Starting phenix.real_space_refine on Fri Mar 6 12:03:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vpd_32063/03_2026/7vpd_32063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vpd_32063/03_2026/7vpd_32063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vpd_32063/03_2026/7vpd_32063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vpd_32063/03_2026/7vpd_32063.map" model { file = "/net/cci-nas-00/data/ceres_data/7vpd_32063/03_2026/7vpd_32063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vpd_32063/03_2026/7vpd_32063.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 168 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 18840 2.51 5 N 5525 2.21 5 O 6280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30924 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9846 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "F" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2396 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "O" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1714 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "P" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1730 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "S" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12673 SG CYS D 60 70.585 109.436 126.834 1.00109.51 S ATOM 12691 SG CYS D 62 69.748 111.035 129.757 1.00113.61 S ATOM 12800 SG CYS D 75 73.483 110.145 129.466 1.00117.90 S ATOM 12826 SG CYS D 78 71.522 107.311 129.927 1.00107.59 S ATOM 19225 SG CYS D 886 110.165 61.407 99.007 1.00 90.51 S ATOM 19789 SG CYS D 962 106.447 61.400 100.326 1.00 82.70 S ATOM 19837 SG CYS D 969 107.029 62.860 96.936 1.00 83.21 S ATOM 19856 SG CYS D 972 107.419 59.275 97.497 1.00 78.77 S ATOM 25721 SG CYS M 90 56.238 156.211 46.011 1.00236.14 S ATOM 25743 SG CYS M 93 53.167 157.823 47.748 1.00237.18 S ATOM 26016 SG CYS M 130 52.799 154.867 45.352 1.00236.71 S ATOM 26035 SG CYS M 133 53.725 158.382 44.112 1.00234.73 S ATOM 25635 SG CYS M 79 58.722 145.036 56.738 1.00239.38 S ATOM 26705 SG CYS N 90 84.033 135.641 47.758 1.00233.86 S ATOM 26727 SG CYS N 93 87.790 134.905 47.356 1.00230.63 S ATOM 27000 SG CYS N 130 85.120 132.758 45.624 1.00232.87 S ATOM 27019 SG CYS N 133 85.655 132.521 49.332 1.00231.61 S ATOM 26619 SG CYS N 79 80.569 142.948 34.348 1.00238.35 S Time building chain proxies: 6.73, per 1000 atoms: 0.22 Number of scatterers: 30924 At special positions: 0 Unit cell: (131.25, 199.5, 215.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 102 16.00 P 168 15.00 Mg 1 11.99 O 6280 8.00 N 5525 7.00 C 18840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 133 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " Number of angles added : 24 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6508 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 42 sheets defined 45.0% alpha, 13.3% beta 68 base pairs and 124 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.621A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.530A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.509A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.880A pdb=" N LEU B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 203 through 221 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.590A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 73 through 81 removed outlier: 3.529A pdb=" N ILE C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 221 through 229 removed outlier: 4.009A pdb=" N LEU C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 241 Processing helix chain 'C' and resid 243 through 253 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.801A pdb=" N LYS C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 337 removed outlier: 3.563A pdb=" N GLY C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 366 through 392 Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.972A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 4.099A pdb=" N PHE C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 439 Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.731A pdb=" N ARG C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 520 through 525 removed outlier: 4.029A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 574 through 580 removed outlier: 4.116A pdb=" N ILE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 586 Processing helix chain 'C' and resid 587 through 598 Processing helix chain 'C' and resid 616 through 624 removed outlier: 3.780A pdb=" N ALA C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 720 removed outlier: 4.110A pdb=" N ASP C 719 " --> pdb=" O ASN C 716 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 720 " --> pdb=" O TYR C 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 716 through 720' Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 906 through 912 removed outlier: 4.184A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 removed outlier: 3.687A pdb=" N LEU C 918 " --> pdb=" O PRO C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 947 Processing helix chain 'C' and resid 966 through 976 Processing helix chain 'C' and resid 1021 through 1026 Processing helix chain 'C' and resid 1054 through 1065 Processing helix chain 'C' and resid 1066 through 1075 removed outlier: 3.665A pdb=" N LEU C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 4.262A pdb=" N VAL C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS C1086 " --> pdb=" O THR C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1115 removed outlier: 3.800A pdb=" N LYS C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 140 through 147 removed outlier: 3.545A pdb=" N ASP D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 188 Processing helix chain 'D' and resid 192 through 228 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.540A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.832A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.555A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 360 removed outlier: 3.990A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.867A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.648A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.815A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 