Starting phenix.real_space_refine on Sat Feb 24 12:19:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atu_15663/02_2024/8atu_15663.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atu_15663/02_2024/8atu_15663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atu_15663/02_2024/8atu_15663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atu_15663/02_2024/8atu_15663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atu_15663/02_2024/8atu_15663.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atu_15663/02_2024/8atu_15663.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 302 5.16 5 C 28038 2.51 5 N 7422 2.21 5 O 8118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 932": "OE1" <-> "OE2" Residue "A ASP 1193": "OD1" <-> "OD2" Residue "A PHE 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1509": "OD1" <-> "OD2" Residue "A GLU 1564": "OE1" <-> "OE2" Residue "A PHE 1790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1888": "OE1" <-> "OE2" Residue "A ASP 2115": "OD1" <-> "OD2" Residue "A ASP 2143": "OD1" <-> "OD2" Residue "A ASP 2187": "OD1" <-> "OD2" Residue "A PHE 2344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2396": "OD1" <-> "OD2" Residue "A TYR 2711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3034": "OD1" <-> "OD2" Residue "A ASP 3429": "OD1" <-> "OD2" Residue "A GLU 3506": "OE1" <-> "OE2" Residue "A GLU 3510": "OE1" <-> "OE2" Residue "A PHE 3689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 932": "OE1" <-> "OE2" Residue "B ASP 1193": "OD1" <-> "OD2" Residue "B PHE 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1509": "OD1" <-> "OD2" Residue "B GLU 1564": "OE1" <-> "OE2" Residue "B PHE 1790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1888": "OE1" <-> "OE2" Residue "B ASP 2115": "OD1" <-> "OD2" Residue "B ASP 2143": "OD1" <-> "OD2" Residue "B ASP 2187": "OD1" <-> "OD2" Residue "B PHE 2344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2396": "OD1" <-> "OD2" Residue "B TYR 2711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3034": "OD1" <-> "OD2" Residue "B ASP 3429": "OD1" <-> "OD2" Residue "B GLU 3506": "OE1" <-> "OE2" Residue "B GLU 3510": "OE1" <-> "OE2" Residue "B PHE 3689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4170": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 43882 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 21940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2837, 21940 Classifications: {'peptide': 2837} Link IDs: {'PCIS': 4, 'PTRANS': 141, 'TRANS': 2691} Chain breaks: 45 Chain: "B" Number of atoms: 21940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2837, 21940 Classifications: {'peptide': 2837} Link IDs: {'PCIS': 4, 'PTRANS': 141, 'TRANS': 2691} Chain breaks: 45 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2095 SG CYS A 328 86.076 66.782 78.733 1.00236.65 S ATOM 2119 SG CYS A 331 85.794 68.456 82.166 1.00239.46 S ATOM 2316 SG CYS A 355 85.364 64.660 81.945 1.00235.55 S ATOM 24035 SG CYS B 328 105.821 136.797 78.724 1.00236.65 S ATOM 24059 SG CYS B 331 106.101 135.123 82.158 1.00239.46 S ATOM 24256 SG CYS B 355 106.532 138.919 81.936 1.00235.55 S Time building chain proxies: 21.97, per 1000 atoms: 0.50 Number of scatterers: 43882 At special positions: 0 Unit cell: (193.05, 204.75, 194.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 302 16.00 O 8118 8.00 N 7422 7.00 C 28038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.16 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4901 " pdb="ZN ZN A4901 " - pdb=" NE2 HIS A 348 " pdb="ZN ZN A4901 " - pdb=" SG CYS A 331 " pdb="ZN ZN A4901 " - pdb=" SG CYS A 328 " pdb="ZN ZN A4901 " - pdb=" SG CYS A 355 " pdb=" ZN B4901 " pdb="ZN ZN B4901 " - pdb=" NE2 HIS B 348 " pdb="ZN ZN B4901 " - pdb=" SG CYS B 331 " pdb="ZN ZN B4901 " - pdb=" SG CYS B 355 " pdb="ZN ZN B4901 " - pdb=" SG CYS B 328 " Number of angles added : 6 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10776 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 32 sheets defined 53.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.41 Creating SS restraints... Processing helix chain 'A' and resid 166 through 180 Processing helix chain 'A' and resid 188 through 208 removed outlier: 4.288A pdb=" N HIS A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 225 through 242 removed outlier: 3.658A pdb=" N ILE A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 263 removed outlier: 3.738A pdb=" N VAL A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 281 through 284 removed outlier: 3.601A pdb=" N TYR A 284 " --> pdb=" O SER A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.569A pdb=" N ARG A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 removed outlier: 3.515A pdb=" N TRP A 296 " --> pdb=" O PHE A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.626A pdb=" N GLN A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 367 through 374 removed outlier: 3.520A pdb=" N THR A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 723 through 729 removed outlier: 3.825A pdb=" N GLU A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 removed outlier: 3.644A pdb=" N THR A 855 " --> pdb=" O PRO A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 869 removed outlier: 3.569A pdb=" N ILE A 866 " --> pdb=" O PRO A 863 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 869 " --> pdb=" O ILE A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1029 Processing helix chain 'A' and resid 1171 through 1177 removed outlier: 3.544A pdb=" N HIS A1177 " --> pdb=" O PHE A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1191 No H-bonds generated for 'chain 'A' and resid 1189 through 1191' Processing helix chain 'A' and resid 1205 through 1213 removed outlier: 3.666A pdb=" N VAL A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1294 Processing helix chain 'A' and resid 1313 through 1324 removed outlier: 3.799A pdb=" N GLN A1317 " --> pdb=" O LYS A1313 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET A1321 " --> pdb=" O GLN A1317 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A1322 " --> pdb=" O ARG A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1337 removed outlier: 3.800A pdb=" N GLU A1329 " --> pdb=" O SER A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1363 Processing helix chain 'A' and resid 1371 through 1384 removed outlier: 3.549A pdb=" N PHE A1384 " --> pdb=" O LYS A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1394 Processing helix chain 'A' and resid 1397 through 1414 Processing helix chain 'A' and resid 1423 through 1434 removed outlier: 4.218A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1442 Processing helix chain 'A' and resid 1444 through 1459 Processing helix chain 'A' and resid 1463 through 1482 removed outlier: 3.619A pdb=" N GLN A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1497 Processing helix chain 'A' and resid 1551 through 1557 removed outlier: 4.245A pdb=" N THR A1555 " --> pdb=" O GLY A1552 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A1557 " --> pdb=" O PHE A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1770 Processing helix chain 'A' and resid 1885 through 1890 Processing helix chain 'A' and resid 1909 through 1940 removed outlier: 3.660A pdb=" N HIS A1913 " --> pdb=" O GLU A1909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1954 Processing helix chain 'A' and resid 1965 through 1999 Processing helix chain 'A' and resid 2010 through 2017 Processing helix chain 'A' and resid 2019 through 2040 Processing helix chain 'A' and resid 2047 through 2054 removed outlier: 3.655A pdb=" N GLN A2051 " --> pdb=" O PRO A2047 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A2054 " --> pdb=" O LEU A2050 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2071 through 2087 Processing helix chain 'A' and resid 2091 through 2104 Processing helix chain 'A' and resid 2113 through 2128 Processing helix chain 'A' and resid 2129 through 2131 No H-bonds generated for 'chain 'A' and resid 2129 through 2131' Processing helix chain 'A' and resid 2132 through 2146 removed outlier: 3.920A pdb=" N GLU A2136 " --> pdb=" O SER A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2147 through 2150 Processing helix chain 'A' and resid 2164 through 2189 Processing helix chain 'A' and resid 2201 through 2206 removed outlier: 4.539A pdb=" N ASN A2205 " --> pdb=" O TRP A2201 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2341 Processing helix chain 'A' and resid 2347 through 2365 removed outlier: 3.522A pdb=" N LEU A2351 " --> pdb=" O HIS A2347 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2389 Processing helix chain 'A' and resid 2394 through 2398 removed outlier: 4.125A pdb=" N ILE A2397 " --> pdb=" O ARG A2394 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A2398 " --> pdb=" O GLY A2395 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2394 through 2398' Processing helix chain 'A' and resid 2400 through 2420 removed outlier: 3.904A pdb=" N ALA A2404 " --> pdb=" O GLY A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2569 through 2574 removed outlier: 3.853A pdb=" N VAL A2573 " --> pdb=" O ARG A2570 " (cutoff:3.500A) Processing helix chain 'A' and resid 2576 through 2600 Processing helix chain 'A' and resid 2635 through 2650 Processing helix chain 'A' and resid 2651 through 2653 No H-bonds generated for 'chain 'A' and resid 2651 through 2653' Processing helix chain 'A' and resid 2656 through 2668 Processing helix chain 'A' and resid 2697 through 2711 Processing helix chain 'A' and resid 2715 through 2732 Processing helix chain 'A' and resid 2747 through 2755 removed outlier: 3.850A pdb=" N ASP A2755 " --> pdb=" O LEU A2751 " (cutoff:3.500A) Processing helix chain 'A' and resid 2755 through 2768 removed outlier: 4.347A pdb=" N ILE A2759 " --> pdb=" O ASP A2755 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A2768 " --> pdb=" O LYS A2764 " (cutoff:3.500A) Processing helix chain 'A' and resid 2782 through 2802 removed outlier: 4.347A pdb=" N SER A2802 " --> pdb=" O VAL A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2804 through 2820 removed outlier: 4.068A pdb=" N PHE A2808 " --> pdb=" O CYS A2804 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2829 Processing helix chain 'A' and resid 2832 through 2845 removed outlier: 3.972A pdb=" N GLU A2845 " --> pdb=" O GLU A2841 " (cutoff:3.500A) Processing helix chain 'A' and resid 2852 through 2873 Processing helix chain 'A' and resid 2914 through 2931 removed outlier: 3.546A pdb=" N LEU A2918 " --> pdb=" O THR A2914 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A2931 " --> pdb=" O ASN A2927 " (cutoff:3.500A) Processing helix chain 'A' and resid 2979 through 2987 removed outlier: 3.959A pdb=" N LEU A2983 " --> pdb=" O TYR A2979 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3000 removed outlier: 3.501A pdb=" N MET A2991 " --> pdb=" O ASN A2987 " (cutoff:3.500A) Processing helix chain 'A' and resid 3031 through 3046 Processing helix chain 'A' and resid 3050 through 3064 Proline residue: A3056 - end of helix Processing helix chain 'A' and resid 3078 through 3089 Processing helix chain 'A' and resid 3091 through 3101 Processing helix chain 'A' and resid 3103 through 3118 Processing helix chain 'A' and resid 3124 through 3132 removed outlier: 3.586A pdb=" N THR A3128 " --> pdb=" O SER A3124 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE A3132 " --> pdb=" O THR A3128 " (cutoff:3.500A) Processing helix chain 'A' and resid 3178 through 3184 removed outlier: 4.448A pdb=" N VAL A3181 " --> pdb=" O PRO A3178 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A3184 " --> pdb=" O VAL A3181 " (cutoff:3.500A) Processing helix chain 'A' and resid 3231 through 3235 removed outlier: 3.745A pdb=" N THR A3234 " --> pdb=" O SER A3231 " (cutoff:3.500A) Processing helix chain 'A' and resid 3321 through 3325 removed outlier: 4.141A pdb=" N LYS A3325 " --> pdb=" O ASP A3321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3321 through 3325' Processing helix chain 'A' and resid 3327 through 3340 Processing helix chain 'A' and resid 3344 through 3353 removed outlier: 3.617A pdb=" N MET A3348 " --> pdb=" O LEU A3344 " (cutoff:3.500A) Processing helix chain 'A' and resid 3357 through 3367 Processing helix chain 'A' and resid 3368 through 3373 removed outlier: 4.072A pdb=" N MET A3373 " --> pdb=" O TYR A3370 " (cutoff:3.500A) Processing helix chain 'A' and resid 3374 through 3387 Processing helix chain 'A' and resid 3389 through 3402 Processing helix chain 'A' and resid 3429 through 3441 removed outlier: 3.671A pdb=" N THR A3441 " --> pdb=" O GLN A3437 " (cutoff:3.500A) Processing helix chain 'A' and resid 3445 through 3467 Processing helix chain 'A' and resid 3483 through 3488 Processing helix chain 'A' and resid 3490 through 3507 Processing helix chain 'A' and resid 3512 through 3517 removed outlier: 3.915A pdb=" N LEU A3516 " --> pdb=" O ASP A3512 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A3517 " --> pdb=" O LEU A3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3512 through 3517' Processing helix chain 'A' and resid 3518 through 3531 Processing helix chain 'A' and resid 3536 through 3553 removed outlier: 4.332A pdb=" N LYS A3540 " --> pdb=" O MET A3536 " (cutoff:3.500A) Processing helix chain 'A' and resid 3553 through 3562 removed outlier: 3.666A pdb=" N PHE A3557 " --> pdb=" O HIS A3553 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A3562 " --> pdb=" O SER A3558 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3616 Processing helix chain 'A' and resid 3619 through 3629 Processing helix chain 'A' and resid 3630 through 3652 Processing helix chain 'A' and resid 3682 through 3694 Processing helix chain 'A' and resid 3696 through 3704 Processing helix chain 'A' and resid 3709 through 3721 Processing helix chain 'A' and resid 3752 through 3771 removed outlier: 3.534A pdb=" N ILE A3771 " --> pdb=" O PHE A3767 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3791 Processing helix chain 'A' and resid 3805 through 3815 Processing helix chain 'A' and resid 3846 through 3850 removed outlier: 3.693A