain E residue 1942 VAL Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2206 TYR Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2304 GLU Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2344 THR Chi-restraints excluded: chain E residue 2358 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 501 optimal weight: 1.9990 chunk 528 optimal weight: 9.9990 chunk 481 optimal weight: 2.9990 chunk 513 optimal weight: 10.0000 chunk 309 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 403 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 464 optimal weight: 3.9990 chunk 485 optimal weight: 0.9980 chunk 511 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 HIS ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 GLN ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1431 ASN ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS D 334 HIS D 437 ASN ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 525 ASN E 548 HIS E 574 GLN E 928 GLN ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 47082 Z= 0.236 Angle : 0.904 18.205 63787 Z= 0.433 Chirality : 0.049 0.379 7342 Planarity : 0.004 0.062 8019 Dihedral : 7.143 178.356 6244 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.74 % Allowed : 24.54 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.11), residues: 5688 helix: -0.32 (0.08), residues: 3686 sheet: -1.51 (0.52), residues: 80 loop : -2.78 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F1897 HIS 0.011 0.001 HIS C 334 PHE 0.046 0.002 PHE E1350 TYR 0.032 0.002 TYR F 175 ARG 0.011 0.001 ARG F1387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 825 time to evaluate : 4.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 126 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7327 (tppt) REVERT: F 154 MET cc_start: 0.7969 (tmm) cc_final: 0.7471 (ppp) REVERT: F 211 PHE cc_start: 0.8122 (t80) cc_final: 0.7915 (t80) REVERT: F 289 LEU cc_start: 0.3883 (OUTLIER) cc_final: 0.3080 (tt) REVERT: F 295 MET cc_start: 0.9286 (tpp) cc_final: 0.8479 (ptm) REVERT: F 416 ARG cc_start: 0.9430 (mmm160) cc_final: 0.8730 (mmm160) REVERT: F 484 MET cc_start: 0.8742 (mtp) cc_final: 0.8483 (mtm) REVERT: F 539 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9055 (mt) REVERT: F 549 ARG cc_start: 0.8787 (mtt-85) cc_final: 0.8145 (mmt90) REVERT: F 551 PHE cc_start: 0.8758 (m-80) cc_final: 0.8442 (m-80) REVERT: F 575 LYS cc_start: 0.8622 (tptt) cc_final: 0.8254 (tttt) REVERT: F 579 ASN cc_start: 0.8728 (t0) cc_final: 0.8462 (t0) REVERT: F 664 MET cc_start: 0.8049 (ttm) cc_final: 0.7790 (ttm) REVERT: F 671 ASN cc_start: 0.8655 (m-40) cc_final: 0.8395 (m110) REVERT: F 691 LEU cc_start: 0.9236 (tp) cc_final: 0.8754 (mt) REVERT: F 759 MET cc_start: 0.9243 (tpp) cc_final: 0.8989 (tpp) REVERT: F 767 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7891 (p0) REVERT: F 937 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8492 (mm) REVERT: F 947 PHE cc_start: 0.8979 (m-80) cc_final: 0.8718 (m-80) REVERT: F 952 LEU cc_start: 0.9235 (pp) cc_final: 0.9002 (mm) REVERT: F 983 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8463 (ptmt) REVERT: F 998 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: F 1118 LYS cc_start: 0.9400 (ptpt) cc_final: 0.9132 (ptpp) REVERT: F 1126 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6741 (tm) REVERT: F 1142 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6500 (tm-30) REVERT: F 1334 MET cc_start: 0.3898 (ptt) cc_final: 0.3566 (ptt) REVERT: F 1353 PHE cc_start: 0.9297 (m-10) cc_final: 0.8879 (m-80) REVERT: F 1488 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8387 (pptt) REVERT: F 1503 MET cc_start: 0.8756 (ttm) cc_final: 0.8436 (ttp) REVERT: F 1527 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7018 (mp) REVERT: F 1536 SER cc_start: 0.8746 (t) cc_final: 0.8442 (t) REVERT: F 1837 PHE cc_start: 0.8593 (m-10) cc_final: 0.8278 (m-80) REVERT: F 1937 TYR cc_start: 0.9097 (m-80) cc_final: 0.8738 (m-80) REVERT: F 1959 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8501 (mmmt) REVERT: F 2008 MET cc_start: 0.8049 (tmm) cc_final: 0.7361 (mtt) REVERT: F 2040 PHE cc_start: 0.6586 (m-80) cc_final: 0.6313 (m-80) REVERT: F 2087 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8693 (p0) REVERT: F 2093 PHE cc_start: 0.9307 (t80) cc_final: 0.8604 (t80) REVERT: F 2213 MET cc_start: 0.8957 (mmm) cc_final: 0.8687 (mmm) REVERT: F 2222 LEU cc_start: 0.8855 (pt) cc_final: 0.8617 (tp) REVERT: F 2247 LEU cc_start: 0.8861 (mt) cc_final: 0.8533 (mp) REVERT: F 2263 ARG cc_start: 0.5560 (tpm170) cc_final: 0.4816 (tpm170) REVERT: F 2282 LYS cc_start: 0.9204 (tttm) cc_final: 0.8809 (mtpp) REVERT: F 2296 GLU cc_start: 0.8913 (pm20) cc_final: 0.8638 (mm-30) REVERT: C 238 LYS cc_start: 0.8873 (tttm) cc_final: 0.8636 (tptp) REVERT: C 335 HIS cc_start: 0.7442 (p-80) cc_final: 0.6006 (t-170) REVERT: C 437 ASN cc_start: 0.8710 (t0) cc_final: 0.7865 (p0) REVERT: C 449 TRP cc_start: 0.7836 (t60) cc_final: 0.7469 (t60) REVERT: C 610 HIS cc_start: 0.9238 (t-170) cc_final: 0.8797 (t-90) REVERT: C 660 MET cc_start: 0.8990 (mmm) cc_final: 0.8754 (mmt) REVERT: C 664 ARG cc_start: 0.8960 (ptt180) cc_final: 0.8681 (ppt170) REVERT: C 707 ARG cc_start: 0.8545 (ttt180) cc_final: 0.8136 (ttt180) REVERT: C 745 MET cc_start: 0.6898 (ptp) cc_final: 0.6484 (ptp) REVERT: D 238 LYS cc_start: 0.8926 (tttm) cc_final: 0.8627 (tptp) REVERT: D 303 MET cc_start: 0.8630 (mmm) cc_final: 0.8400 (mmm) REVERT: D 317 LEU cc_start: 0.9526 (tt) cc_final: 0.9183 (mp) REVERT: D 449 TRP cc_start: 0.7829 (t60) cc_final: 0.7468 (t60) REVERT: D 547 LYS cc_start: 0.8888 (mttt) cc_final: 0.8654 (mttm) REVERT: D 609 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8231 (tp30) REVERT: D 610 HIS cc_start: 0.9195 (t-170) cc_final: 0.8791 (t-170) REVERT: D 660 MET cc_start: 0.8852 (mmp) cc_final: 0.8469 (mmt) REVERT: D 661 ARG cc_start: 0.8926 (ptp-170) cc_final: 0.8601 (ptp90) REVERT: D 720 MET cc_start: 0.8024 (mtm) cc_final: 0.7564 (ptm) REVERT: E 126 LYS cc_start: 0.7979 (mtmt) cc_final: 0.7693 (mtmt) REVERT: E 135 VAL cc_start: 0.9149 (m) cc_final: 0.8946 (p) REVERT: E 154 MET cc_start: 0.8265 (tmm) cc_final: 0.7675 (ppp) REVERT: E 186 TYR cc_start: 0.9089 (t80) cc_final: 0.8732 (t80) REVERT: E 295 MET cc_start: 0.9106 (tpt) cc_final: 0.8687 (ptm) REVERT: E 297 LYS cc_start: 0.7735 (mtpp) cc_final: 0.7197 (ttmm) REVERT: E 393 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8144 (tt) REVERT: E 416 ARG cc_start: 0.9283 (mmm160) cc_final: 0.8629 (mmm160) REVERT: E 469 GLU cc_start: 0.8934 (tp30) cc_final: 0.8604 (tp30) REVERT: E 539 LEU cc_start: 0.9320 (tp) cc_final: 0.9080 (mt) REVERT: E 545 PHE cc_start: 0.9151 (m-80) cc_final: 0.8939 (m-80) REVERT: E 549 ARG cc_start: 0.8982 (mtt-85) cc_final: 0.8400 (mmm-85) REVERT: E 574 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8717 (mm-40) REVERT: E 575 LYS cc_start: 0.9007 (tptt) cc_final: 0.8629 (tptm) REVERT: E 594 LEU cc_start: 0.9172 (mm) cc_final: 0.8970 (mt) REVERT: E 668 GLN cc_start: 0.8830 (mm110) cc_final: 0.8411 (mm-40) REVERT: E 691 LEU cc_start: 0.9340 (tp) cc_final: 0.8929 (mt) REVERT: E 710 ILE cc_start: 0.8960 (pp) cc_final: 0.8730 (pp) REVERT: E 718 LYS cc_start: 0.8936 (tttt) cc_final: 0.8702 (mtpt) REVERT: E 