492 removed outlier: 3.530A pdb=" N TYR D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 529 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 589 Processing helix chain 'D' and resid 606 through 617 Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.631A pdb=" N GLU D 640 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 672 Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 723 removed outlier: 3.878A pdb=" N GLY D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 removed outlier: 3.608A pdb=" N ARG D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 840 through 877 removed outlier: 3.611A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 916 removed outlier: 3.663A pdb=" N SER D 914 " --> pdb=" O ASP D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 958 through 962 Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.557A pdb=" N TYR D 973 " --> pdb=" O CYS D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 999 removed outlier: 3.561A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1005 removed outlier: 4.549A pdb=" N THR D1005 " --> pdb=" O GLY D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1107 removed outlier: 3.538A pdb=" N VAL D1104 " --> pdb=" O ASN D1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1129 removed outlier: 4.182A pdb=" N GLN D1128 " --> pdb=" O VAL D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 3.937A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1208 Processing helix chain 'D' and resid 1213 through 1223 Processing helix chain 'D' and resid 1231 through 1237 removed outlier: 3.668A pdb=" N ILE D1237 " --> pdb=" O GLU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1252 Processing helix chain 'D' and resid 1258 through 1265 removed outlier: 3.523A pdb=" N LYS D1262 " --> pdb=" O THR D1258 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 24 Processing helix chain 'E' and resid 26 through 45 Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.565A pdb=" N ILE E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 223 removed outlier: 4.128A pdb=" N ASP F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 252 Processing helix chain 'F' and resid 257 through 292 removed outlier: 4.542A pdb=" N ARG F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 317 Processing helix chain 'F' and resid 325 through 346 removed outlier: 3.624A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TRP F 333 " --> pdb=" O TYR F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 374 Processing helix chain 'F' and resid 378 through 387 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 429 through 450 Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 471 through 476 Processing helix chain 'F' and resid 482 through 497 Processing helix chain 'F' and resid 498 through 499 No H-bonds generated for 'chain 'F' and resid 498 through 499' Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 503 through 510 removed outlier: 4.233A pdb=" N ASP F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR F 509 " --> pdb=" O VAL F 505 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 26 removed outlier: 3.512A pdb=" N VAL M 26 " --> pdb=" O ALA M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 101 through 116 removed outlier: 3.952A pdb=" N GLU M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'N' and resid 13 through 26 Processing helix chain 'N' and resid 32 through 43 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 101 through 116 removed outlier: 4.226A pdb=" N GLU N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 removed outlier: 4.137A pdb=" N ALA N 134 " --> pdb=" O CYS N 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 250 through 255 Processing helix chain 'S' and resid 257 through 267 Processing helix chain 'S' and resid 271 through 278 Processing helix chain 'S' and resid 279 through 286 Processing helix chain 'S' and resid 290 through 304 removed outlier: 3.774A pdb=" N MET S 304 " --> pdb=" O LYS S 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 15 removed outlier: 6.300A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.754A pdb=" N SER A 53 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 13 removed outlier: 3.678A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP B 188 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 181 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP B 190 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU B 179 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU B 192 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS B 177 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B 194 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 175 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL B 196 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS B 173 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR B 198 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B 171 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 99 removed outlier: 7.538A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.056A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.391A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 100 removed outlier: 5.467A pdb=" N LEU C 93 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR C 128 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE C 95 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLU C 126 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP C 97 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 142 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 134 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 362 through 364 removed outlier: 6.203A pdb=" N SER C 165 " --> pdb=" O ASN C 442 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY C 484 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.698A pdb=" N ASP C 180 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB8, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.753A pdb=" N ARG C 491 " --> pdb=" O GLU C 499 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 