pdb=" N GLY A3850 " --> pdb=" O PRO A3847 " (cutoff:3.500A) Processing helix chain 'A' and resid 3865 through 3872 removed outlier: 3.580A pdb=" N VAL A3869 " --> pdb=" O THR A3865 " (cutoff:3.500A) Processing helix chain 'A' and resid 3982 through 3992 Processing helix chain 'A' and resid 4069 through 4077 removed outlier: 4.202A pdb=" N MET A4077 " --> pdb=" O VAL A4073 " (cutoff:3.500A) Processing helix chain 'A' and resid 4078 through 4086 removed outlier: 3.691A pdb=" N LEU A4082 " --> pdb=" O GLY A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4154 through 4165 removed outlier: 4.014A pdb=" N LEU A4158 " --> pdb=" O PRO A4154 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A4162 " --> pdb=" O LEU A4158 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A4163 " --> pdb=" O ALA A4159 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4175 removed outlier: 3.670A pdb=" N VAL A4173 " --> pdb=" O GLY A4169 " (cutoff:3.500A) Processing helix chain 'A' and resid 4177 through 4190 Processing helix chain 'A' and resid 4211 through 4224 removed outlier: 3.847A pdb=" N LEU A4217 " --> pdb=" O PRO A4213 " (cutoff:3.500A) Processing helix chain 'A' and resid 4228 through 4242 removed outlier: 3.811A pdb=" N VAL A4232 " --> pdb=" O THR A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4242 through 4256 removed outlier: 3.555A pdb=" N LEU A4246 " --> pdb=" O GLY A4242 " (cutoff:3.500A) Processing helix chain 'A' and resid 4315 through 4332 Processing helix chain 'A' and resid 4357 through 4365 removed outlier: 4.051A pdb=" N LEU A4361 " --> pdb=" O PRO A4357 " (cutoff:3.500A) Processing helix chain 'A' and resid 4368 through 4378 Processing helix chain 'A' and resid 4391 through 4405 Processing helix chain 'A' and resid 4406 through 4413 Proline residue: A4410 - end of helix removed outlier: 3.711A pdb=" N LEU A4413 " --> pdb=" O PRO A4410 " (cutoff:3.500A) Processing helix chain 'A' and resid 4432 through 4445 Processing helix chain 'A' and resid 4478 through 4496 Processing helix chain 'B' and resid 166 through 180 Processing helix chain 'B' and resid 188 through 208 removed outlier: 4.288A pdb=" N HIS B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.658A pdb=" N ILE B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 263 removed outlier: 3.739A pdb=" N VAL B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 281 through 284 removed outlier: 3.601A pdb=" N TYR B 284 " --> pdb=" O SER B 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.569A pdb=" N ARG B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 296 removed outlier: 3.516A pdb=" N TRP B 296 " --> pdb=" O PHE B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.626A pdb=" N GLN B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.520A pdb=" N THR B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 723 through 729 removed outlier: 3.826A pdb=" N GLU B 727 " --> pdb=" O PRO B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.644A pdb=" N THR B 855 " --> pdb=" O PRO B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 869 removed outlier: 3.569A pdb=" N ILE B 866 " --> pdb=" O PRO B 863 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 869 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1029 Processing helix chain 'B' and resid 1171 through 1177 removed outlier: 3.544A pdb=" N HIS B1177 " --> pdb=" O PHE B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1191 No H-bonds generated for 'chain 'B' and resid 1189 through 1191' Processing helix chain 'B' and resid 1205 through 1213 removed outlier: 3.667A pdb=" N VAL B1209 " --> pdb=" O SER B1205 " (cutoff:3.500A) Processing helix chain 'B' and resid 1291 through 1294 Processing helix chain 'B' and resid 1313 through 1324 removed outlier: 3.799A pdb=" N GLN B1317 " --> pdb=" O LYS B1313 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET B1321 " --> pdb=" O GLN B1317 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B1322 " --> pdb=" O ARG B1318 " (cutoff:3.500A) Processing helix chain 'B' and resid 1325 through 1337 removed outlier: 3.801A pdb=" N GLU B1329 " --> pdb=" O SER B1325 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1363 Processing helix chain 'B' and resid 1371 through 1384 removed outlier: 3.549A pdb=" N PHE B1384 " --> pdb=" O LYS B1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 1384 through 1394 Processing helix chain 'B' and resid 1397 through 1414 Processing helix chain 'B' and resid 1423 through 1434 removed outlier: 4.218A pdb=" N VAL B1427 " --> pdb=" O ALA B1423 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1442 Processing helix chain 'B' and resid 1444 through 1459 Processing helix chain 'B' and resid 1463 through 1482 removed outlier: 3.619A pdb=" N GLN B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1487 through 1497 Processing helix chain 'B' and resid 1551 through 1557 removed outlier: 4.246A pdb=" N THR B1555 " --> pdb=" O GLY B1552 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU B1557 " --> pdb=" O PHE B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1759 through 1770 Processing helix chain 'B' and resid 1885 through 1890 Processing helix chain 'B' and resid 1909 through 1940 removed outlier: 3.660A pdb=" N HIS B1913 " --> pdb=" O GLU B1909 " (cutoff:3.500A) Processing helix chain 'B' and resid 1949 through 1954 Processing helix chain 'B' and resid 1965 through 1999 Processing helix chain 'B' and resid 2010 through 2017 Processing helix chain 'B' and resid 2019 through 2040 Processing helix chain 'B' and resid 2047 through 2054 removed outlier: 3.655A pdb=" N GLN B2051 " --> pdb=" O PRO B2047 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B2054 " --> pdb=" O LEU B2050 " (cutoff:3.500A) Processing helix chain 'B' and resid 2055 through 2067 Processing helix chain 'B' and resid 2071 through 2087 Processing helix chain 'B' and resid 2091 through 2104 Processing helix chain 'B' and resid 2113 through 2128 Processing helix chain 'B' and resid 2129 through 2131 No H-bonds generated for 'chain 'B' and resid 2129 through 2131' Processing helix chain 'B' and resid 2132 through 2146 removed outlier: 3.919A pdb=" N GLU B2136 " --> pdb=" O SER B2132 " (cutoff:3.500A) Processing helix chain 'B' and resid 2147 through 2150 Processing helix chain 'B' and resid 2164 through 2189 Processing helix chain 'B' and resid 2201 through 2206 removed outlier: 4.539A pdb=" N ASN B2205 " --> pdb=" O TRP B2201 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2341 Processing helix chain 'B' and resid 2347 through 2365 removed outlier: 3.522A pdb=" N LEU B2351 " --> pdb=" O HIS B2347 " (cutoff:3.500A) Processing helix chain 'B' and resid 2376 through 2389 Processing helix chain 'B' and resid 2394 through 2398 removed outlier: 4.126A pdb=" N ILE B2397 " --> pdb=" O ARG B2394 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B2398 " --> pdb=" O GLY B2395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2394 through 2398' Processing helix chain 'B' and resid 2400 through 2420 removed outlier: 3.905A pdb=" N ALA B2404 " --> pdb=" O GLY B2400 " (cutoff:3.500A) Processing helix chain 'B' and resid 2569 through 2574 removed outlier: 3.854A pdb=" N VAL B2573 " --> pdb=" O ARG B2570 " (cutoff:3.500A) Processing helix chain 'B' and resid 2576 through 2600 Processing helix chain 'B' and resid 2635 through 2650 Processing helix chain 'B' and resid 2651 through 2653 No H-bonds generated for 'chain 'B' and resid 2651 through 2653' Processing helix chain 'B' and resid 2656 through 2668 Processing helix chain 'B' and resid 2697 through 2711 Processing helix chain 'B' and resid 2715 through 2732 Processing helix chain 'B' and resid 2747 through 2755 removed outlier: 3.849A pdb=" N ASP B2755 " --> pdb=" O LEU B2751 " (cutoff:3.500A) Processing helix chain 'B' and resid 2755 through 2768 removed outlier: 4.347A pdb=" N ILE B2759 " --> pdb=" O ASP B2755 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B2768 " --> pdb=" O LYS B2764 " (cutoff:3.500A) Processing helix chain 'B' and resid 2782 through 2802 removed outlier: 4.347A pdb=" N SER B2802 " --> pdb=" O VAL B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2804 through 2820 removed outlier: 4.068A pdb=" N PHE B2808 " --> pdb=" O CYS B2804 " (cutoff:3.500A) Processing helix chain 'B' and resid 2824 through 2829 Processing helix chain 'B' and resid 2832 through 2845 removed outlier: 3.972A pdb=" N GLU B2845 " --> pdb=" O GLU B2841 " (cutoff:3.500A) Processing helix chain 'B' and resid 2852 through 2873 Processing helix chain 'B' and resid 2914 through 2931 removed outlier: 3.546A pdb=" N LEU B2918 " --> pdb=" O THR B2914 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B2931 " --> pdb=" O ASN B2927 " (cutoff:3.500A) Processing helix chain 'B' and resid 2979 through 2987 removed outlier: 3.959A pdb=" N LEU B2983 " --> pdb=" O TYR B2979 " (cutoff:3.500A) Processing helix chain 'B' and resid 2987 through 3000 removed outlier: 3.502A pdb=" N MET B2991 " --> pdb=" O ASN B2987 " (cutoff:3.500A) Processing helix chain 'B' and resid 3031 through 3046 Processing helix chain 'B' and resid 3050 through 3064 Proline residue: B3056 - end of helix Processing helix chain 'B' and resid 3078 through 3089 Processing helix chain 'B' and resid 3091 through 3101 Processing helix chain 'B' and resid 3103 through 3118 Processing helix chain 'B' and resid 3124 through 3132 removed outlier: 3.587A pdb=" N THR B3128 " --> pdb=" O SER B3124 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE B3132 " --> pdb=" O THR B3128 " (cutoff:3.500A) Processing helix chain 'B' and resid 3178 through 3184 removed outlier: 4.447A pdb=" N VAL B3181 " --> pdb=" O PRO B3178 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B3184 " --> pdb=" O VAL B3181 " (cutoff:3.500A) Processing helix chain 'B' and resid 3231 through 3235 removed outlier: 3.745A pdb=" N THR B3234 " --> pdb=" O SER B3231 " (cutoff:3.500A) Processing helix chain 'B' and resid 3321 through 3325 removed outlier: 4.141A pdb=" N LYS B3325 " --> pdb=" O ASP B3321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3321 through 3325' Processing helix chain 'B' and resid 3327 through 3340 Processing helix chain 'B' and resid 3344 through 3353 removed outlier: 3.616A pdb=" N MET B3348 " --> pdb=" O LEU B3344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3357 through 3367 Processing helix chain 'B' and resid 3368 through 3373 removed outlier: 4.072A pdb=" N MET B3373 " --> pdb=" O TYR B3370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3374 through 3387 Processing helix chain 'B' and resid 3389 through 3402 Processing helix chain 'B' and resid 3429 through 3441 removed outlier: 3.671A pdb=" N THR B3441 " --> pdb=" O GLN B3437 " (cutoff:3.500A) Processing helix chain 'B' and resid 3445 through 3467 Processing helix chain 'B' and resid 3483 through 3488 Processing helix chain 'B' and resid 3490 through 3507 Processing helix chain 'B' and resid 3512 through 3517 removed outlier: 3.915A pdb=" N LEU B3516 " --> pdb=" O ASP B3512 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B3517 " --> pdb=" O LEU B3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3512 through 3517' Processing helix chain 'B' and resid 3518 through 3531 Processing helix chain 'B' and resid 3536 through 3553 removed outlier: 4.332A pdb=" N LYS B3540 " --> pdb=" O MET B3536 " (cutoff:3.500A) Processing helix chain 'B' and resid 3553 through 3562 removed outlier: 3.666A pdb=" N PHE B3557 " --> pdb=" O HIS B3553 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B3562 " --> pdb=" O SER B3558 " (cutoff:3.500A) Processing helix chain 'B' and resid 3606 through 3616 Processing helix chain 'B' and resid 3619 through 3629 Processing helix chain 'B' and resid 3630 through 3652 Processing helix chain 'B' and resid 3682 through 3694 Processing helix chain 'B' and resid 3696 through 3704 Processing helix chain 'B' and resid 3709 through 3721 Processing helix chain 'B' and resid 3752 through 3771 removed outlier: 3.534A pdb=" N ILE B3771 " --> pdb=" O PHE B3767 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3791 Processing helix chain 'B' and resid 3805 through 3815 Processing helix chain 'B' and resid 3846 through 3850 removed outlier: 3.692A pdb=" N GLY B3850 " --> pdb=" O PRO B3847 " (cutoff:3.500A) Processing helix chain 'B' and resid 3865 through 3872 removed outlier: 3.581A pdb=" N VAL B3869 " --> pdb=" O THR B3865 " (cutoff:3.500A) Processing helix chain 'B' and resid 3982 through 3992 Processing helix chain 'B' and resid 4069 through 4077 removed outlier: 4.202A pdb=" N MET B4077 " --> pdb=" O VAL B4073 " (cutoff:3.500A) Processing helix chain 'B' and resid 4078 through 4086 removed outlier: 3.691A pdb=" N LEU B4082 " --> pdb=" O GLY B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4154 through 4165 removed outlier: 4.014A pdb=" N LEU B4158 " --> pdb=" O PRO B4154 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B4162 " --> pdb=" O LEU B4158 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B4163 " --> pdb=" O ALA B4159 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4175 removed outlier: 3.669A pdb=" N VAL B4173 " --> pdb=" O GLY B4169 " (cutoff:3.500A) Processing helix chain 'B' and resid 4177 through 4190 Processing helix chain 'B' and resid 4211 through 4224 removed outlier: 3.847A pdb=" N LEU B4217 " --> pdb=" O PRO B4213 " (cutoff:3.500A) Processing helix chain 'B' and resid 4228 through 4242 removed outlier: 3.811A pdb=" N VAL B4232 " --> pdb=" O THR B4228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4242 through 4256 removed outlier: 3.555A pdb=" N LEU B4246 " --> pdb=" O GLY B4242 " (cutoff:3.500A) Processing helix chain 'B' and resid 4315 through 4332 Processing helix chain 'B' and resid 4357 through 4365 removed outlier: 4.050A pdb=" N LEU B4361 " --> pdb=" O PRO B4357 " (cutoff:3.500A) Processing helix chain 'B' and resid 4368 through 4378 Processing helix chain 'B' and resid 4391 through 4405 Processing helix chain 'B' and resid 4406 through 4413 Proline residue: B4410 - end of helix removed outlier: 3.711A pdb=" N LEU B4413 " --> pdb=" O PRO B4410 " (cutoff:3.500A) Processing helix chain 'B' and resid 4432 through 4445 Processing helix chain 'B' and resid 4478 through 4496 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 64 removed outlier: 5.611A pdb=" N ARG A 59 " --> pdb=" O GLN A 965 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLN A 965 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY A 61 " --> pdb=" O PHE A 963 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A 963 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 942 " --> pdb=" O CYS A 955 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 72 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 70 through 72 current: chain 'A' and resid 81 through 86 removed outlier: 5.553A pdb=" N ASP A 95 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N THR A 101 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 120 Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 165 removed outlier: 3.546A pdb=" N LEU A 223 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 392 removed outlier: 7.416A pdb=" N ALA A 403 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE A 391 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA A 401 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 503 through 513 removed outlier: 7.385A pdb=" N VAL A 503 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS A 576 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU A 505 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR A 574 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE A 507 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 572 " --> pdb=" O ILE A 507 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 509 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG A 721 " --> pdb=" O PRO A 628 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU A 630 " --> pdb=" O CYS A 719 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N CYS A 719 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 632 " --> pdb=" O VAL A 717 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 731 through 738 removed outlier: 5.444A pdb=" N ILE A 733 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A 750 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A 824 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 858 through 862 removed outlier: 3.854A pdb=" N SER A 858 " --> pdb=" O THR A 906 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS A 902 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP A 916 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 922 " --> pdb=" O ASP A 916 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1031 through 1033 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1031 through 1033 current: chain 'A' and resid 1075 through 1079 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1075 through 1079 current: chain 'A' and resid 1198 through 1203 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1039 through 1041 removed outlier: 4.017A pdb=" N VAL A1186 " --> pdb=" O VAL A1122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1564 through 1565 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1564 through 1565 current: chain 'A' and resid 1788 through 1806 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1788 through 1806 current: chain 'A' and resid 1829 through 1834 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1577 through 1581 Processing sheet with id=AB6, first strand: chain 'A' and resid 2877 through 2880 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2877 through 2880 current: chain 'A' and resid 3251 through 3252 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 3855 through 3861 Processing sheet with id=AB8, first strand: chain 'B' and resid 57 through 64 removed outlier: 5.610A pdb=" N ARG B 59 " --> pdb=" O GLN B 965 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLN B 965 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY B 61 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE B 963 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 942 " --> pdb=" O CYS B 955 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 70 through 72 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 70 through 72 current: chain 'B' and resid 81 through 86 removed outlier: 5.553A pdb=" N ASP B 95 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N THR B 101 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 120 Processing sheet with id=AC2, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AC3, first strand: chain 'B' and resid 160 through 165 removed outlier: 3.547A pdb=" N LEU B 223 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 314 through 316 Processing sheet with id=AC5, first strand: chain 'B' and resid 388 through 392 removed outlier: 7.415A pdb=" N ALA B 403 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE B 391 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA B 401 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 503 through 513 removed outlier: 7.385A pdb=" N VAL B 503 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS B 576 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU B 505 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR B 574 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE B 507 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 572 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 509 " --> pdb=" O GLY B 570 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG B 721 " --> pdb=" O PRO B 628 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B 630 " --> pdb=" O CYS B 719 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS B 719 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 632 " --> pdb=" O VAL B 717 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 731 through 738 removed outlier: 5.443A pdb=" N ILE B 733 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 750 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 824 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 858 through 862 removed outlier: 3.854A pdb=" N SER B 858 " --> pdb=" O THR B 906 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS B 902 " --> pdb=" O LEU B 862 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 916 " --> pdb=" O ILE B 922 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 922 " --> pdb=" O ASP B 916 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1031 through 1033 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1031 through 1033 current: chain 'B' and resid 1075 through 1079 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1075 through 1079 current: chain 'B' and resid 1198 through 1203 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 1039 through 1041 removed outlier: 4.016A pdb=" N VAL B1186 " --> pdb=" O VAL B1122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1564 through 1565 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1564 through 1565 current: chain 'B' and resid 1788 through 1806 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1788 through 1806 current: chain 'B' and resid 1829 through 1834 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1577 through 1581 Processing sheet with id=AD4, first strand: chain 'B' and resid 2877 through 2880 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2877 through 2880 current: chain 'B' and resid 3251 through 3252 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 3855 through 3861 2216 hydrogen bonds defined for protein. 6468 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: 25.05 Time building geometry restraints manager: 16.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14148 1.34 - 1.46: 9493 1.46 - 1.58: 20617 1.58 - 1.70: 4 1.70 - 1.82: 438 Bond restraints: 44700 Sorted by residual: bond pdb=" CB PRO B1807 " pdb=" CG PRO B1807 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 1.00e+01 bond pdb=" CB PRO B1426 " pdb=" CG PRO B1426 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 1.00e+01 bond pdb=" CB PRO A1807 " pdb=" CG PRO A1807 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 1.00e+01 bond pdb=" CB PRO A1426 " pdb=" CG PRO A1426 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 9.95e+00 bond pdb=" C VAL A4409 " pdb=" N PRO A4410 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 5.02e+00 ... (remaining 44695 not shown) Histogram of bond angle deviations from ideal: 94.15 - 102.17: 157 102.17 - 110.20: 8991 110.20 - 118.22: 26595 118.22 - 126.24: 24230 126.24 - 134.27: 751 Bond angle restraints: 60724 Sorted by residual: angle pdb=" CA PRO A1807 " pdb=" N PRO A1807 " pdb=" CD PRO A1807 " ideal model delta sigma weight residual 112.00 94.15 17.85 1.40e+00 5.10e-01 1.63e+02 angle pdb=" CA PRO B1807 " pdb=" N PRO B1807 " pdb=" CD PRO B1807 " ideal model delta sigma weight residual 112.00 94.16 17.84 1.40e+00 5.10e-01 1.62e+02 angle pdb=" CA PRO B1426 " pdb=" N PRO B1426 " pdb=" CD PRO B1426 " ideal model delta sigma weight residual 112.00 98.52 13.48 1.40e+00 5.10e-01 9.27e+01 angle pdb=" CA PRO A1426 " pdb=" N PRO A1426 " pdb=" CD PRO A1426 " ideal model delta sigma weight residual 112.00 98.56 13.44 1.40e+00 5.10e-01 9.22e+01 angle pdb=" N VAL B2850 " pdb=" CA VAL B2850 " pdb=" C VAL B2850 " ideal model delta sigma weight residual 113.20 108.11 5.09 9.60e-01 1.09e+00 2.81e+01 ... (remaining 60719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 23421 17.98 - 35.96: 2811 35.96 - 53.94: 656 53.94 - 71.93: 128 71.93 - 89.91: 38 Dihedral angle restraints: 27054 sinusoidal: 10586 harmonic: 16468 Sorted by residual: dihedral pdb=" CA SER B2941 " pdb=" C SER B2941 " pdb=" N ALA B2942 " pdb=" CA ALA B2942 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER A2941 " pdb=" C SER A2941 " pdb=" N ALA A2942 " pdb=" CA ALA A2942 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER A2398 " pdb=" C SER A2398 " pdb=" N TRP A2399 " pdb=" CA TRP A2399 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 27051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6001 0.053 - 0.106: 1097 0.106 - 0.158: 246 0.158 - 0.211: 14 0.211 - 0.264: 6 Chirality restraints: 7364 Sorted by residual: chirality pdb=" CG LEU A1939 " pdb=" CB LEU A1939 " pdb=" CD1 LEU A1939 " pdb=" CD2 LEU A1939 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU B1939 " pdb=" CB LEU B1939 " pdb=" CD1 LEU B1939 " pdb=" CD2 LEU B1939 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL B3693 " pdb=" CA VAL B3693 " pdb=" CG1 VAL B3693 " pdb=" CG2 VAL B3693 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 7361 not shown) Planarity restraints: 7594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1806 " -0.124 5.00e-02 4.00e+02 1.70e-01 4.65e+01 pdb=" N PRO A1807 " 0.294 5.00e-02 4.00e+02 pdb=" CA PRO A1807 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO A1807 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B1806 " 0.124 5.00e-02 4.00e+02 1.70e-01 4.64e+01 pdb=" N PRO B1807 " -0.294 5.00e-02 4.00e+02 pdb=" CA PRO B1807 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO B1807 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B1425 " 0.100 5.00e-02 4.00e+02 1.42e-01 3.20e+01 pdb=" N PRO B1426 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO B1426 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B1426 " 0.072 5.00e-02 4.00e+02 ... (remaining 7591 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 10007 2.79 - 3.32: 40139 3.32 - 3.85: 74741 3.85 - 4.37: 82286 4.37 - 4.90: 143484 Nonbonded interactions: 350657 Sorted by model distance: nonbonded pdb=" O SER B3616 " pdb=" OG SER B3616 " model vdw 2.263 2.440 nonbonded pdb=" O SER A3616 " pdb=" OG SER A3616 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASP B3443 " pdb=" OG1 THR B3446 " model vdw 2.273 2.440 nonbonded pdb=" OD1 ASP A3443 " pdb=" OG1 THR A3446 " model vdw 2.273 2.440 nonbonded pdb=" OH TYR A 945 " pdb=" OD1 ASP A 950 " model vdw 2.283 2.440 ... (remaining 350652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 13.160 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 122.690 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.210 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 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 : 0.003 0.158 44700 Z= 0.217 Angle : 0.764 17.851 60724 Z= 0.375 Chirality : 0.044 0.264 7364 Planarity : 0.007 0.170 7594 Dihedral : 16.626 89.907 16278 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.36 % Allowed : 22.19 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.10), residues: 5490 helix: -0.44 (0.09), residues: 2756 sheet: 0.19 (0.19), residues: 776 loop : -1.15 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2710 HIS 0.007 0.001 HIS A1845 PHE 0.051 0.001 PHE A3689 TYR 0.040 0.001 TYR B2711 ARG 0.006 0.000 ARG A2717 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 348 time to evaluate : 4.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2030 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7735 (pp) REVERT: A 3101 MET cc_start: 0.7087 (ptp) cc_final: 0.6840 (ptt) REVERT: B 309 MET cc_start: 0.3239 (tmm) cc_final: 0.2822 (ttp) REVERT: B 3101 MET cc_start: 0.7051 (ptp) cc_final: 0.6803 (ptt) outliers start: 18 outliers final: 7 residues processed: 360 average time/residue: 0.5122 time to fit residues: 320.2121 Evaluate side-chains 331 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 323 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2582 MET Chi-restraints excluded: chain A residue 3333 LEU Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 2582 MET Chi-restraints excluded: chain B residue 3333 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 477 optimal weight: 6.9990 chunk 429 optimal weight: 0.7980 chunk 238 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 289 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 443 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 513 optimal weight: 0.5980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 ASN A2200 GLN ** A2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 HIS A4245 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1376 ASN B2200 GLN ** B2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3966 HIS B4245 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 44700 Z= 0.288 Angle : 0.612 10.023 60724 Z= 0.294 Chirality : 0.041 0.310 7364 Planarity : 0.005 0.086 7594 Dihedral : 4.104 51.066 5932 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.44 % Allowed : 20.93 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.11), residues: 5490 helix: 0.83 (0.10), residues: 2794 sheet: 0.27 (0.19), residues: 764 loop : -0.79 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2719 HIS 0.009 0.001 HIS B2777 PHE 0.018 0.002 PHE A2704 TYR 0.012 0.001 TYR A2979 ARG 0.006 0.000 ARG A1934 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 351 time to evaluate : 5.