947 PHE cc_start: 0.9163 (m-80) cc_final: 0.8755 (m-80) REVERT: E 998 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: E 1020 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8206 (tt) REVERT: E 1099 LEU cc_start: 0.9230 (mm) cc_final: 0.8883 (pp) REVERT: E 1106 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8554 (mmt-90) REVERT: E 1118 LYS cc_start: 0.9445 (ptpt) cc_final: 0.9167 (ptpt) REVERT: E 1190 TYR cc_start: 0.7856 (t80) cc_final: 0.7573 (t80) REVERT: E 1297 TYR cc_start: 0.8092 (m-80) cc_final: 0.7505 (m-80) REVERT: E 1334 MET cc_start: 0.4151 (ptt) cc_final: 0.3892 (ptt) REVERT: E 1351 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8654 (ttp-110) REVERT: E 1488 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8378 (pptt) REVERT: E 1527 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7268 (mp) REVERT: E 1536 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8228 (t) REVERT: E 1711 MET cc_start: 0.7832 (ttm) cc_final: 0.6956 (ppp) REVERT: E 1724 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: E 1727 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: E 1769 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: E 1837 PHE cc_start: 0.8425 (m-10) cc_final: 0.8200 (m-80) REVERT: E 1897 TRP cc_start: 0.8213 (m100) cc_final: 0.7882 (m-10) REVERT: E 2020 ARG cc_start: 0.8800 (ptt180) cc_final: 0.8527 (ttp-170) REVERT: E 2038 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6778 (tm130) REVERT: E 2040 PHE cc_start: 0.6683 (m-80) cc_final: 0.5757 (m-80) REVERT: E 2087 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8453 (p0) REVERT: E 2092 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8604 (tp-100) REVERT: E 2093 PHE cc_start: 0.9313 (t80) cc_final: 0.8750 (t80) REVERT: E 2176 GLU cc_start: 0.9214 (tt0) cc_final: 0.8944 (tm-30) REVERT: E 2213 MET cc_start: 0.9096 (mmm) cc_final: 0.8797 (mmm) REVERT: E 2226 HIS cc_start: 0.8793 (OUTLIER) cc_final: 0.8561 (t-90) REVERT: E 2247 LEU cc_start: 0.8760 (mt) cc_final: 0.8282 (mp) REVERT: E 2263 ARG cc_start: 0.4954 (tmt-80) cc_final: 0.4022 (tpm170) REVERT: E 2282 LYS cc_start: 0.9297 (tttm) cc_final: 0.8885 (mtpp) REVERT: E 2292 MET cc_start: 0.8478 (ptp) cc_final: 0.8267 (ptp) REVERT: E 2296 GLU cc_start: 0.8881 (pm20) cc_final: 0.8353 (mt-10) REVERT: E 2350 GLU cc_start: 0.8882 (tt0) cc_final: 0.8586 (pt0) REVERT: E 2357 LEU cc_start: 0.9179 (mt) cc_final: 0.8919 (pp) REVERT: E 2364 TRP cc_start: 0.8933 (t60) cc_final: 0.8682 (t60) outliers start: 187 outliers final: 141 residues processed: 957 average time/residue: 0.4752 time to fit residues: 766.5693 Evaluate side-chains 947 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 780 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 149 HIS Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 687 ILE Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 937 LEU Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 956 HIS Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 978 SER Chi-restraints excluded: chain F residue 983 LYS Chi-restraints excluded: chain F residue 998 GLU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1106 ARG Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1155 PHE Chi-restraints excluded: chain F residue 1200 MET Chi-restraints excluded: chain F residue 1233 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1382 THR Chi-restraints excluded: chain F residue 1390 GLU Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1411 GLU Chi-restraints excluded: chain F residue 1434 LEU Chi-restraints excluded: chain F residue 1435 LEU Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1614 