498 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 517 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR C 500 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TYR C 502 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP C 513 " --> pdb=" O TYR C 502 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 504 " --> pdb=" O THR C 511 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.753A pdb=" N ARG C 491 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 629 Processing sheet with id=AC2, first strand: chain 'C' and resid 634 through 639 removed outlier: 5.344A pdb=" N VAL C 636 " --> pdb=" O THR C 647 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR C 647 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 638 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC4, first strand: chain 'C' and resid 992 through 993 removed outlier: 7.588A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 722 " --> pdb=" O ILE C 902 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ILE C 901 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU C 706 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU C 903 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA C 708 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 734 through 746 removed outlier: 3.725A pdb=" N HIS C 741 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 857 " --> pdb=" O HIS C 741 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 835 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA C 860 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL C 833 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N LYS C 862 " --> pdb=" O GLY C 831 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N GLY C 831 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 831 " --> pdb=" O VAL C 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 754 through 755 removed outlier: 3.668A pdb=" N GLU C 754 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 892 through 893 Processing sheet with id=AC8, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 3.607A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1052 through 1053 removed outlier: 3.638A pdb=" N LYS D 420 " --> pdb=" O PHE C1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1121 through 1123 removed outlier: 3.660A pdb=" N LEU D 10 " --> pdb=" O ASP D1226 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP D1226 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AD3, first strand: chain 'D' and resid 135 through 139 removed outlier: 5.343A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 336 through 337 Processing sheet with id=AD5, first strand: chain 'D' and resid 430 through 432 Processing sheet with id=AD6, first strand: chain 'D' and resid 443 through 444 removed outlier: 5.885A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AD9, first strand: chain 'D' and resid 892 through 894 removed outlier: 4.228A pdb=" N MET D 919 " --> pdb=" O ARG D 957 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1070 through 1073 Processing sheet with id=AE2, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id=AE3, first strand: chain 'D' and resid 1254 through 1257 removed outlier: 3.507A pdb=" N GLU E 83 " --> pdb=" O ARG D1254 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D1256 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR E 81 " --> pdb=" O GLU D1256 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 65 through 68 Processing sheet with id=AE5, first strand: chain 'M' and resid 96 through 99 removed outlier: 5.462A pdb=" N HIS M 87 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE M 126 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE N 127 " --> pdb=" O ALA M 121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR M 123 " --> pdb=" O GLU N 125 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU N 125 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS N 87 " --> pdb=" O ILE N 126 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 30 through 31 1267 hydrogen bonds defined for protein. 3591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 177 hydrogen bonds 350 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 124 stacking parallelities Total time for adding SS restraints: 8.21 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8212 1.33 - 1.45: 6095 1.45 - 1.58: 16956 1.58 - 1.70: 334 1.70 - 1.82: 178 Bond restraints: 31775 Sorted by residual: bond pdb=" O3' DG O 71 " pdb=" P DG O 72 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" C VAL C 825 " pdb=" N PRO C 826 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.34e-02 5.57e+03 6.47e+00 bond pdb=" C HIS D 494 " pdb=" N PRO D 495 " ideal model delta sigma weight residual 1.332 1.361 -0.030 1.26e-02 6.30e+03 5.55e+00 bond pdb=" O3' DG P 22 " pdb=" P DA P 23 " ideal model delta sigma weight residual 1.607 1.641 -0.034 1.50e-02 4.44e+03 5.20e+00 bond pdb=" CA SER C 420 " pdb=" C SER C 420 " ideal model delta sigma weight residual 1.520 1.493 0.027 1.21e-02 6.83e+03 5.06e+00 ... (remaining 31770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 42191 1.93 - 3.86: 1258 3.86 - 5.80: 206 5.80 - 7.73: 35 7.73 - 9.66: 9 Bond angle restraints: 43699 Sorted by residual: angle pdb=" N GLU F 412 " pdb=" CA GLU F 412 " pdb=" C GLU F 412 " ideal model delta sigma weight residual 111.36 103.98 7.38 1.09e+00 8.42e-01 4.58e+01 angle pdb=" N ARG D 67 " pdb=" CA ARG D 67 " pdb=" C ARG D 67 " ideal model delta sigma weight residual 110.43 118.91 -8.48 1.31e+00 5.83e-01 4.19e+01 angle pdb=" N GLN C 421 " pdb=" CA GLN C 421 " pdb=" C GLN C 421 " ideal model delta sigma weight residual 113.20 105.89 7.31 1.21e+00 6.83e-01 3.65e+01 angle pdb=" O3' DC O 23 " pdb=" C3' DC O 23 " pdb=" C2' DC O 23 " ideal model delta sigma weight residual 111.50 103.30 8.20 1.50e+00 4.44e-01 2.99e+01 angle pdb=" N LYS D 66 " pdb=" CA LYS D 66 " pdb=" C LYS D 66 " ideal model delta sigma weight residual 111.36 117.30 -5.94 1.09e+00 8.42e-01 2.97e+01 ... (remaining 43694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 17837 35.89 - 71.78: 1060 71.78 - 107.67: 32 107.67 - 143.56: 