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.2814 (tmm) cc_final: 0.2468 (ttp) REVERT: A 1429 LEU cc_start: 0.6614 (tt) cc_final: 0.6298 (tt) REVERT: A 1942 ILE cc_start: 0.3865 (OUTLIER) cc_final: 0.3515 (mt) REVERT: A 1998 LEU cc_start: 0.8146 (tp) cc_final: 0.7836 (tt) REVERT: A 2030 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7609 (pt) REVERT: A 2777 HIS cc_start: 0.0991 (OUTLIER) cc_final: 0.0664 (p-80) REVERT: A 2880 ARG cc_start: 0.5798 (OUTLIER) cc_final: 0.4364 (mmt-90) REVERT: A 3043 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8681 (tt) REVERT: A 3250 MET cc_start: 0.7988 (mmp) cc_final: 0.7729 (mmp) REVERT: A 3676 MET cc_start: 0.5970 (tmm) cc_final: 0.5606 (ppp) REVERT: A 3699 MET cc_start: 0.6697 (mmp) cc_final: 0.6375 (mmm) REVERT: A 3810 ARG cc_start: 0.5745 (OUTLIER) cc_final: 0.4288 (mtm180) REVERT: A 3848 MET cc_start: 0.7504 (mtp) cc_final: 0.7179 (mtp) REVERT: B 309 MET cc_start: 0.2768 (tmm) cc_final: 0.2471 (ttp) REVERT: B 1429 LEU cc_start: 0.6669 (tt) cc_final: 0.6350 (tt) REVERT: B 1942 ILE cc_start: 0.4007 (OUTLIER) cc_final: 0.3634 (mt) REVERT: B 1998 LEU cc_start: 0.8110 (tp) cc_final: 0.7811 (tt) REVERT: B 2777 HIS cc_start: 0.0989 (OUTLIER) cc_final: 0.0659 (p-80) REVERT: B 2880 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.4460 (mmt-90) REVERT: B 3043 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8683 (tt) REVERT: B 3250 MET cc_start: 0.7993 (mmp) cc_final: 0.7729 (mmp) REVERT: B 3676 MET cc_start: 0.5961 (tmm) cc_final: 0.5602 (ppp) REVERT: B 3699 MET cc_start: 0.6683 (mmp) cc_final: 0.6360 (mmm) REVERT: B 3810 ARG cc_start: 0.5769 (OUTLIER) cc_final: 0.4299 (mtm180) outliers start: 172 outliers final: 90 residues processed: 495 average time/residue: 0.5083 time to fit residues: 442.5851 Evaluate side-chains 428 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 327 time to evaluate : 4.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1556 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1881 HIS Chi-restraints excluded: chain A residue 1888 GLU Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2349 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2668 SER Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2828 THR Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2880 ARG Chi-restraints excluded: chain A residue 2926 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3043 LEU Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3550 CYS Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3679 THR Chi-restraints excluded: chain A residue 3690 LEU Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 4002 ILE Chi-restraints excluded: chain A residue 4173 VAL Chi-restraints excluded: chain A residue 4216 VAL Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1204 THR Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1381 THR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1556 SER Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1881 HIS Chi-restraints excluded: chain B residue 1888 GLU Chi-restraints excluded: chain B residue 1942 ILE Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2349 ASP Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2668 SER Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2828 THR Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2880 ARG Chi-restraints excluded: chain B residue 2926 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3043 LEU Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3550 CYS Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3679 THR Chi-restraints excluded: chain B residue 3690 LEU Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4173 VAL Chi-restraints excluded: chain B residue 4216 VAL Chi-restraints excluded: chain B residue 4319 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 285 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 427 optimal weight: 0.9980 chunk 349 optimal weight: 20.0000 chunk 141 optimal weight: 0.8980 chunk 514 optimal weight: 4.9990 chunk 556 optimal weight: 9.9990 chunk 458 optimal weight: 0.8980 chunk 510 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 413 optimal weight: 9.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3076 GLN A3377 ASN A3845 GLN ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 HIS B3076 GLN B3377 ASN B3845 GLN ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3966 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 44700 Z= 0.194 Angle : 0.540 9.730 60724 Z= 0.256 Chirality : 0.039 0.257 7364 Planarity : 0.004 0.066 7594 Dihedral : 3.918 51.831 5922 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.86 % Allowed : 20.99 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.11), residues: 5490 helix: 1.32 (0.10), residues: 2802 sheet: 0.32 (0.19), residues: 758 loop : -0.61 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2170 HIS 0.005 0.001 HIS A3099 PHE 0.013 0.001 PHE A2353 TYR 0.009 0.001 TYR A2870 ARG 0.003 0.000 ARG B1934 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 358 time to evaluate : 4.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.2743 (tmm) cc_final: 0.2398 (ttp) REVERT: A 1183 CYS cc_start: 0.4560 (OUTLIER) cc_final: 0.4135 (t) REVERT: A 1538 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.4889 (mt) REVERT: A 1814 SER cc_start: 0.6986 (OUTLIER) cc_final: 0.6746 (m) REVERT: A 1942 ILE cc_start: 0.4195 (OUTLIER) cc_final: 0.3860 (mt) REVERT: A 2030 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7595 (pt) REVERT: A 2143 ASP cc_start: 0.7745 (t0) cc_final: 0.7486 (t0) REVERT: A 2327 ARG cc_start: 0.5191 (ptt90) cc_final: 0.4955 (mmm160) REVERT: A 2352 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8945 (mp) REVERT: A 2876 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8221 (mtpt) REVERT: A 2880 ARG cc_start: 0.5829 (OUTLIER) cc_final: 0.4469 (mmt-90) REVERT: A 3058 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8403 (pp) REVERT: A 3535 ASN cc_start: 0.5666 (OUTLIER) cc_final: 0.5443 (m110) REVERT: A 3699 MET cc_start: 0.6587 (mmp) cc_final: 0.6307 (mmm) REVERT: A 3760 GLU cc_start: 0.7499 (tt0) cc_final: 0.7100 (tt0) REVERT: A 3810 ARG cc_start: 0.5800 (OUTLIER) cc_final: 0.4383 (mtt180) REVERT: A 3848 MET cc_start: 0.7445 (mtp) cc_final: 0.7104 (mtp) REVERT: B 309 MET cc_start: 0.2744 (tmm) cc_final: 0.2405 (ttp) REVERT: B 1183 CYS cc_start: 0.4526 (OUTLIER) cc_final: 0.4118 (t) REVERT: B 1538 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.5023 (tt) REVERT: B 1814 SER cc_start: 0.7015 (OUTLIER) cc_final: 0.6664 (m) REVERT: B 1942 ILE cc_start: 0.4206 (OUTLIER) cc_final: 0.3869 (mt) REVERT: B 2143 ASP cc_start: 0.7756 (t0) cc_final: 0.7506 (t0) REVERT: B 2327 ARG cc_start: 0.5186 (ptt90) cc_final: 0.4966 (mmm160) REVERT: B 2352 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8949 (mp) REVERT: B 2876 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8229 (mtpt) REVERT: B 2880 ARG cc_start: 0.5836 (OUTLIER) cc_final: 0.4470 (mmt-90) REVERT: B 3058 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8404 (pp) REVERT: B 3535 ASN cc_start: 0.5664 (OUTLIER) cc_final: 0.5447 (m110) REVERT: B 3699 MET cc_start: 0.6506 (mmp) cc_final: 0.6233 (mmm) REVERT: B 3760 GLU cc_start: 0.7500 (tt0) cc_final: 0.6907 (tt0) REVERT: B 3810 ARG cc_start: 0.5822 (OUTLIER) cc_final: 0.4359 (mtm180) outliers start: 193 outliers final: 105 residues processed: 521 average time/residue: 0.5080 time to fit residues: 461.8825 Evaluate side-chains 455 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 329 time to evaluate : 4.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1556 SER Chi-restraints excluded: chain A residue 1814 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2027 ILE Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2322 THR Chi-restraints excluded: chain A residue 2328 CYS Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2349 ASP Chi-restraints excluded: chain A residue 2352 LEU Chi-restraints excluded: chain A residue 2722 VAL Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2828 THR Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2876 LYS Chi-restraints excluded: chain A residue 2880 ARG Chi-restraints excluded: chain A residue 2935 SER Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3058 LEU Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3222 GLU Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3508 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3550 CYS Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 4002 ILE Chi-restraints excluded: chain A residue 4216 VAL Chi-restraints excluded: chain A residue 4234 LEU Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1556 SER Chi-restraints excluded: chain B residue 1814 SER Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1942 ILE Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2027 ILE Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2322 THR Chi-restraints excluded: chain B residue 2328 CYS Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2349 ASP Chi-restraints excluded: chain B residue 2352 LEU Chi-restraints excluded: chain B residue 2722 VAL Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2828 THR Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2876 LYS Chi-restraints excluded: chain B residue 2880 ARG Chi-restraints excluded: chain B residue 2935 SER Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3058 LEU Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3222 GLU Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3508 LEU Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3550 CYS Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4216 VAL Chi-restraints excluded: chain B residue 4234 LEU Chi-restraints excluded: chain B residue 4319 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 508 optimal weight: 0.4980 chunk 387 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 chunk 345 optimal weight: 9.9990 chunk 516 optimal weight: 20.0000 chunk 547 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 489 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN A 244 GLN A 378 GLN A1456 ASN ** A1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2797 GLN A2931 GLN A3226 GLN ** A3374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 HIS A4156 HIS A4319 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 244 GLN B 378 GLN ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2797 GLN B2931 GLN B3226 GLN ** B3374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3966 HIS B4156 HIS B4319 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 44700 Z= 0.515 Angle : 0.783 16.065 60724 Z= 0.379 Chirality : 0.047 0.239 7364 Planarity : 0.005 0.063 7594 Dihedral : 4.726 49.833 5922 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.89 % Allowed : 20.46 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.11), residues: 5490 helix: 0.84 (0.10), residues: 2786 sheet: 0.12 (0.20), residues: 700 loop : -0.89 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B2719 HIS 0.013 0.002 HIS B2777 PHE 0.026 0.003 PHE B2353 TYR 0.017 0.002 TYR B2979 ARG 0.005 0.001 ARG B 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 362 time to evaluate : 5.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.2821 (tmm) cc_final: 0.2596 (ttp) REVERT: A 378 GLN cc_start: 0.2549 (OUTLIER) cc_final: 0.2205 (tp-100) REVERT: A 1538 LEU cc_start: 0.5331 (OUTLIER) cc_final: 0.4788 (tt) REVERT: A 1564 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6676 (pm20) REVERT: A 1942 ILE cc_start: 0.4760 (OUTLIER) cc_final: 0.4408 (mt) REVERT: A 2327 ARG cc_start: 0.5633 (ptt90) cc_final: 0.5085 (mmm160) REVERT: A 2352 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9071 (mp) REVERT: A 2576 GLU cc_start: 0.7562 (pm20) cc_final: 0.6788 (mm-30) REVERT: A 2876 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8237 (mtpt) REVERT: A 2880 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.4393 (mmt-90) REVERT: A 3052 MET cc_start: 0.8582 (ptp) cc_final: 0.8272 (ptp) REVERT: A 3116 ARG cc_start: 0.7087 (ttm170) cc_final: 0.6535 (tpt90) REVERT: A 3184 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: A 3389 SER cc_start: 0.7521 (t) cc_final: 0.7276 (p) REVERT: A 3510 GLU cc_start: 0.7733 (pp20) cc_final: 0.7391 (pp20) REVERT: A 3810 ARG cc_start: 0.5907 (OUTLIER) cc_final: 0.4339 (mtt180) REVERT: A 4247 ILE cc_start: 0.1852 (OUTLIER) cc_final: 0.1125 (mt) REVERT: B 222 HIS cc_start: 0.0434 (OUTLIER) cc_final: -0.0766 (m-70) REVERT: B 309 MET cc_start: 0.2815 (tmm) cc_final: 0.2593 (ttp) REVERT: B 378 GLN cc_start: 0.2549 (OUTLIER) cc_final: 0.2197 (tp-100) REVERT: B 1538 LEU cc_start: 0.5132 (OUTLIER) cc_final: 0.4553 (tt) REVERT: B 1564 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: B 1942 ILE cc_start: 0.4718 (OUTLIER) cc_final: 0.4355 (mt) REVERT: B 1975 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7385 (tp-100) REVERT: B 2327 ARG cc_start: 0.5636 (ptt90) cc_final: 0.5086 (mmm160) REVERT: B 2352 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9070 (mp) REVERT: B 2576 GLU cc_start: 0.7518 (pm20) cc_final: 0.6789 (mm-30) REVERT: B 2876 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8241 (mtpt) REVERT: B 2880 ARG cc_start: 0.5836 (OUTLIER) cc_final: 0.4388 (mmt-90) REVERT: B 3052 MET cc_start: 0.8588 (ptp) cc_final: 0.8283 (ptp) REVERT: B 3116 ARG cc_start: 0.7086 (ttm170) cc_final: 0.6536 (tpt90) REVERT: B 3184 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7610 (mp10) REVERT: B 3389 SER cc_start: 0.7528 (t) cc_final: 0.7285 (p) REVERT: B 3510 GLU cc_start: 0.7683 (pp20) cc_final: 0.7348 (pp20) REVERT: B 3760 GLU cc_start: 0.7412 (tt0) cc_final: 0.6787 (tt0) REVERT: B 3810 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.4336 (mtm180) REVERT: B 4247 ILE cc_start: 0.1794 (OUTLIER) cc_final: 0.1139 (mt) outliers start: 294 outliers final: 166 residues processed: 622 average time/residue: 0.5078 time to fit residues: 547.7260 Evaluate side-chains 519 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 331 time to evaluate : 4.