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1890 GLN Chi-restraints excluded: chain F residue 1901 LEU Chi-restraints excluded: chain F residue 1905 LEU Chi-restraints excluded: chain F residue 1942 VAL Chi-restraints excluded: chain F residue 2077 ILE Chi-restraints excluded: chain F residue 2087 ASP Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2172 GLU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2230 ILE Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 574 GLN Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 654 PHE Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 884 PHE Chi-restraints excluded: chain E residue 928 GLN Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 978 SER Chi-restraints excluded: chain E residue 998 GLU Chi-restraints excluded: chain E residue 1020 LEU Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1093 LEU Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1200 MET Chi-restraints excluded: chain E residue 1217 ASN Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1350 PHE Chi-restraints excluded: chain E residue 1351 ARG Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1370 LEU Chi-restraints excluded: chain E residue 1382 THR Chi-restraints excluded: chain E residue 1399 LEU Chi-restraints excluded: chain E residue 1411 GLU Chi-restraints excluded: chain E residue 1434 LEU Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1527 LEU Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1614 LEU Chi-restraints excluded: chain E residue 1633 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1724 GLU Chi-restraints excluded: chain E residue 1727 GLU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1769 GLU Chi-restraints excluded: chain E residue 1874 LEU Chi-restraints excluded: chain E residue 1901 LEU Chi-restraints excluded: chain E residue 1905 LEU Chi-restraints excluded: chain E residue 1942 VAL Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2206 TYR Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2344 THR Chi-restraints excluded: chain E residue 2358 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 337 optimal weight: 3.9990 chunk 543 optimal weight: 2.9990 chunk 331 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 chunk 377 optimal weight: 0.0770 chunk 569 optimal weight: 0.6980 chunk 524 optimal weight: 0.0980 chunk 453 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 350 optimal weight: 0.9990 chunk 278 optimal weight: 0.4980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 934 GLN F1217 ASN F1383 ASN ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1511 GLN E1712 HIS ** E1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.276 47082 Z= 0.364 Angle : 1.045 59.136 63787 Z= 0.545 Chirality : 0.051 0.700 7342 Planarity : 0.007 0.234 8019 Dihedral : 7.153 178.345 6244 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.27 % Favored : 90.69 % Rotamer: Outliers : 3.57 % Allowed : 24.76 % Favored : 71.67 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.11), residues: 5688 helix: -0.33 (0.08), residues: 3684 sheet: -1.52 (0.52), residues: 80 loop : -2.80 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F1897 HIS 0.379 0.005 HIS F 149 PHE 0.046 0.002 PHE E1350 TYR 0.037 0.002 TYR E1232 ARG 0.016 0.001 ARG E 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 785 time to evaluate : 4.