7 143.56 - 179.45: 13 Dihedral angle restraints: 18949 sinusoidal: 8840 harmonic: 10109 Sorted by residual: dihedral pdb=" CA ALA C 907 " pdb=" C ALA C 907 " pdb=" N VAL C 908 " pdb=" CA VAL C 908 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA HIS F 354 " pdb=" C HIS F 354 " pdb=" N MET F 355 " pdb=" CA MET F 355 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C4' DT P 76 " pdb=" C3' DT P 76 " pdb=" O3' DT P 76 " pdb=" P DG P 77 " ideal model delta sinusoidal sigma weight residual -140.00 39.45 -179.45 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 18946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4001 0.055 - 0.109: 813 0.109 - 0.164: 133 0.164 - 0.218: 14 0.218 - 0.273: 8 Chirality restraints: 4969 Sorted by residual: chirality pdb=" CA ARG D 67 " pdb=" N ARG D 67 " pdb=" C ARG D 67 " pdb=" CB ARG D 67 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE D 846 " pdb=" N ILE D 846 " pdb=" C ILE D 846 " pdb=" CB ILE D 846 " both_signs ideal model delta sigma weight residual False 2.43 2.17 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE D 880 " pdb=" N ILE D 880 " pdb=" C ILE D 880 " pdb=" CB ILE D 880 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4966 not shown) Planarity restraints: 5138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 576 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.79e+00 pdb=" N PRO D 577 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 577 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 577 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 462 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO C 463 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 494 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO D 495 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 495 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 495 " 0.033 5.00e-02 4.00e+02 ... (remaining 5135 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 289 2.56 - 3.15: 26526 3.15 - 3.73: 52307 3.73 - 4.32: 67604 4.32 - 4.90: 107817 Nonbonded interactions: 254543 Sorted by model distance: nonbonded pdb=" OD2 ASP N 65 " pdb="ZN ZN N 202 " model vdw 1.979 2.230 nonbonded pdb=" OE2 GLU N 105 " pdb="ZN ZN N 203 " model vdw 1.998 2.230 nonbonded pdb=" OE2 GLU M 105 " pdb="ZN ZN M 203 " model vdw 2.072 2.230 nonbonded pdb=" OD2 ASP D 539 " pdb="MG MG D1401 " model vdw 2.081 2.170 nonbonded pdb=" O GLU M 27 " pdb=" NE ARG M 77 " model vdw 2.198 3.120 ... (remaining 254538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 35.130 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.005 0.061 31803 Z= 0.218 Angle : 0.806 15.531 43723 Z= 0.447 Chirality : 0.046 0.273 4969 Planarity : 0.005 0.086 5138 Dihedral : 20.159 179.445 12441 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.44 % Allowed : 19.79 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3513 helix: 1.08 (0.14), residues: 1405 sheet: -1.02 (0.25), residues: 411 loop : -0.67 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 239 TYR 0.034 0.001 TYR E 32 PHE 0.034 0.002 PHE D 226 TRP 0.009 0.002 TRP D 718 HIS 0.020 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00467 (31775) covalent geometry : angle 0.79233 (43699) hydrogen bonds : bond 0.14599 ( 1443) hydrogen bonds : angle 5.87951 ( 3941) metal coordination : bond 0.00473 ( 28) metal coordination : angle 6.30105 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 391 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6534 (ttm) cc_final: 0.6199 (mtm) REVERT: A 213 LYS cc_start: 0.9211 (tptp) cc_final: 0.8815 (tmtt) REVERT: B 78 LEU cc_start: 0.8243 (mp) cc_final: 0.7966 (tt) REVERT: C 55 LYS cc_start: 0.8931 (ptpt) cc_final: 0.8683 (ptpp) REVERT: C 648 ASN cc_start: 0.4805 (t0) cc_final: 0.3763 (t0) REVERT: C 821 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8064 (p) REVERT: D 43 LYS cc_start: 0.7818 (tppt) cc_final: 0.7579 (mptt) REVERT: D 312 MET cc_start: 0.8728 (mmt) cc_final: 0.8432 (mmm) REVERT: D 379 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7358 (t0) REVERT: D 405 MET cc_start: 0.7996 (mtt) cc_final: 0.7602 (mtt) REVERT: D 862 THR cc_start: 0.8601 (p) cc_final: 0.8193 (t) REVERT: D 1006 MET cc_start: -0.0174 (mmt) cc_final: -0.1119 (mtm) REVERT: F 260 LEU cc_start: 0.9182 (tp) cc_final: 0.8871 (pp) REVERT: F 276 ASN cc_start: 0.9000 (m110) cc_final: 0.8633 (p0) REVERT: F 283 LEU cc_start: 0.9215 (mt) cc_final: 0.8988 (mt) REVERT: F 360 ASN cc_start: 0.9217 (p0) cc_final: 0.8977 (p0) outliers start: 13 outliers final: 2 residues processed: 399 average time/residue: 0.2304 time to fit residues: 141.5373 Evaluate side-chains 316 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 312 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 1190 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN B 82 GLN B 152 ASN B 185 GLN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN C 913 ASN C 916 GLN D 304 GLN D 440 GLN E 64 HIS F 305 GLN F 468 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.156849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.114102 restraints weight = 78489.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.114173 restraints weight = 51473.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.115040 restraints weight = 45708.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.115097 restraints weight = 38571.