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1556 SER Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1778 ILE Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1873 ILE Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 1986 LEU Chi-restraints excluded: chain A residue 2027 ILE Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2083 VAL Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2322 THR Chi-restraints excluded: chain A residue 2328 CYS Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2352 LEU Chi-restraints excluded: chain A residue 2375 VAL Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2589 LEU Chi-restraints excluded: chain A residue 2668 SER Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2828 THR Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2876 LYS Chi-restraints excluded: chain A residue 2880 ARG Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3114 SER Chi-restraints excluded: chain A residue 3119 VAL Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3184 GLN Chi-restraints excluded: chain A residue 3186 THR Chi-restraints excluded: chain A residue 3222 GLU Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3240 SER Chi-restraints excluded: chain A residue 3255 THR Chi-restraints excluded: chain A residue 3270 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3370 TYR Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3508 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3545 LEU Chi-restraints excluded: chain A residue 3550 CYS Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3610 LEU Chi-restraints excluded: chain A residue 3690 LEU Chi-restraints excluded: chain A residue 3764 VAL Chi-restraints excluded: chain A residue 3786 CYS Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 3981 MET Chi-restraints excluded: chain A residue 4173 VAL Chi-restraints excluded: chain A residue 4216 VAL Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4478 VAL Chi-restraints excluded: chain A residue 4493 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1381 THR Chi-restraints excluded: chain B residue 1444 THR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1556 SER Chi-restraints excluded: chain B residue 1564 GLU Chi-restraints excluded: chain B residue 1778 ILE Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1873 ILE Chi-restraints excluded: chain B residue 1888 GLU Chi-restraints excluded: chain B residue 1942 ILE Chi-restraints excluded: chain B residue 1975 GLN Chi-restraints excluded: chain B residue 1986 LEU Chi-restraints excluded: chain B residue 2027 ILE Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2083 VAL Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2322 THR Chi-restraints excluded: chain B residue 2328 CYS Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2352 LEU Chi-restraints excluded: chain B residue 2375 VAL Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2573 VAL Chi-restraints excluded: chain B residue 2583 LEU Chi-restraints excluded: chain B residue 2589 LEU Chi-restraints excluded: chain B residue 2668 SER Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2728 LEU Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2828 THR Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2852 SER Chi-restraints excluded: chain B residue 2876 LYS Chi-restraints excluded: chain B residue 2880 ARG Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3114 SER Chi-restraints excluded: chain B residue 3119 VAL Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3184 GLN Chi-restraints excluded: chain B residue 3186 THR Chi-restraints excluded: chain B residue 3222 GLU Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3240 SER Chi-restraints excluded: chain B residue 3255 THR Chi-restraints excluded: chain B residue 3270 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3370 TYR Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3508 LEU Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3545 LEU Chi-restraints excluded: chain B residue 3550 CYS Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3610 LEU Chi-restraints excluded: chain B residue 3690 LEU Chi-restraints excluded: chain B residue 3764 VAL Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 3981 MET Chi-restraints excluded: chain B residue 4173 VAL Chi-restraints excluded: chain B residue 4216 VAL Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4478 VAL Chi-restraints excluded: chain B residue 4493 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 455 optimal weight: 1.9990 chunk 310 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 407 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 466 optimal weight: 0.6980 chunk 378 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 279 optimal weight: 7.9990 chunk 491 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 HIS A1365 ASN ** A2578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 HIS B1365 ASN ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3966 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44700 Z= 0.184 Angle : 0.571 10.435 60724 Z= 0.270 Chirality : 0.040 0.190 7364 Planarity : 0.004 0.058 7594 Dihedral : 4.085 24.445 5918 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.60 % Allowed : 22.71 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.11), residues: 5490 helix: 1.35 (0.10), residues: 2814 sheet: 0.20 (0.19), residues: 740 loop : -0.76 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1358 HIS 0.005 0.001 HIS A1363 PHE 0.018 0.001 PHE B1091 TYR 0.012 0.001 TYR A2870 ARG 0.006 0.000 ARG A1934 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 367 time to evaluate : 4.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.0344 (OUTLIER) cc_final: -0.0860 (m-70) REVERT: A 309 MET cc_start: 0.2857 (tmm) cc_final: 0.2587 (ttp) REVERT: A 378 GLN cc_start: 0.3050 (OUTLIER) cc_final: 0.2591 (tp-100) REVERT: A 1192 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.5951 (tp) REVERT: A 1328 HIS cc_start: 0.5937 (m90) cc_final: 0.5709 (m90) REVERT: A 1829 ARG cc_start: 0.3965 (pmt170) cc_final: 0.3534 (mtt-85) REVERT: A 1966 GLU cc_start: 0.6477 (tm-30) cc_final: 0.6260 (tm-30) REVERT: A 2327 ARG cc_start: 0.5320 (ptt90) cc_final: 0.5044 (mmm160) REVERT: A 2828 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8664 (p) REVERT: A 2876 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8185 (mtpt) REVERT: A 3052 MET cc_start: 0.8498 (ptp) cc_final: 0.8179 (ptp) REVERT: A 3396 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7697 (pp) REVERT: A 3510 GLU cc_start: 0.7560 (pp20) cc_final: 0.7194 (pp20) REVERT: A 3760 GLU cc_start: 0.7593 (tt0) cc_final: 0.6915 (tt0) REVERT: A 3810 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.4441 (mtm180) REVERT: B 309 MET cc_start: 0.2846 (tmm) cc_final: 0.2579 (ttp) REVERT: B 378 GLN cc_start: 0.3455 (OUTLIER) cc_final: 0.2789 (tp-100) REVERT: B 1192 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5906 (tp) REVERT: B 1328 HIS cc_start: 0.5847 (m90) cc_final: 0.5579 (m90) REVERT: B 1829 ARG cc_start: 0.3945 (pmt170) cc_final: 0.3500 (mtt-85) REVERT: B 1863 ARG cc_start: 0.3549 (OUTLIER) cc_final: 0.3208 (mtm180) REVERT: B 2327 ARG cc_start: 0.5318 (ptt90) cc_final: 0.5041 (mmm160) REVERT: B 2828 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8662 (p) REVERT: B 2876 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8188 (mtpt) REVERT: B 3052 MET cc_start: 0.8479 (ptp) cc_final: 0.8155 (ptp) REVERT: B 3396 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7729 (pp) REVERT: B 3510 GLU cc_start: 0.7584 (pp20) cc_final: 0.7234 (pp20) REVERT: B 3810 ARG cc_start: 0.5922 (OUTLIER) cc_final: 0.4457 (mtt180) REVERT: B 4408 MET cc_start: -0.1881 (tpp) cc_final: -0.2085 (tpp) outliers start: 180 outliers final: 114 residues processed: 518 average time/residue: 0.5219 time to fit residues: 466.2188 Evaluate side-chains 475 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 347 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1860 VAL Chi-restraints excluded: chain A residue 1877 PHE Chi-restraints excluded: chain A residue 1989 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2328 CYS Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2722 VAL Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2828 THR Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2876 LYS Chi-restraints excluded: chain A residue 2935 SER Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3127 SER Chi-restraints excluded: chain A residue 3186 THR Chi-restraints excluded: chain A residue 3222 GLU Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3381 VAL Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3550 CYS Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3721 HIS Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3828 SER Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 4216 VAL Chi-restraints excluded: chain A residue 4234 LEU Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1192 LEU Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1863 ARG Chi-restraints excluded: chain B residue 1989 ASN Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2722 VAL Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2828 THR Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2876 LYS Chi-restraints excluded: chain B residue 2935 SER Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3186 THR Chi-restraints excluded: chain B residue 3222 GLU Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3381 VAL Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3550 CYS Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3721 HIS Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3828 SER Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4216 VAL Chi-restraints excluded: chain B residue 4234 LEU Chi-restraints excluded: chain B residue 4315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 184 optimal weight: 0.3980 chunk 492 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 321 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 547 optimal weight: 10.0000 chunk 454 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 287 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3966 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 44700 Z= 0.311 Angle : 0.637 11.838 60724 Z= 0.301 Chirality : 0.042 0.246 7364 Planarity : 0.004 0.054 7594 Dihedral : 4.169 25.461 5918 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.49 % Allowed : 22.67 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 5490 helix: 1.33 (0.10), residues: 2810 sheet: 0.10 (0.19), residues: 744 loop : -0.74 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1358 HIS 0.013 0.001 HIS B1363 PHE 0.020 0.002 PHE A2353 TYR 0.014 0.002 TYR A1883 ARG 0.009 0.000 ARG A1934 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 357 time to evaluate : 4.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.0339 (OUTLIER) cc_final: -0.0882 (m-70) REVERT: A 309 MET cc_start: 0.2774 (tmm) cc_final: 0.2532 (ttp) REVERT: A 378 GLN cc_start: 0.2947 (OUTLIER) cc_final: 0.2568 (tp-100) REVERT: A 1328 HIS cc_start: 0.6004 (m90) cc_final: 0.5714 (m90) REVERT: A 1829 ARG cc_start: 0.3912 (pmt170) cc_final: 0.3574 (mtt-85) REVERT: A 1966 GLU cc_start: 0.6411 (tm-30) cc_final: 0.6202 (tm-30) REVERT: A 2327 ARG cc_start: 0.5482 (ptt90) cc_final: 0.5121 (mmm160) REVERT: A 2352 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8959 (mp) REVERT: A 2711 TYR cc_start: 0.6457 (t80) cc_final: 0.6200 (t80) REVERT: A 3052 MET cc_start: 0.8496 (ptp) cc_final: 0.8282 (ptp) REVERT: A 3116 ARG cc_start: 0.6989 (ttm170) cc_final: 0.6378 (tpt90) REVERT: A 3130 MET cc_start: 0.7748 (tpp) cc_final: 0.7464 (tpp) REVERT: A 3226 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8428 (tp40) REVERT: A 3510 GLU cc_start: 0.7593 (pp20) cc_final: 0.7217 (pp20) REVERT: A 3521 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7453 (tt) REVERT: A 3760 GLU cc_start: 0.7588 (tt0) cc_final: 0.6788 (tt0) REVERT: A 3810 ARG cc_start: 0.5944 (OUTLIER) cc_final: 0.4455 (mtm180) REVERT: A 3817 LEU cc_start: 0.4832 (mp) cc_final: 0.3992 (tt) REVERT: A 3828 SER cc_start: 0.5785 (OUTLIER) cc_final: 0.5566 (p) REVERT: B 222 HIS cc_start: 0.0375 (OUTLIER) cc_final: -0.0821 (m-70) REVERT: B 309 MET cc_start: 0.2757 (tmm) cc_final: 0.2498 (ttp) REVERT: B 378 GLN cc_start: 0.2934 (OUTLIER) cc_final: 0.2564 (tp-100) REVERT: B 1829 ARG cc_start: 0.3895 (pmt170) cc_final: 0.3538 (mtt-85) REVERT: B 1966 GLU cc_start: 0.6382 (tm-30) cc_final: 0.6178 (tm-30) REVERT: B 2327 ARG cc_start: 0.5482 (ptt90) cc_final: 0.5122 (mmm160) REVERT: B 2352 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8959 (mp) REVERT: B 3052 MET cc_start: 0.8541 (ptp) cc_final: 0.8311 (ptp) REVERT: B 3116 ARG cc_start: 0.6895 (ttm170) cc_final: 0.6337 (tpt90) REVERT: B 3130 MET cc_start: 0.7744 (tpp) cc_final: 0.7441 (tpp) REVERT: B 3226 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8424 (tp40) REVERT: B 3389 SER cc_start: 0.7554 (t) cc_final: 0.7254 (p) REVERT: B 3510 GLU cc_start: 0.7600 (pp20) cc_final: 0.7222 (pp20) REVERT: B 3521 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7460 (tt) REVERT: B 3810 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.4475 (mtt180) REVERT: B 3828 SER cc_start: 0.5780 (OUTLIER) cc_final: 0.5564 (p) outliers start: 224 outliers final: 158 residues processed: 554 average time/residue: 