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 126 LYS cc_start: 0.7879 (mtmt) cc_final: 0.7325 (tppt) REVERT: F 154 MET cc_start: 0.7963 (tmm) cc_final: 0.7470 (ppp) REVERT: F 289 LEU cc_start: 0.3885 (OUTLIER) cc_final: 0.3077 (tt) REVERT: F 295 MET cc_start: 0.9289 (tpp) cc_final: 0.8471 (ptm) REVERT: F 416 ARG cc_start: 0.9429 (mmm160) cc_final: 0.8730 (mmm160) REVERT: F 484 MET cc_start: 0.8740 (mtp) cc_final: 0.8468 (mtm) REVERT: F 539 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9054 (mt) REVERT: F 549 ARG cc_start: 0.8783 (mtt-85) cc_final: 0.8146 (mmt90) REVERT: F 551 PHE cc_start: 0.8765 (m-80) cc_final: 0.8455 (m-80) REVERT: F 579 ASN cc_start: 0.8730 (t0) cc_final: 0.8466 (t0) REVERT: F 664 MET cc_start: 0.8129 (ttm) cc_final: 0.7807 (ttm) REVERT: F 671 ASN cc_start: 0.8688 (m-40) cc_final: 0.8383 (m110) REVERT: F 691 LEU cc_start: 0.9256 (tp) cc_final: 0.8753 (mt) REVERT: F 718 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8554 (mmmm) REVERT: F 759 MET cc_start: 0.9251 (tpp) cc_final: 0.8966 (tpp) REVERT: F 767 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7887 (p0) REVERT: F 937 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8487 (mm) REVERT: F 947 PHE cc_start: 0.8998 (m-80) cc_final: 0.8735 (m-80) REVERT: F 952 LEU cc_start: 0.9225 (pp) cc_final: 0.8985 (mm) REVERT: F 983 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8460 (ptmt) REVERT: F 998 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: F 1118 LYS cc_start: 0.9399 (ptpt) cc_final: 0.9137 (ptpp) REVERT: F 1126 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6731 (tm) REVERT: F 1142 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6497 (tm-30) REVERT: F 1334 MET cc_start: 0.3892 (ptt) cc_final: 0.3595 (ptt) REVERT: F 1353 PHE cc_start: 0.9295 (m-10) cc_final: 0.8873 (m-80) REVERT: F 1488 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8389 (pptt) REVERT: F 1503 MET cc_start: 0.8727 (ttm) cc_final: 0.8415 (ttp) REVERT: F 1527 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7017 (mp) REVERT: F 1536 SER cc_start: 0.8738 (t) cc_final: 0.8435 (t) REVERT: F 1731 LYS cc_start: 0.9339 (tmtt) cc_final: 0.8936 (mmtm) REVERT: F 1837 PHE cc_start: 0.8596 (m-10) cc_final: 0.8274 (m-80) REVERT: F 1937 TYR cc_start: 0.9097 (m-80) cc_final: 0.8736 (m-80) REVERT: F 1959 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8500 (mmmt) REVERT: F 2008 MET cc_start: 0.8047 (tmm) cc_final: 0.7350 (mtt) REVERT: F 2040 PHE cc_start: 0.6603 (m-80) cc_final: 0.6309 (m-80) REVERT: F 2093 PHE cc_start: 0.9319 (t80) cc_final: 0.8608 (t80) REVERT: F 2213 MET cc_start: 0.8958 (mmm) cc_final: 0.8684 (mmm) REVERT: F 2222 LEU cc_start: 0.8858 (pt) cc_final: 0.8619 (tp) REVERT: F 2247 LEU cc_start: 0.8859 (mt) cc_final: 0.8532 (mp) REVERT: F 2263 ARG cc_start: 0.5608 (tpm170) cc_final: 0.4819 (tpm170) REVERT: F 2282 LYS cc_start: 0.9202 (tttm) cc_final: 0.8807 (mtpp) REVERT: F 2296 GLU cc_start: 0.8908 (pm20) cc_final: 0.8638 (mm-30) REVERT: C 238 LYS cc_start: 0.8872 (tttm) cc_final: 0.8638 (tptp) REVERT: C 335 HIS cc_start: 0.7466 (p-80) cc_final: 0.5985 (t-170) REVERT: C 449 TRP cc_start: 0.7833 (t60) cc_final: 0.7465 (t60) REVERT: C 610 HIS cc_start: 0.9236 (t-170) cc_final: 0.8792 (t-90) REVERT: C 664 ARG cc_start: 0.8958 (ptt180) cc_final: 0.8680 (ppt170) REVERT: C 707 ARG cc_start: 0.8542 (ttt180) cc_final: 0.8135 (ttt180) REVERT: C 745 MET cc_start: 0.6894 (ptp) cc_final: 0.6479 (ptp) REVERT: D 238 LYS cc_start: 0.8906 (tttm) cc_final: 0.8630 (tptp) REVERT: D 303 MET cc_start: 0.8627 (mmm) cc_final: 0.8398 (mmm) REVERT: D 317 LEU cc_start: 0.9524 (tt) cc_final: 0.9179 (mp) REVERT: D 449 TRP cc_start: 0.7827 (t60) cc_final: 0.7464 (t60) REVERT: D 547 LYS cc_start: 0.8884 (mttt) cc_final: 0.8651 (mttm) REVERT: D 610 HIS cc_start: 0.9195 (t-170) cc_final: 0.8750 (t-170) REVERT: D 660 MET cc_start: 0.8853 (mmp) cc_final: 0.8457 (mmt) REVERT: D 661 ARG cc_start: 0.8924 (ptp-170) cc_final: 0.8493 (ptp90) REVERT: D 720 MET cc_start: 0.8022 (mtm) cc_final: 0.7569 (ptm) REVERT: E 126 LYS cc_start: 0.7977 (mtmt) cc_final: 0.7691 (mtmt) REVERT: E 135 VAL cc_start: 0.9159 (m) cc_final: 0.8957 (p) REVERT: E 154 MET cc_start: 0.8262 (tmm) cc_final: 0.7676 (ppp) REVERT: E 186 TYR cc_start: 0.9088 (t80) cc_final: 0.8729 (t80) REVERT: E 295 MET cc_start: 0.9131 (tpt) cc_final: 0.8689 (ptm) REVERT: E 297 LYS cc_start: 0.7730 (mtpp) cc_final: 0.7192 (ttmm) REVERT: E 393 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8141 (tt) REVERT: E 416 ARG cc_start: 0.9291 (mmm160) cc_final: 0.8593 (mmm160) REVERT: E 458 TRP cc_start: 0.8762 (m100) cc_final: 0.7946 (m100) REVERT: E 469 GLU cc_start: 0.8931 (tp30) cc_final: 0.8601 (tp30) REVERT: E 539 LEU cc_start: 0.9319 (tp) cc_final: 0.9080 (mt) REVERT: E 545 PHE cc_start: 0.9153 (m-80) cc_final: 0.8927 (m-80) REVERT: E 549 ARG cc_start: 0.8995 (mtt-85) cc_final: 0.8386 (mmm-85) REVERT: E 575 LYS cc_start: 0.9010 (tptt) cc_final: 0.8227 (tptp) REVERT: E 668 GLN cc_start: 0.8824 (mm110) cc_final: 0.8409 (mm-40) REVERT: E 691 LEU cc_start: 0.9339 (tp) cc_final: 0.8928 (mt) REVERT: E 710 ILE cc_start: 0.8959 (pp) cc_final: 0.8730 (pp) REVERT: E 768 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.8009 (p) REVERT: E 947 PHE cc_start: 0.9160 (m-80) cc_final: 0.8750 (m-80) REVERT: E 998 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8423 (pm20) REVERT: E 1020 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8158 (tt) REVERT: E 1099 LEU cc_start: 0.9212 (mm) cc_final: 0.8862 (pp) REVERT: E 1106 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.8553 (mmt-90) REVERT: E 1118 LYS cc_start: 0.9428 (ptpt) cc_final: 0.9166 (ptpt) REVERT: E 1190 TYR cc_start: 0.7854 (t80) cc_final: 0.7572 (t80) REVERT: E 1297 TYR cc_start: 0.8088 (m-80) cc_final: 0.7499 (m-80) REVERT: E 1334 MET cc_start: 0.4146 (ptt) cc_final: 0.3861 (ptt) REVERT: E 1351 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8651 (ttp-110) REVERT: E 1485 VAL cc_start: 0.9294 (m) cc_final: 0.9036 (m) REVERT: E 1488 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8388 (pptt) REVERT: E 1527 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7267 (mp) REVERT: E 1536 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8207 (t) REVERT: E 1711 MET cc_start: 0.7849 (ttm) cc_final: 0.6968 (ppp) REVERT: E 1724 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8094 (mm-30) REVERT: E 1837 PHE cc_start: 0.8423 (m-10) cc_final: 0.8206 (m-80) REVERT: E 1897 TRP cc_start: 0.8211 (m100) cc_final: 0.7872 (m-10) REVERT: E 2020 ARG cc_start: 0.8798 (ptt180) cc_final: 0.8525 (ttp-170) REVERT: E 2038 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6776 (tm130) REVERT: E 2040 PHE cc_start: 0.6676 (m-80) cc_final: 0.5753 (m-80) REVERT: E 2087 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8450 (p0) REVERT: E 2092 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8601 (tp-100) REVERT: E 2093 PHE cc_start: 0.9310 (t80) cc_final: 0.8746 (t80) REVERT: E 2174 TYR cc_start: 0.8437 (t80) cc_final: 0.8205 (t80) REVERT: E 2176 GLU cc_start: 0.9216 (tt0) cc_final: 0.8943 (tm-30) REVERT: E 2213 MET cc_start: 0.9097 (mmm) cc_final: 0.8795 (mmm) REVERT: E 2226 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.8561 (t-90) REVERT: E 2247 LEU cc_start: 0.8762 (mt) cc_final: 0.8282 (mp) REVERT: E 2263 ARG cc_start: 0.4952 (tmt-80) cc_final: 0.4016 (tpm170) REVERT: E 2282 LYS cc_start: 0.9301 (tttm) cc_final: 0.8888 (mtpp) REVERT: E 2296 GLU cc_start: 0.8879 (pm20) cc_final: 0.8449 (mt-10) REVERT: E 2350 GLU cc_start: 0.8882 (tt0) cc_final: 0.8584 (pt0) REVERT: E 2357 LEU cc_start: 0.9225 (mt) cc_final: 0.8878 (pp) REVERT: E 2364 TRP cc_start: 0.8926 (t60) cc_final: 0.8662 (t60) outliers start: 178 outliers final: 144 residues processed: 909 average time/residue: 0.4750 time to fit residues: 727.2536 Evaluate side-chains 946 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 778 time to evaluate : 4.