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.116011 restraints weight = 34522.273| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31803 Z= 0.157 Angle : 0.685 12.077 43723 Z= 0.359 Chirality : 0.044 0.228 4969 Planarity : 0.005 0.059 5138 Dihedral : 21.100 179.918 5659 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.64 % Allowed : 18.27 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3513 helix: 1.25 (0.14), residues: 1421 sheet: -0.62 (0.27), residues: 368 loop : -0.54 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 182 TYR 0.031 0.001 TYR E 32 PHE 0.020 0.002 PHE B 63 TRP 0.011 0.001 TRP D 718 HIS 0.008 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00356 (31775) covalent geometry : angle 0.67563 (43699) hydrogen bonds : bond 0.04529 ( 1443) hydrogen bonds : angle 4.53109 ( 3941) metal coordination : bond 0.00565 ( 28) metal coordination : angle 4.97202 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 368 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.6764 (pm20) cc_final: 0.6497 (pm20) REVERT: A 213 LYS cc_start: 0.9233 (tptp) cc_final: 0.8654 (tmtt) REVERT: B 24 GLU cc_start: 0.6412 (mm-30) cc_final: 0.6183 (mm-30) REVERT: B 79 ASN cc_start: 0.8488 (m-40) cc_final: 0.8256 (m-40) REVERT: B 232 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6868 (pt) REVERT: C 442 ASN cc_start: 0.8701 (t0) cc_final: 0.8369 (t0) REVERT: C 608 GLU cc_start: 0.6948 (tt0) cc_final: 0.6728 (tt0) REVERT: C 648 ASN cc_start: 0.5689 (t0) cc_final: 0.4718 (t0) REVERT: C 749 LYS cc_start: 0.8590 (tppt) cc_final: 0.8359 (ttmt) REVERT: C 759 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8617 (tp) REVERT: C 803 GLU cc_start: 0.8776 (mp0) cc_final: 0.8456 (mp0) REVERT: C 806 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9129 (mt) REVERT: C 913 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.7707 (p0) REVERT: D 70 PHE cc_start: 0.8230 (p90) cc_final: 0.7802 (p90) REVERT: D 113 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6963 (ptt180) REVERT: D 296 LEU cc_start: 0.8501 (mt) cc_final: 0.8040 (mt) REVERT: D 344 TYR cc_start: 0.8690 (m-80) cc_final: 0.7959 (m-80) REVERT: D 861 ARG cc_start: 0.6419 (mmm160) cc_final: 0.6103 (mtp180) REVERT: F 233 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: F 245 PHE cc_start: 0.7910 (m-10) cc_final: 0.7636 (m-10) REVERT: F 276 ASN cc_start: 0.8919 (m110) cc_final: 0.8493 (p0) REVERT: F 283 LEU cc_start: 0.9244 (mt) cc_final: 0.9019 (mt) REVERT: F 360 ASN cc_start: 0.9068 (p0) cc_final: 0.8775 (p0) REVERT: F 479 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.7022 (t80) REVERT: N 79 CYS cc_start: 0.4960 (OUTLIER) cc_final: 0.4438 (m) outliers start: 78 outliers final: 31 residues processed: 418 average time/residue: 0.2032 time to fit residues: 135.9694 Evaluate side-chains 343 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 304 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 913 ASN Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 101 optimal weight: 0.7980 chunk 74 optimal weight: 0.0570 chunk 160 optimal weight: 2.9990 chunk 324 optimal weight: 50.0000 chunk 347 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 239 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 304 GLN D 416 ASN ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.156309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.113395 restraints weight = 78763.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.113208 restraints weight = 51119.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.114255 restraints weight = 46693.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.114214 restraints weight = 38893.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.115797 restraints weight = 34844.164| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31803 Z= 0.159 Angle : 0.649 13.612 43723 Z= 0.340 Chirality : 0.043 0.277 4969 Planarity : 0.004 0.055 5138 Dihedral : 21.034 179.794 5654 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.71 % Allowed : 19.89 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3513 helix: 1.26 (0.14), residues: 1430 sheet: -0.51 (0.26), residues: 377 loop : -0.57 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 313 TYR 0.030 0.001 TYR E 32 PHE 0.018 0.002 PHE A 30 TRP 0.017 0.002 TRP F 333 HIS 0.008 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00366 (31775) covalent geometry : angle 0.64189 (43699) hydrogen bonds : bond 0.04131 ( 1443) hydrogen bonds : angle 4.38052 ( 3941) metal coordination : bond 0.00542 ( 28) metal coordination : angle 4.20513 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 337 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.6774 (pm20) cc_final: 0.6473 (pm20) REVERT: A 213 LYS cc_start: 0.9242 (tptp) cc_final: 0.8866 (tmtt) REVERT: B 40 ARG cc_start: 0.7482 (tpp-160) cc_final: 0.7249 (tpt-90) REVERT: C 94 THR cc_start: 0.6949 (OUTLIER) cc_final: 0.6684 (p) REVERT: C 442 ASN cc_start: 0.8760 (t0) cc_final: 0.8353 (t0) REVERT: C 517 LEU cc_start: 0.8355 (mp) cc_final: 0.7813 (mp) REVERT: C 608 GLU cc_start: 0.6969 (tt0) cc_final: 0.6756 (tt0) REVERT: C 648 ASN cc_start: 0.5798 (t0) cc_final: 0.4747 (t0) REVERT: C 710 MET cc_start: 0.8529 (ptm) cc_final: 0.8223 (ptp) REVERT: C 749 LYS cc_start: 0.8689 (tppt) cc_final: 0.8456 (ttmt) REVERT: C 803 GLU cc_start: 0.8786 (mp0) cc_final: 0.8557 (mp0) REVERT: C 806 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9068 (mt) REVERT: D 81 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7318 (tm-30) REVERT: D 113 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6861 (ptt180) REVERT: D 242 ARG cc_start: 0.8670 (ptp-170) cc_final: 0.8400 (ptp-170) REVERT: D 296 LEU cc_start: 0.8457 (mt) cc_final: 0.7877 (mt) REVERT: D 344 TYR cc_start: 0.8752 (m-80) cc_final: 0.8112 (m-80) REVERT: D 1006 MET cc_start: 0.1895 (mtm) cc_final: 0.0900 (mmt) REVERT: F 245 PHE cc_start: 0.8085 (m-10) cc_final: 0.7688 (m-10) REVERT: F 283 LEU cc_start: 0.9235 (mt) cc_final: 0.8994 (mt) REVERT: F 360 ASN cc_start: 0.9056 (p0) cc_final: 0.8756 (p0) REVERT: N 50 THR cc_start: -0.4222 (OUTLIER) cc_final: -0.4423 (t) REVERT: N 79 CYS cc_start: 0.5108 (OUTLIER) cc_final: 0.4591 (m) outliers start: 80 outliers final: 41 residues processed: 392 average time/residue: 0.2000 time to fit residues: 127.1902 Evaluate side-chains 343 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 730 ASP Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 121 optimal weight: 0.9980 chunk 211 optimal weight: 0.3980 chunk 319 optimal weight: 50.0000 chunk 164 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 316 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 338 optimal weight: 8.9990 chunk 323 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN B 89 HIS ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN ** C 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.156717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113666 restraints weight = 78384.