0.5144 time to fit residues: 491.3862 Evaluate side-chains 514 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 342 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1436 MET Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1556 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1860 VAL Chi-restraints excluded: chain A residue 1986 LEU Chi-restraints excluded: chain A residue 1989 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2027 ILE Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2322 THR Chi-restraints excluded: chain A residue 2328 CYS Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2352 LEU Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2595 LEU Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2828 THR Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3088 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3114 SER Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3175 THR Chi-restraints excluded: chain A residue 3186 THR Chi-restraints excluded: chain A residue 3222 GLU Chi-restraints excluded: chain A residue 3226 GLN Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3240 SER Chi-restraints excluded: chain A residue 3270 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3359 LEU Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3381 VAL Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3508 LEU Chi-restraints excluded: chain A residue 3521 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3545 LEU Chi-restraints excluded: chain A residue 3550 CYS Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3610 LEU Chi-restraints excluded: chain A residue 3690 LEU Chi-restraints excluded: chain A residue 3721 HIS Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3828 SER Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 4173 VAL Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1192 LEU Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1436 MET Chi-restraints excluded: chain B residue 1444 THR Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1556 SER Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1989 ASN Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2027 ILE Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2322 THR Chi-restraints excluded: chain B residue 2328 CYS Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2352 LEU Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2583 LEU Chi-restraints excluded: chain B residue 2595 LEU Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2728 LEU Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2828 THR Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3088 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3114 SER Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3186 THR Chi-restraints excluded: chain B residue 3222 GLU Chi-restraints excluded: chain B residue 3226 GLN Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3240 SER Chi-restraints excluded: chain B residue 3270 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3381 VAL Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3508 LEU Chi-restraints excluded: chain B residue 3521 LEU Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3545 LEU Chi-restraints excluded: chain B residue 3550 CYS Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3610 LEU Chi-restraints excluded: chain B residue 3690 LEU Chi-restraints excluded: chain B residue 3721 HIS Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3828 SER Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 527 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 312 optimal weight: 1.9990 chunk 399 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 chunk 460 optimal weight: 0.8980 chunk 305 optimal weight: 20.0000 chunk 545 optimal weight: 1.9990 chunk 341 optimal weight: 6.9990 chunk 332 optimal weight: 20.0000 chunk 251 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 GLN ** A2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1297 GLN ** B1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3966 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 44700 Z= 0.348 Angle : 0.657 12.225 60724 Z= 0.313 Chirality : 0.043 0.384 7364 Planarity : 0.005 0.055 7594 Dihedral : 4.320 25.710 5918 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.09 % Allowed : 22.15 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.11), residues: 5490 helix: 1.25 (0.10), residues: 2806 sheet: 0.02 (0.19), residues: 728 loop : -0.84 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1358 HIS 0.009 0.001 HIS B1363 PHE 0.022 0.002 PHE A2353 TYR 0.017 0.002 TYR A1883 ARG 0.006 0.001 ARG A1934 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 354 time to evaluate : 4.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.0361 (OUTLIER) cc_final: -0.0848 (m-70) REVERT: A 309 MET cc_start: 0.2875 (tmm) cc_final: 0.2656 (ttp) REVERT: A 1304 ARG cc_start: 0.4978 (mmt90) cc_final: 0.4670 (mpt180) REVERT: A 1328 HIS cc_start: 0.5998 (m90) cc_final: 0.5663 (m90) REVERT: A 1335 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5834 (mm) REVERT: A 1829 ARG cc_start: 0.3835 (pmt170) cc_final: 0.3542 (mtt-85) REVERT: A 1883 TYR cc_start: 0.6103 (t80) cc_final: 0.5824 (t80) REVERT: A 1966 GLU cc_start: 0.6601 (tm-30) cc_final: 0.6379 (tm-30) REVERT: A 1975 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7368 (tp-100) REVERT: A 2327 ARG cc_start: 0.5531 (ptt90) cc_final: 0.5159 (mmm160) REVERT: A 2352 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9103 (mp) REVERT: A 2394 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6478 (ptt90) REVERT: A 2876 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8158 (mtpt) REVERT: A 3083 TRP cc_start: 0.7767 (m-10) cc_final: 0.7154 (m-10) REVERT: A 3116 ARG cc_start: 0.6884 (ttm170) cc_final: 0.6339 (tpt90) REVERT: A 3226 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8447 (tp40) REVERT: A 3396 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7685 (pp) REVERT: A 3510 GLU cc_start: 0.7595 (pp20) cc_final: 0.7227 (pp20) REVERT: A 3521 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7433 (tt) REVERT: A 3810 ARG cc_start: 0.6051 (OUTLIER) cc_final: 0.4503 (mtt180) REVERT: A 3817 LEU cc_start: 0.4881 (mp) cc_final: 0.4070 (tt) REVERT: A 3828 SER cc_start: 0.5829 (OUTLIER) cc_final: 0.5583 (p) REVERT: A 3856 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6854 (tpt170) REVERT: A 4247 ILE cc_start: 0.1973 (OUTLIER) cc_final: 0.1231 (mt) REVERT: B 222 HIS cc_start: 0.0333 (OUTLIER) cc_final: -0.0867 (m-70) REVERT: B 309 MET cc_start: 0.2868 (tmm) cc_final: 0.2649 (ttp) REVERT: B 1335 LEU cc_start: 0.6105 (OUTLIER) cc_final: 0.5858 (mm) REVERT: B 1829 ARG cc_start: 0.3823 (pmt170) cc_final: 0.3589 (mtt-85) REVERT: B 1863 ARG cc_start: 0.3768 (mtm180) cc_final: 0.3547 (mtm180) REVERT: B 1883 TYR cc_start: 0.6069 (t80) cc_final: 0.5822 (t80) REVERT: B 1966 GLU cc_start: 0.6674 (tm-30) cc_final: 0.6439 (tm-30) REVERT: B 1975 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7406 (tp-100) REVERT: B 2327 ARG cc_start: 0.5534 (ptt90) cc_final: 0.5161 (mmm160) REVERT: B 2352 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9102 (mp) REVERT: B 2394 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6469 (ptt90) REVERT: B 2576 GLU cc_start: 0.7337 (pm20) cc_final: 0.6662 (mm-30) REVERT: B 2876 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8160 (mtpt) REVERT: B 3052 MET cc_start: 0.8528 (ptp) cc_final: 0.8314 (ptp) REVERT: B 3083 TRP cc_start: 0.7772 (m-10) cc_final: 0.7162 (m-10) REVERT: B 3116 ARG cc_start: 0.6886 (ttm170) cc_final: 0.6347 (tpt90) REVERT: B 3226 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8443 (tp40) REVERT: B 3389 SER cc_start: 0.7464 (t) cc_final: 0.7165 (p) REVERT: B 3510 GLU cc_start: 0.7612 (pp20) cc_final: 0.7240 (pp20) REVERT: B 3521 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7440 (tt) REVERT: B 3681 ASP cc_start: 0.7248 (t0) cc_final: 0.7045 (t0) REVERT: B 3810 ARG cc_start: 0.6044 (OUTLIER) cc_final: 0.4465 (mtt180) REVERT: B 3817 LEU cc_start: 0.4907 (mp) cc_final: 0.4088 (tt) REVERT: B 3828 SER cc_start: 0.5831 (OUTLIER) cc_final: 0.5589 (p) REVERT: B 3856 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6861 (tpt170) REVERT: B 4247 ILE cc_start: 0.1910 (OUTLIER) cc_final: 0.1238 (mt) outliers start: 254 outliers final: 188 residues processed: 576 average time/residue: 0.5379 time to fit residues: 533.3542 Evaluate side-chains 557 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 344 time to evaluate : 5.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 348 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1365 ASN Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1556 SER Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1860 VAL Chi-restraints excluded: chain A residue 1975 GLN Chi-restraints excluded: chain A residue 1986 LEU Chi-restraints excluded: chain A residue 1989 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2027 ILE Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2322 THR Chi-restraints excluded: chain A residue 2328 CYS Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2352 LEU Chi-restraints excluded: chain A residue 2375 VAL Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2394 ARG Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2595 LEU Chi-restraints excluded: chain A residue 2668 SER Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2828 THR Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2876 LYS Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3088 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3114 SER Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3175 THR Chi-restraints excluded: chain A residue 3186 THR Chi-restraints excluded: chain A residue 3221 LYS Chi-restraints excluded: chain A residue 3222 GLU Chi-restraints excluded: chain A residue 3226 GLN Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3240 SER Chi-restraints excluded: chain A residue 3270 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3359 LEU Chi-restraints excluded: chain A residue 3370 TYR Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3381 VAL Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3508 LEU Chi-restraints excluded: chain A residue 3521 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3545 LEU Chi-restraints excluded: chain A residue 3550 CYS Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3610 LEU Chi-restraints excluded: chain A residue 3690 LEU Chi-restraints excluded: chain A residue 3721 HIS Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3828 SER Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 3856 ARG Chi-restraints excluded: chain A residue 4064 THR Chi-restraints excluded: chain A residue 4232 VAL Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain A residue 4478 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1192 LEU Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1335 LEU Chi-restraints excluded: chain B residue 1365 ASN Chi-restraints excluded: chain B residue 1436 MET Chi-restraints excluded: chain B residue 1444 THR Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1556 SER Chi-restraints excluded: chain B residue 1832 VAL Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1975 GLN Chi-restraints excluded: chain B residue 1986 LEU Chi-restraints excluded: chain B residue 1989 ASN Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2027 ILE Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2106 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2180 ASP Chi-restraints excluded: chain B residue 2322 THR Chi-restraints excluded: chain B residue 2328 CYS Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2352 LEU Chi-restraints excluded: chain B residue 2375 VAL Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2394 ARG Chi-restraints excluded: chain B residue 2583 LEU Chi-restraints excluded: chain B residue 2595 LEU Chi-restraints excluded: chain B residue 2668 SER Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2728 LEU Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2828 THR Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2876 LYS Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3088 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3114 SER Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3175 THR Chi-restraints excluded: chain B residue 3186 THR Chi-restraints excluded: chain B residue 3221 LYS Chi-restraints excluded: chain B residue 3222 GLU Chi-restraints excluded: chain B residue 3226 GLN Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3240 SER Chi-restraints excluded: chain B residue 3270 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3321 ASP Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3370 TYR Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3381 VAL Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3508 LEU Chi-restraints excluded: chain B residue 3521 LEU Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3545 LEU Chi-restraints excluded: chain B residue 3550 CYS Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3610 LEU Chi-restraints excluded: chain B residue 3690 LEU Chi-restraints excluded: chain B residue 3721 HIS Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3828 SER Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 3856 ARG Chi-restraints excluded: chain B residue 4064 THR Chi-restraints excluded: chain B residue 4232 VAL Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4315 LEU Chi-restraints excluded: chain B residue 4319 HIS Chi-restraints excluded: chain B residue 4478 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 337 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 325 optimal weight: 10.0000 chunk 164 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 346 optimal weight: 5.9990 chunk 371 optimal weight: 0.9980 chunk 269 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 428 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 HIS ** A2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 HIS ** B2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3966 