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 633 GLN Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain F residue 687 ILE Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain F residue 767 ASN Chi-restraints excluded: chain F residue 937 LEU Chi-restraints excluded: chain F residue 953 LEU Chi-restraints excluded: chain F residue 956 HIS Chi-restraints excluded: chain F residue 962 LEU Chi-restraints excluded: chain F residue 978 SER Chi-restraints excluded: chain F residue 983 LYS Chi-restraints excluded: chain F residue 998 GLU Chi-restraints excluded: chain F residue 1050 LEU Chi-restraints excluded: chain F residue 1057 VAL Chi-restraints excluded: chain F residue 1106 ARG Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1114 GLU Chi-restraints excluded: chain F residue 1126 LEU Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1155 PHE Chi-restraints excluded: chain F residue 1200 MET Chi-restraints excluded: chain F residue 1233 LEU Chi-restraints excluded: chain F residue 1283 ILE Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1365 GLN Chi-restraints excluded: chain F residue 1382 THR Chi-restraints excluded: chain F residue 1390 GLU Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1399 LEU Chi-restraints excluded: chain F residue 1411 GLU Chi-restraints excluded: chain F residue 1434 LEU Chi-restraints excluded: chain F residue 1435 LEU Chi-restraints excluded: chain F residue 1488 LYS Chi-restraints excluded: chain F residue 1506 HIS Chi-restraints excluded: chain F residue 1527 LEU Chi-restraints excluded: chain F residue 1614 LEU Chi-restraints excluded: chain F residue 1640 PHE Chi-restraints excluded: chain F residue 1667 LEU Chi-restraints excluded: chain F residue 1703 LEU Chi-restraints excluded: chain F residue 1755 VAL Chi-restraints excluded: chain F residue 1890 GLN Chi-restraints excluded: chain F residue 1901 LEU Chi-restraints excluded: chain F residue 1905 LEU Chi-restraints excluded: chain F residue 1942 VAL Chi-restraints excluded: chain F residue 2077 ILE Chi-restraints excluded: chain F residue 2132 VAL Chi-restraints excluded: chain F residue 2172 GLU Chi-restraints excluded: chain F residue 2226 HIS Chi-restraints excluded: chain F residue 2230 ILE Chi-restraints excluded: chain F residue 2323 LEU Chi-restraints excluded: chain F residue 2350 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 577 PHE Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 633 GLN Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 654 PHE Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain E residue 797 THR Chi-restraints excluded: chain E residue 884 PHE Chi-restraints excluded: chain E residue 928 GLN Chi-restraints excluded: chain E residue 953 LEU Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 978 SER Chi-restraints excluded: chain E residue 998 GLU Chi-restraints excluded: chain E residue 1020 LEU Chi-restraints excluded: chain E residue 1050 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1057 VAL Chi-restraints excluded: chain E residue 1093 LEU Chi-restraints excluded: chain E residue 1106 