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112820 restraints weight = 51883.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.113802 restraints weight = 45635.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114356 restraints weight = 37121.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114664 restraints weight = 34066.780| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31803 Z= 0.143 Angle : 0.641 15.517 43723 Z= 0.332 Chirality : 0.042 0.295 4969 Planarity : 0.004 0.052 5138 Dihedral : 20.982 179.521 5651 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.38 % Allowed : 20.37 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3513 helix: 1.35 (0.14), residues: 1430 sheet: -0.39 (0.27), residues: 371 loop : -0.54 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 267 TYR 0.028 0.001 TYR E 32 PHE 0.023 0.001 PHE D1209 TRP 0.019 0.001 TRP D 105 HIS 0.007 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00327 (31775) covalent geometry : angle 0.63485 (43699) hydrogen bonds : bond 0.03903 ( 1443) hydrogen bonds : angle 4.25438 ( 3941) metal coordination : bond 0.00474 ( 28) metal coordination : angle 3.88899 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 329 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.6945 (m-10) cc_final: 0.6193 (m-10) REVERT: B 40 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.7116 (tpt-90) REVERT: B 78 LEU cc_start: 0.8139 (mp) cc_final: 0.7789 (tt) REVERT: C 94 THR cc_start: 0.6913 (OUTLIER) cc_final: 0.6613 (p) REVERT: C 442 ASN cc_start: 0.8717 (t0) cc_final: 0.8317 (t0) REVERT: C 517 LEU cc_start: 0.8329 (mp) cc_final: 0.7778 (mp) REVERT: C 648 ASN cc_start: 0.6119 (t0) cc_final: 0.5074 (t0) REVERT: C 710 MET cc_start: 0.8562 (ptm) cc_final: 0.8282 (ptp) REVERT: C 749 LYS cc_start: 0.8710 (tppt) cc_final: 0.8463 (ttmt) REVERT: C 803 GLU cc_start: 0.8831 (mp0) cc_final: 0.8473 (mp0) REVERT: C 806 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9119 (mt) REVERT: D 69 ARG cc_start: 0.8009 (ptm160) cc_final: 0.7734 (ptm160) REVERT: D 81 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7374 (tm-30) REVERT: D 113 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6881 (ptt180) REVERT: D 242 ARG cc_start: 0.8647 (ptp-170) cc_final: 0.8325 (ptp-170) REVERT: D 261 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8925 (mp) REVERT: D 344 TYR cc_start: 0.8734 (m-80) cc_final: 0.8173 (m-80) REVERT: D 670 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7849 (tm-30) REVERT: D 1061 VAL cc_start: 0.6787 (OUTLIER) cc_final: 0.6210 (p) REVERT: D 1191 MET cc_start: 0.8823 (pmm) cc_final: 0.8103 (pmm) REVERT: F 245 PHE cc_start: 0.8186 (m-10) cc_final: 0.7746 (m-10) REVERT: F 283 LEU cc_start: 0.9254 (mt) cc_final: 0.9018 (mt) REVERT: F 441 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7680 (pp20) REVERT: F 479 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6781 (t80) REVERT: N 79 CYS cc_start: 0.5041 (OUTLIER) cc_final: 0.4536 (m) outliers start: 100 outliers final: 58 residues processed: 406 average time/residue: 0.1991 time to fit residues: 131.2950 Evaluate side-chains 353 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 288 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 598 MET Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 823 LYS Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1087 HIS Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 216 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 354 optimal weight: 10.0000 chunk 242 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 325 optimal weight: 50.0000 chunk 363 optimal weight: 40.0000 chunk 292 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN C 741 HIS ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 304 GLN D 416 ASN ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.152496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.109967 restraints weight = 77609.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108734 restraints weight = 54718.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109881 restraints weight = 55634.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109799 restraints weight = 43049.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.110160 restraints weight = 38662.817| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 31803 Z= 0.273 Angle : 0.731 16.265 43723 Z= 0.380 Chirality : 0.045 0.346 4969 Planarity : 0.005 0.059 5138 Dihedral : 21.006 178.383 5651 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.06 % Allowed : 21.08 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3513 helix: 1.08 (0.14), residues: 1428 sheet: -0.64 (0.27), residues: 394 loop : -0.64 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 556 TYR 0.043 0.002 TYR E 32 PHE 0.028 0.002 PHE D1209 TRP 0.026 0.002 TRP C 231 HIS 0.008 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00631 (31775) covalent geometry : angle 0.72284 (43699) hydrogen bonds : bond 0.04472 ( 1443) hydrogen bonds : angle 4.54476 ( 3941) metal coordination : bond 0.00999 ( 28) metal coordination : angle 4.78102 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 299 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 ASN cc_start: 0.8558 (m-40) cc_final: 0.8347 (p0) REVERT: C 94 THR cc_start: 0.7086 (OUTLIER) cc_final: 0.6762 (p) REVERT: C 398 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.7067 (mt) REVERT: C 442 ASN cc_start: 0.8807 (t0) cc_final: 0.8523 (t0) REVERT: C 517 LEU cc_start: 0.8693 (mp) cc_final: 0.8226 (mp) REVERT: C 648 ASN cc_start: 0.6225 (t0) cc_final: 0.5030 (t0) REVERT: C 710 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8536 (ptp) REVERT: C 749 LYS cc_start: 0.8705 (tppt) cc_final: 0.8503 (ttmt) REVERT: C 803 GLU cc_start: 0.8718 (mp0) cc_final: 0.8272 (mp0) REVERT: C 806 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9078 (mt) REVERT: C 819 ARG cc_start: 0.8253 (tmm-80) cc_final: 0.7926 (tmm-80) REVERT: C 999 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7068 (ttp80) REVERT: D 69 ARG cc_start: 0.8232 (ptm160) cc_final: 0.7935 (ptm160) REVERT: D 134 TYR cc_start: 0.7685 (m-80) cc_final: 0.7329 (m-10) REVERT: D 242 ARG cc_start: 0.8664 (ptp-170) cc_final: 0.8446 (ptp-170) REVERT: D 277 LEU cc_start: 0.8350 (mt) cc_final: 0.7762 (mt) REVERT: D 670 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7872 (tm-30) REVERT: F 245 PHE cc_start: 0.8232 (m-10) cc_final: 0.7824 (m-10) REVERT: F 283 LEU cc_start: 0.9259 (mt) cc_final: 0.9022 (mt) REVERT: F 298 MET cc_start: 0.5189 (tpp) cc_final: 0.4877 (tpp) REVERT: F 324 TYR cc_start: 0.8200 (m-80) cc_final: 0.7965 (m-80) REVERT: F 479 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.6719 (t80) REVERT: N 79 CYS cc_start: 0.4887 (OUTLIER) cc_final: 0.4411 (m) outliers start: 120 outliers final: 86 residues processed: 389 average time/residue: 0.1952 time to fit residues: 125.0329 Evaluate side-chains 365 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 272 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 999 ARG Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 520 LYS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 823 LYS Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 873 VAL Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 276 ASN Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain S residue 304 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 95 optimal weight: 2.9990 chunk 320 optimal weight: 50.0000 chunk 311 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 267 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 245 optimal weight: 0.8980 chunk 338 optimal weight: 10.0000 chunk 269 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN D 416 ASN ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.155101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.111188 restraints weight = 78018.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.110648 restraints weight = 53051.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.111379 restraints weight = 45328.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112015 restraints weight = 37480.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.112165 restraints weight = 34082.105| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31803 Z= 0.149 Angle : 0.660 18.968 43723 Z= 0.339 Chirality : 0.043 0.297 4969 Planarity : 0.004 0.057 5138 Dihedral : 20.970 179.326 5651 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.18 % Allowed : 23.14 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3513 helix: 1.26 (0.14), residues: 1423 sheet: -0.50 (0.27), residues: 393 loop : -0.58 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 485 TYR 0.031 0.001 TYR E 32 PHE 0.032 0.002 PHE D 226 TRP 0.021 0.002 TRP C 231 HIS 0.019 0.001 HIS C 741 Details of bonding type rmsd covalent geometry : bond 0.00343 (31775) covalent geometry : angle 0.65437 (43699) hydrogen bonds : bond 0.03824 ( 1443) hydrogen bonds : angle 4.29819 ( 3941) metal coordination : bond 0.00440 ( 28) metal coordination : angle 3.85244 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 306 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.7076 (ttm) cc_final: 0.6582 (mtm) REVERT: A 213 LYS cc_start: 0.9186 (tptp) cc_final: 0.8948 (tptp) REVERT: B 78 LEU cc_start: 0.8118 (mp) cc_final: 0.7835 (tt) REVERT: B 152 ASN cc_start: 0.8608 (m-40) cc_final: 0.8361 (p0) REVERT: C 52 ASP cc_start: 0.7269 (p0) cc_final: 0.6956 (p0) REVERT: C 244 GLU cc_start: 0.8272 (pm20) cc_final: 0.8070 (pm20) REVERT: C 359 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.6341 (t80) REVERT: C 442 ASN cc_start: 0.8761 (t0) cc_final: 0.8479 (t0) REVERT: C 517 LEU cc_start: 0.8532 (mp) cc_final: 0.8072 (mp) REVERT: C 648 ASN cc_start: 0.6109 (t0) cc_final: 0.4899 (t0) REVERT: C 803 GLU cc_start: 0.8794 (mp0) cc_final: 0.8281 (mp0) REVERT: C 806 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9085 (mt) REVERT: C 999 ARG cc_start: 0.7096 (mtp85) cc_final: 0.6646 (ttp80) REVERT: D 69 ARG cc_start: 0.8149 (ptm160) cc_final: 0.7794 (ptm160) REVERT: D 81 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7344 (tm-30) REVERT: D 242 ARG cc_start: 0.8613 (ptp-170) cc_final: 0.8354 (ptp-170) REVERT: D 344 TYR cc_start: 0.8670 (m-80) cc_final: 0.8002 (m-80) REVERT: D 670 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7817 (tm-30) REVERT: D 828 PRO cc_start: 0.8714 (Cg_endo) cc_final: 0.8485 (Cg_exo) REVERT: D 836 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7331 (ttt180) REVERT: D 1191 MET cc_start: 0.8643 (pmm) cc_final: 0.8299 (ptp) REVERT: F 245 PHE cc_start: 0.8291 (m-10) cc_final: 0.8072 (m-10) REVERT: F 283 LEU cc_start: 0.9244 (mt) cc_final: 0.9011 (mt) REVERT: F 298 MET cc_start: 0.5439 (tpp) cc_final: 0.5123 (tpp) REVERT: F 324 TYR cc_start: 0.8201 (m-80) cc_final: 0.7941 (m-80) REVERT: F 479 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6406 (t80) REVERT: N 79 CYS cc_start: 0.5049 (OUTLIER) cc_final: 0.4591 (m) outliers start: 94 outliers final: 61 residues processed: 375 average time/residue: 0.2021 time to fit residues: 123.7573 Evaluate side-chains 342 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 276 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 823 LYS Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 836 ARG Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain S residue 304 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 169 optimal weight: 8.9990 chunk 240 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 342 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 316 optimal weight: 0.9990 chunk 349 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 HIS D 304 GLN ** D 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.154091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.110500 restraints weight = 78575.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.109020 restraints weight = 54972.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.109958 restraints weight = 51108.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110579 restraints weight = 40746.