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 44700 Z= 0.326 Angle : 0.647 12.452 60724 Z= 0.309 Chirality : 0.043 0.277 7364 Planarity : 0.005 0.054 7594 Dihedral : 4.320 25.412 5918 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.81 % Allowed : 22.29 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.11), residues: 5490 helix: 1.24 (0.10), residues: 2802 sheet: -0.01 (0.19), residues: 728 loop : -0.86 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1358 HIS 0.021 0.001 HIS B 348 PHE 0.025 0.002 PHE B2353 TYR 0.016 0.002 TYR A1883 ARG 0.010 0.001 ARG A1934 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 349 time to evaluate : 4.671 Fit side-chains REVERT: A 222 HIS cc_start: 0.0357 (OUTLIER) cc_final: -0.0854 (m-70) REVERT: A 1304 ARG cc_start: 0.4922 (mmt90) cc_final: 0.4686 (mpt180) REVERT: A 1335 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5827 (mm) REVERT: A 1829 ARG cc_start: 0.3869 (pmt170) cc_final: 0.3606 (mtt-85) REVERT: A 1966 GLU cc_start: 0.6612 (tm-30) cc_final: 0.6384 (tm-30) REVERT: A 1975 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7400 (tp-100) REVERT: A 2327 ARG cc_start: 0.5503 (ptt90) cc_final: 0.5163 (mmm160) REVERT: A 2352 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9106 (mp) REVERT: A 2394 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6489 (ptt90) REVERT: A 2880 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.4434 (mmt-90) REVERT: A 3083 TRP cc_start: 0.7810 (m-10) cc_final: 0.7189 (m-10) REVERT: A 3116 ARG cc_start: 0.6947 (ttm170) cc_final: 0.6364 (tpt90) REVERT: A 3226 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8428 (tp40) REVERT: A 3510 GLU cc_start: 0.7599 (pp20) cc_final: 0.7231 (pp20) REVERT: A 3521 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7439 (tt) REVERT: A 3810 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.4597 (mtt180) REVERT: A 3817 LEU cc_start: 0.4907 (mp) cc_final: 0.4084 (tt) REVERT: A 3828 SER cc_start: 0.5858 (OUTLIER) cc_final: 0.5594 (p) REVERT: A 3856 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6849 (tpt170) REVERT: A 4247 ILE cc_start: 0.1981 (OUTLIER) cc_final: 0.1238 (mt) REVERT: B 222 HIS cc_start: 0.0332 (OUTLIER) cc_final: -0.0868 (m-70) REVERT: B 1335 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5851 (mm) REVERT: B 1829 ARG cc_start: 0.3867 (pmt170) cc_final: 0.3595 (mtt-85) REVERT: B 1863 ARG cc_start: 0.3707 (mtm180) cc_final: 0.3504 (mtm180) REVERT: B 1883 TYR cc_start: 0.6122 (t80) cc_final: 0.5803 (t80) REVERT: B 1966 GLU cc_start: 0.6590 (tm-30) cc_final: 0.6366 (tm-30) REVERT: B 1975 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7416 (tp-100) REVERT: B 2327 ARG cc_start: 0.5506 (ptt90) cc_final: 0.5161 (mmm160) REVERT: B 2352 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9106 (mp) REVERT: B 2394 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6075 (ptt90) REVERT: B 2576 GLU cc_start: 0.7444 (pm20) cc_final: 0.6809 (mm-30) REVERT: B 2586 MET cc_start: 0.6957 (mtm) cc_final: 0.6747 (mtm) REVERT: B 2880 ARG cc_start: 0.5837 (OUTLIER) cc_final: 0.4433 (mmt-90) REVERT: B 3052 MET cc_start: 0.8531 (ptp) cc_final: 0.8330 (ptp) REVERT: B 3083 TRP cc_start: 0.7812 (m-10) cc_final: 0.7191 (m-10) REVERT: B 3116 ARG cc_start: 0.6943 (ttm170) cc_final: 0.6372 (tpt90) REVERT: B 3226 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8423 (tp40) REVERT: B 3389 SER cc_start: 0.7437 (t) cc_final: 0.7140 (p) REVERT: B 3396 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7742 (pp) REVERT: B 3510 GLU cc_start: 0.7611 (pp20) cc_final: 0.7238 (pp20) REVERT: B 3521 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7446 (tt) REVERT: B 3681 ASP cc_start: 0.7212 (t0) cc_final: 0.7007 (t0) REVERT: B 3698 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6375 (tt) REVERT: B 3810 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.4579 (mtm180) REVERT: B 3817 LEU cc_start: 0.4931 (mp) cc_final: 0.4106 (tt) REVERT: B 3828 SER cc_start: 0.5808 (OUTLIER) cc_final: 0.5545 (p) REVERT: B 3856 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6858 (tpt170) REVERT: B 4247 ILE cc_start: 0.1922 (OUTLIER) cc_final: 0.1247 (mt) outliers start: 240 outliers final: 194 residues processed: 560 average time/residue: 0.5280 time to fit residues: 508.4071 Evaluate side-chains 566 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 346 time to evaluate : 4.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1365 ASN Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1436 MET Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1556 SER Chi-restraints excluded: chain A residue 1558 THR Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1860 VAL Chi-restraints excluded: chain A residue 1975 GLN Chi-restraints excluded: chain A residue 1986 LEU Chi-restraints excluded: chain A residue 1989 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2027 ILE Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2083 VAL Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2132 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2322 THR Chi-restraints excluded: chain A residue 2328 CYS Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2352 LEU Chi-restraints excluded: chain A residue 2375 VAL Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2394 ARG Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2595 LEU Chi-restraints excluded: chain A residue 2668 SER Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2748 THR Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2777 HIS Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2828 THR Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2880 ARG Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3088 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3114 SER Chi-restraints excluded: chain A residue 3119 VAL Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3175 THR Chi-restraints excluded: chain A residue 3186 THR Chi-restraints excluded: chain A residue 3222 GLU Chi-restraints excluded: chain A residue 3226 GLN Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3240 SER Chi-restraints excluded: chain A residue 3270 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3331 LEU Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3359 LEU Chi-restraints excluded: chain A residue 3370 TYR Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3381 VAL Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3508 LEU Chi-restraints excluded: chain A residue 3521 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3545 LEU Chi-restraints excluded: chain A residue 3550 CYS Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3610 LEU Chi-restraints excluded: chain A residue 3690 LEU Chi-restraints excluded: chain A residue 3721 HIS Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3828 SER Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 3856 ARG Chi-restraints excluded: chain A residue 4064 THR Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain A residue 4478 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1192 LEU Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1335 LEU Chi-restraints excluded: chain B residue 1365 ASN Chi-restraints excluded: chain B residue 1381 THR Chi-restraints excluded: chain B residue 1436 MET Chi-restraints excluded: chain B residue 1444 THR Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1556 SER Chi-restraints excluded: chain B residue 1832 VAL Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1975 GLN Chi-restraints excluded: chain B residue 1989 ASN Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2027 ILE Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2083 VAL Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2132 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2180 ASP Chi-restraints excluded: chain B residue 2322 THR Chi-restraints excluded: chain B residue 2328 CYS Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2352 LEU Chi-restraints excluded: chain B residue 2375 VAL Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2394 ARG Chi-restraints excluded: chain B residue 2583 LEU Chi-restraints excluded: chain B residue 2595 LEU Chi-restraints excluded: chain B residue 2668 SER Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2728 LEU Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2828 THR Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2880 ARG Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3088 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3114 SER Chi-restraints excluded: chain B residue 3119 VAL Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3186 THR Chi-restraints excluded: chain B residue 3222 GLU Chi-restraints excluded: chain B residue 3226 GLN Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3240 SER Chi-restraints excluded: chain B residue 3270 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3323 VAL Chi-restraints excluded: chain B residue 3331 LEU Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3370 TYR Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3381 VAL Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3508 LEU Chi-restraints excluded: chain B residue 3521 LEU Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3545 LEU Chi-restraints excluded: chain B residue 3550 CYS Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3610 LEU Chi-restraints excluded: chain B residue 3690 LEU Chi-restraints excluded: chain B residue 3698 ILE Chi-restraints excluded: chain B residue 3721 HIS Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3828 SER Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 3856 ARG Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4064 THR Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4315 LEU Chi-restraints excluded: chain B residue 4319 HIS Chi-restraints excluded: chain B residue 4478 VAL Chi-restraints excluded: chain B residue 4493 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 496 optimal weight: 0.8980 chunk 522 optimal weight: 2.9990 chunk 476 optimal weight: 3.9990 chunk 508 optimal weight: 7.9990 chunk 305 optimal weight: 0.1980 chunk 221 optimal weight: 2.9990 chunk 399 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 459 optimal weight: 0.9980 chunk 480 optimal weight: 2.9990 chunk 506 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN A 348 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 348 HIS ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3966 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44700 Z= 0.198 Angle : 0.578 10.897 60724 Z= 0.272 Chirality : 0.040 0.265 7364 Planarity : 0.004 0.051 7594 Dihedral : 4.042 22.254 5918 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.88 % Allowed : 23.19 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.12), residues: 5490 helix: 1.51 (0.10), residues: 2810 sheet: 0.10 (0.19), residues: 728 loop : -0.79 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1358 HIS 0.006 0.001 HIS B1363 PHE 0.020 0.001 PHE A1091 TYR 0.013 0.001 TYR B2711 ARG 0.008 0.000 ARG A1934 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 361 time to evaluate : 4.858 Fit side-chains revert: symmetry clash REVERT: A 151 GLN cc_start: 0.3115 (OUTLIER) cc_final: 0.0641 (mt0) REVERT: A 222 HIS cc_start: 0.0431 (OUTLIER) cc_final: -0.0755 (m-70) REVERT: A 1304 ARG cc_start: 0.4835 (mmt90) cc_final: 0.4565 (mpt180) REVERT: A 1335 LEU cc_start: 0.5887 (OUTLIER) cc_final: 0.5636 (mm) REVERT: A 1829 ARG cc_start: 0.4067 (pmt170) cc_final: 0.3828 (mtt-85) REVERT: A 1966 GLU cc_start: 0.6613 (tm-30) cc_final: 0.6366 (tm-30) REVERT: A 1975 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7316 (tp-100) REVERT: A 2327 ARG cc_start: 0.5426 (ptt90) cc_final: 0.5145 (mmm160) REVERT: A 3083 TRP cc_start: 0.7609 (m-10) cc_final: 0.7014 (m-10) REVERT: A 3226 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8373 (tp40) REVERT: A 3396 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7774 (pp) REVERT: A 3810 ARG cc_start: 0.6052 (OUTLIER) cc_final: 0.4563 (mtm180) REVERT: A 3817 LEU cc_start: 0.4886 (mp) cc_final: 0.4047 (tt) REVERT: A 3828 SER cc_start: 0.5973 (OUTLIER) cc_final: 0.5764 (p) REVERT: A 3856 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6857 (tpt170) REVERT: B 222 HIS cc_start: 0.0475 (OUTLIER) cc_final: -0.0643 (m-70) REVERT: B 1829 ARG cc_start: 0.4054 (pmt170) cc_final: 0.3816 (mtt-85) REVERT: B 1863 ARG cc_start: 0.3677 (mtm180) cc_final: 0.3472 (mtm180) REVERT: B 1966 GLU cc_start: 0.6704 (tm-30) cc_final: 0.6446 (tm-30) REVERT: B 1975 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7362 (tp-100) REVERT: B 2327 ARG cc_start: 0.5442 (ptt90) cc_final: 0.5143 (mmm160) REVERT: B 2582 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.6255 (ttp) REVERT: B 2586 MET cc_start: 0.7012 (mtm) cc_final: 0.6768 (mtm) REVERT: B 3052 MET cc_start: 0.8477 (ptp) cc_final: 0.8196 (ptp) REVERT: B 3083 TRP cc_start: 0.7631 (m-10) cc_final: 0.7031 (m-10) REVERT: B 3116 ARG cc_start: 0.6980 (ttm170) cc_final: 0.6395 (tpt90) REVERT: B 3226 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8367 (tp40) REVERT: B 3396 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7736 (pp) REVERT: B 3810 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.4574 (mtm180) REVERT: B 3817 LEU cc_start: 0.4907 (mp) cc_final: 0.4064 (tt) REVERT: B 3856 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6864 (tpt170) REVERT: B 4247 ILE cc_start: 0.1786 (OUTLIER) cc_final: 0.1122 (mt) outliers start: 194 outliers final: 154 residues processed: 529 average time/residue: 0.5399 time to fit residues: 494.7266 Evaluate side-chains 509 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 338 time to evaluate : 5.