ARG Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1120 ILE Chi-restraints excluded: chain E residue 1126 LEU Chi-restraints excluded: chain E residue 1200 MET Chi-restraints excluded: chain E residue 1217 ASN Chi-restraints excluded: chain E residue 1233 LEU Chi-restraints excluded: chain E residue 1283 ILE Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1300 LEU Chi-restraints excluded: chain E residue 1350 PHE Chi-restraints excluded: chain E residue 1351 ARG Chi-restraints excluded: chain E residue 1365 GLN Chi-restraints excluded: chain E residue 1370 LEU Chi-restraints excluded: chain E residue 1382 THR Chi-restraints excluded: chain E residue 1399 LEU Chi-restraints excluded: chain E residue 1411 GLU Chi-restraints excluded: chain E residue 1434 LEU Chi-restraints excluded: chain E residue 1442 TYR Chi-restraints excluded: chain E residue 1452 ASP Chi-restraints excluded: chain E residue 1488 LYS Chi-restraints excluded: chain E residue 1527 LEU Chi-restraints excluded: chain E residue 1536 SER Chi-restraints excluded: chain E residue 1614 LEU Chi-restraints excluded: chain E residue 1633 LEU Chi-restraints excluded: chain E residue 1640 PHE Chi-restraints excluded: chain E residue 1667 LEU Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1724 GLU Chi-restraints excluded: chain E residue 1755 VAL Chi-restraints excluded: chain E residue 1874 LEU Chi-restraints excluded: chain E residue 1901 LEU Chi-restraints excluded: chain E residue 1905 LEU Chi-restraints excluded: chain E residue 1942 VAL Chi-restraints excluded: chain E residue 2038 GLN Chi-restraints excluded: chain E residue 2077 ILE Chi-restraints excluded: chain E residue 2087 ASP Chi-restraints excluded: chain E residue 2132 VAL Chi-restraints excluded: chain E residue 2206 TYR Chi-restraints excluded: chain E residue 2226 HIS Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2344 THR Chi-restraints excluded: chain E residue 2358 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 360 optimal weight: 0.0370 chunk 483 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 418 optimal weight: 10.0000 chunk 67 optimal weight: 0.0040 chunk 126 optimal weight: 20.0000 chunk 454 optimal weight: 0.0970 chunk 190 optimal weight: 0.0970 chunk 466 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.2468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 934 GLN F1383 ASN ** F1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1910 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.082524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.066200 restraints weight = 289970.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.068483 restraints weight = 174441.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.070073 restraints weight = 119312.277| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.276 47082 Z= 0.364 Angle : 1.045 59.131 63787 Z= 0.545 Chirality : 0.051 0.700 7342 Planarity : 0.007 0.234 8019 Dihedral : 7.153 178.345 6244 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 26.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.27 % Favored : 90.69 % Rotamer: Outliers : 3.39 % Allowed : 24.98 % Favored : 71.63 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.11), residues: 5688 helix: -0.33 (0.08), residues: 3684 sheet: -1.52 (0.52), residues: 80 loop : -2.80 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F1897 HIS 0.379 0.005 HIS F 149 PHE 0.046 0.002 PHE E1350 TYR 0.037 0.002 TYR E1232 ARG 0.016 0.001 ARG E 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13012.98 seconds wall clock time: 225 minutes 16.34 seconds (13516.34 seconds total)