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 348 HIS Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1436 MET Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1860 VAL Chi-restraints excluded: chain A residue 1975 GLN Chi-restraints excluded: chain A residue 1989 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2106 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2595 LEU Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2722 VAL Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2828 THR Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3088 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3114 SER Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3186 THR Chi-restraints excluded: chain A residue 3221 LYS Chi-restraints excluded: chain A residue 3222 GLU Chi-restraints excluded: chain A residue 3226 GLN Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3323 VAL Chi-restraints excluded: chain A residue 3331 LEU Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3550 CYS Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3721 HIS Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3828 SER Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 3856 ARG Chi-restraints excluded: chain A residue 4064 THR Chi-restraints excluded: chain A residue 4232 VAL Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain A residue 4478 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 899 THR Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1192 LEU Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1381 THR Chi-restraints excluded: chain B residue 1436 MET Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1556 SER Chi-restraints excluded: chain B residue 1832 VAL Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1975 GLN Chi-restraints excluded: chain B residue 1989 ASN Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2106 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2180 ASP Chi-restraints excluded: chain B residue 2328 CYS Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2582 MET Chi-restraints excluded: chain B residue 2583 LEU Chi-restraints excluded: chain B residue 2595 LEU Chi-restraints excluded: chain B residue 2668 SER Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2722 VAL Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2828 THR Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3088 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3114 SER Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3186 THR Chi-restraints excluded: chain B residue 3222 GLU Chi-restraints excluded: chain B residue 3226 GLN Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3331 LEU Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3550 CYS Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3721 HIS Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 3856 ARG Chi-restraints excluded: chain B residue 4064 THR Chi-restraints excluded: chain B residue 4232 VAL Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4315 LEU Chi-restraints excluded: chain B residue 4319 HIS Chi-restraints excluded: chain B residue 4478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 333 optimal weight: 5.9990 chunk 537 optimal weight: 0.0020 chunk 328 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 373 optimal weight: 5.9990 chunk 563 optimal weight: 9.9990 chunk 518 optimal weight: 0.0270 chunk 449 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 346 optimal weight: 6.9990 chunk 275 optimal weight: 0.0060 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 44700 Z= 0.245 Angle : 0.769 59.175 60724 Z= 0.411 Chirality : 0.048 1.481 7364 Planarity : 0.005 0.198 7594 Dihedral : 4.040 22.242 5918 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.64 % Allowed : 23.37 % Favored : 72.99 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.12), residues: 5490 helix: 1.51 (0.10), residues: 2808 sheet: 0.11 (0.19), residues: 728 loop : -0.78 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1358 HIS 0.310 0.003 HIS B 348 PHE 0.020 0.001 PHE A1091 TYR 0.012 0.001 TYR A2870 ARG 0.008 0.000 ARG A1934 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 336 time to evaluate : 4.743 Fit side-chains REVERT: A 151 GLN cc_start: 0.3688 (OUTLIER) cc_final: 0.2611 (pm20) REVERT: A 222 HIS cc_start: 0.0429 (OUTLIER) cc_final: -0.0754 (m-70) REVERT: A 1304 ARG cc_start: 0.4835 (mmt90) cc_final: 0.4567 (mpt180) REVERT: A 1335 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5635 (mm) REVERT: A 1829 ARG cc_start: 0.4066 (pmt170) cc_final: 0.3827 (mtt-85) REVERT: A 1966 GLU cc_start: 0.6613 (tm-30) cc_final: 0.6365 (tm-30) REVERT: A 1975 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7316 (tp-100) REVERT: A 2327 ARG cc_start: 0.5423 (ptt90) cc_final: 0.5145 (mmm160) REVERT: A 3083 TRP cc_start: 0.7629 (m-10) cc_final: 0.7031 (m-10) REVERT: A 3226 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8373 (tp40) REVERT: A 3396 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7774 (pp) REVERT: A 3810 ARG cc_start: 0.6053 (OUTLIER) cc_final: 0.4564 (mtm180) REVERT: A 3817 LEU cc_start: 0.4887 (mp) cc_final: 0.4047 (tt) REVERT: A 3828 SER cc_start: 0.5969 (OUTLIER) cc_final: 0.5763 (p) REVERT: A 3856 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6866 (tpt170) REVERT: B 151 GLN cc_start: 0.3698 (OUTLIER) cc_final: 0.2614 (pm20) REVERT: B 222 HIS cc_start: 0.0518 (OUTLIER) cc_final: -0.0612 (m-70) REVERT: B 1829 ARG cc_start: 0.4056 (pmt170) cc_final: 0.3817 (mtt-85) REVERT: B 1863 ARG cc_start: 0.3679 (mtm180) cc_final: 0.3469 (mtm180) REVERT: B 1883 TYR cc_start: 0.6258 (t80) cc_final: 0.6042 (t80) REVERT: B 1966 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6443 (tm-30) REVERT: B 1975 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7372 (tp-100) REVERT: B 2327 ARG cc_start: 0.5441 (ptt90) cc_final: 0.5143 (mmm160) REVERT: B 2586 MET cc_start: 0.7000 (mtm) cc_final: 0.6757 (mtm) REVERT: B 2711 TYR cc_start: 0.6589 (t80) cc_final: 0.6296 (t80) REVERT: B 2876 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8158 (mtpt) REVERT: B 3052 MET cc_start: 0.8477 (ptp) cc_final: 0.8177 (ptp) REVERT: B 3083 TRP cc_start: 0.7630 (m-10) cc_final: 0.7028 (m-10) REVERT: B 3116 ARG cc_start: 0.6980 (ttm170) cc_final: 0.6395 (tpt90) REVERT: B 3226 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8367 (tp40) REVERT: B 3396 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7735 (pp) REVERT: B 3810 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.4575 (mtm180) REVERT: B 3817 LEU cc_start: 0.4909 (mp) cc_final: 0.4064 (tt) REVERT: B 3856 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6873 (tpt170) REVERT: B 4247 ILE cc_start: 0.1785 (OUTLIER) cc_final: 0.1122 (mt) outliers start: 182 outliers final: 159 residues processed: 492 average time/residue: 0.5155 time to fit residues: 436.1852 Evaluate side-chains 512 residues out of total 4994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 335 time to evaluate : 4.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1436 MET Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1538 LEU Chi-restraints excluded: chain A residue 1558 THR Chi-restraints excluded: chain A residue 1832 VAL Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1860 VAL Chi-restraints excluded: chain A residue 1975 GLN Chi-restraints excluded: chain A residue 1989 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2038 LEU Chi-restraints excluded: chain A residue 2049 VAL Chi-restraints excluded: chain A residue 2071 THR Chi-restraints excluded: chain A residue 2074 ILE Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2097 SER Chi-restraints excluded: chain A residue 2106 SER Chi-restraints excluded: chain A residue 2132 SER Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2582 MET Chi-restraints excluded: chain A residue 2583 LEU Chi-restraints excluded: chain A residue 2595 LEU Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2722 VAL Chi-restraints excluded: chain A residue 2774 THR Chi-restraints excluded: chain A residue 2827 GLN Chi-restraints excluded: chain A residue 2828 THR Chi-restraints excluded: chain A residue 2840 LEU Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3039 ILE Chi-restraints excluded: chain A residue 3050 VAL Chi-restraints excluded: chain A residue 3088 VAL Chi-restraints excluded: chain A residue 3091 THR Chi-restraints excluded: chain A residue 3095 LEU Chi-restraints excluded: chain A residue 3114 SER Chi-restraints excluded: chain A residue 3119 VAL Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3186 THR Chi-restraints excluded: chain A residue 3221 LYS Chi-restraints excluded: chain A residue 3222 GLU Chi-restraints excluded: chain A residue 3226 GLN Chi-restraints excluded: chain A residue 3239 VAL Chi-restraints excluded: chain A residue 3291 LEU Chi-restraints excluded: chain A residue 3302 THR Chi-restraints excluded: chain A residue 3323 VAL Chi-restraints excluded: chain A residue 3331 LEU Chi-restraints excluded: chain A residue 3334 LEU Chi-restraints excluded: chain A residue 3371 CYS Chi-restraints excluded: chain A residue 3396 LEU Chi-restraints excluded: chain A residue 3535 ASN Chi-restraints excluded: chain A residue 3550 CYS Chi-restraints excluded: chain A residue 3559 LEU Chi-restraints excluded: chain A residue 3721 HIS Chi-restraints excluded: chain A residue 3791 THR Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3828 SER Chi-restraints excluded: chain A residue 3853 HIS Chi-restraints excluded: chain A residue 3856 ARG Chi-restraints excluded: chain A residue 4232 VAL Chi-restraints excluded: chain A residue 4315 LEU Chi-restraints excluded: chain A residue 4319 HIS Chi-restraints excluded: chain A residue 4478 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 899 THR Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1183 CYS Chi-restraints excluded: chain B residue 1192 LEU Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain B residue 1299 VAL Chi-restraints excluded: chain B residue 1381 THR Chi-restraints excluded: chain B residue 1436 MET Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1512 MET Chi-restraints excluded: chain B residue 1538 LEU Chi-restraints excluded: chain B residue 1556 SER Chi-restraints excluded: chain B residue 1832 VAL Chi-restraints excluded: chain B residue 1833 VAL Chi-restraints excluded: chain B residue 1860 VAL Chi-restraints excluded: chain B residue 1975 GLN Chi-restraints excluded: chain B residue 1989 ASN Chi-restraints excluded: chain B residue 2008 THR Chi-restraints excluded: chain B residue 2035 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2071 THR Chi-restraints excluded: chain B residue 2074 ILE Chi-restraints excluded: chain B residue 2080 LEU Chi-restraints excluded: chain B residue 2097 SER Chi-restraints excluded: chain B residue 2106 SER Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2180 ASP Chi-restraints excluded: chain B residue 2328 CYS Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2386 LEU Chi-restraints excluded: chain B residue 2583 LEU Chi-restraints excluded: chain B residue 2595 LEU Chi-restraints excluded: chain B residue 2668 SER Chi-restraints excluded: chain B residue 2715 LEU Chi-restraints excluded: chain B residue 2722 VAL Chi-restraints excluded: chain B residue 2774 THR Chi-restraints excluded: chain B residue 2777 HIS Chi-restraints excluded: chain B residue 2827 GLN Chi-restraints excluded: chain B residue 2828 THR Chi-restraints excluded: chain B residue 2840 LEU Chi-restraints excluded: chain B residue 2876 LYS Chi-restraints excluded: chain B residue 2944 VAL Chi-restraints excluded: chain B residue 3039 ILE Chi-restraints excluded: chain B residue 3050 VAL Chi-restraints excluded: chain B residue 3088 VAL Chi-restraints excluded: chain B residue 3091 THR Chi-restraints excluded: chain B residue 3095 LEU Chi-restraints excluded: chain B residue 3114 SER Chi-restraints excluded: chain B residue 3119 VAL Chi-restraints excluded: chain B residue 3121 THR Chi-restraints excluded: chain B residue 3186 THR Chi-restraints excluded: chain B residue 3222 GLU Chi-restraints excluded: chain B residue 3226 GLN Chi-restraints excluded: chain B residue 3239 VAL Chi-restraints excluded: chain B residue 3291 LEU Chi-restraints excluded: chain B residue 3302 THR Chi-restraints excluded: chain B residue 3331 LEU Chi-restraints excluded: chain B residue 3334 LEU Chi-restraints excluded: chain B residue 3371 CYS Chi-restraints excluded: chain B residue 3396 LEU Chi-restraints excluded: chain B residue 3535 ASN Chi-restraints excluded: chain B residue 3550 CYS Chi-restraints excluded: chain B residue 3559 LEU Chi-restraints excluded: chain B residue 3690 LEU Chi-restraints excluded: chain B residue 3721 HIS Chi-restraints excluded: chain B residue 3791 THR Chi-restraints excluded: chain B residue 3810 ARG Chi-restraints excluded: chain B residue 3853 HIS Chi-restraints excluded: chain B residue 3856 ARG Chi-restraints excluded: chain B residue 4002 ILE Chi-restraints excluded: chain B residue 4232 VAL Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4315 LEU Chi-restraints excluded: chain B residue 4319 HIS Chi-restraints excluded: chain B residue 4478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 356 optimal weight: 20.0000 chunk 478 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 414 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 449 optimal weight: 0.9990 chunk 188 optimal weight: 0.0170 chunk 461 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.219060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157994 restraints weight = 76119.777| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 3.81 r_work: 0.3697 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 44700 Z= 0.238 Angle : 0.754 57.209 60724 Z= 0.402 Chirality : 0.045 1.150 7364 Planarity : 0.005 0.171 7594 Dihedral : 4.041 22.242 5918 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.66 % Allowed : 23.33 % Favored : 73.01 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.12), residues: 5490 helix: 1.51 (0.10), residues: 2810 sheet: 0.11 (0.19), residues: 728 loop : -0.78 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1358 HIS 0.266 0.002 HIS B 348 PHE 0.017 0.001 PHE B1091 TYR 0.012 0.001 TYR A2870 ARG 0.007 0.000 ARG B1304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11321.69 seconds wall clock time: 206 minutes 16.99 seconds (12376.99 seconds total)