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.110860 restraints weight = 37028.640| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31803 Z= 0.185 Angle : 0.679 13.627 43723 Z= 0.349 Chirality : 0.043 0.381 4969 Planarity : 0.005 0.151 5138 Dihedral : 20.977 179.430 5651 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.52 % Allowed : 23.38 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3513 helix: 1.19 (0.14), residues: 1427 sheet: -0.50 (0.28), residues: 385 loop : -0.60 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 247 TYR 0.036 0.001 TYR E 32 PHE 0.032 0.002 PHE D1209 TRP 0.025 0.002 TRP C 231 HIS 0.004 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00430 (31775) covalent geometry : angle 0.67199 (43699) hydrogen bonds : bond 0.03945 ( 1443) hydrogen bonds : angle 4.35349 ( 3941) metal coordination : bond 0.00640 ( 28) metal coordination : angle 4.06524 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 291 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.9221 (tptp) cc_final: 0.8957 (tptp) REVERT: B 152 ASN cc_start: 0.8678 (m-40) cc_final: 0.8376 (p0) REVERT: C 52 ASP cc_start: 0.7263 (p0) cc_final: 0.6987 (p0) REVERT: C 359 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6383 (t80) REVERT: C 442 ASN cc_start: 0.8847 (t0) cc_final: 0.8550 (t0) REVERT: C 499 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7287 (pm20) REVERT: C 517 LEU cc_start: 0.8721 (mp) cc_final: 0.8247 (mp) REVERT: C 648 ASN cc_start: 0.6218 (t0) cc_final: 0.4937 (t0) REVERT: C 806 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9121 (mt) REVERT: C 819 ARG cc_start: 0.8103 (tmm-80) cc_final: 0.7648 (tmm-80) REVERT: C 999 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6852 (ttp80) REVERT: D 69 ARG cc_start: 0.8276 (ptm160) cc_final: 0.7999 (ptm160) REVERT: D 670 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7847 (tm-30) REVERT: D 828 PRO cc_start: 0.8724 (Cg_endo) cc_final: 0.8461 (Cg_exo) REVERT: D 836 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7388 (ttt180) REVERT: D 1006 MET cc_start: 0.1346 (mpp) cc_final: 0.0257 (mmt) REVERT: D 1191 MET cc_start: 0.8683 (pmm) cc_final: 0.8364 (ptp) REVERT: F 245 PHE cc_start: 0.8391 (m-10) cc_final: 0.8186 (m-10) REVERT: F 283 LEU cc_start: 0.9269 (mt) cc_final: 0.9048 (mt) REVERT: F 298 MET cc_start: 0.5580 (tpp) cc_final: 0.5227 (tpp) REVERT: F 324 TYR cc_start: 0.8196 (m-80) cc_final: 0.7888 (m-80) REVERT: N 79 CYS cc_start: 0.5089 (OUTLIER) cc_final: 0.4651 (m) outliers start: 104 outliers final: 79 residues processed: 370 average time/residue: 0.1959 time to fit residues: 118.5584 Evaluate side-chains 366 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 281 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 598 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 999 ARG Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 823 LYS Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 836 ARG Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1231 LEU Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 276 ASN Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain S residue 304 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 164 optimal weight: 3.9990 chunk 354 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 191 optimal weight: 0.0970 chunk 275 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 79 ASN B 82 GLN ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 HIS ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.155983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.113326 restraints weight = 78777.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.109927 restraints weight = 59446.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.111361 restraints weight = 49798.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.111994 restraints weight = 39851.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.112095 restraints weight = 36058.088| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31803 Z= 0.135 Angle : 0.660 13.500 43723 Z= 0.339 Chirality : 0.043 0.323 4969 Planarity : 0.004 0.077 5138 Dihedral : 20.912 179.825 5651 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.84 % Allowed : 24.05 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3513 helix: 1.29 (0.14), residues: 1435 sheet: -0.39 (0.27), residues: 397 loop : -0.56 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 242 TYR 0.028 0.001 TYR E 32 PHE 0.040 0.001 PHE D1209 TRP 0.038 0.002 TRP C 199 HIS 0.012 0.001 HIS E 64 Details of bonding type rmsd covalent geometry : bond 0.00310 (31775) covalent geometry : angle 0.65525 (43699) hydrogen bonds : bond 0.03692 ( 1443) hydrogen bonds : angle 4.22218 ( 3941) metal coordination : bond 0.00348 ( 28) metal coordination : angle 3.58798 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 307 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.7118 (ttm) cc_final: 0.6752 (mtm) REVERT: A 213 LYS cc_start: 0.9183 (tptp) cc_final: 0.8953 (tptp) REVERT: B 152 ASN cc_start: 0.8759 (m-40) cc_final: 0.8432 (p0) REVERT: C 52 ASP cc_start: 0.7252 (p0) cc_final: 0.7005 (p0) REVERT: C 285 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8310 (mt-10) REVERT: C 359 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.6051 (t80) REVERT: C 442 ASN cc_start: 0.8785 (t0) cc_final: 0.8469 (t0) REVERT: C 499 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: C 517 LEU cc_start: 0.8504 (mp) cc_final: 0.8031 (mp) REVERT: C 648 ASN cc_start: 0.6092 (t0) cc_final: 0.4868 (t0) REVERT: C 749 LYS cc_start: 0.8769 (tptt) cc_final: 0.8482 (mttm) REVERT: C 806 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9135 (mt) REVERT: C 819 ARG cc_start: 0.8278 (tmm-80) cc_final: 0.7934 (tmm-80) REVERT: C 1015 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8744 (tp) REVERT: D 69 ARG cc_start: 0.8232 (ptm160) cc_final: 0.7875 (ptm160) REVERT: D 81 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7350 (tm-30) REVERT: D 256 MET cc_start: 0.8055 (tpp) cc_final: 0.7778 (tpp) REVERT: D 344 TYR cc_start: 0.8672 (m-80) cc_final: 0.8092 (m-80) REVERT: D 670 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7789 (tm-30) REVERT: D 828 PRO cc_start: 0.8706 (Cg_endo) cc_final: 0.8441 (Cg_exo) REVERT: D 1006 MET cc_start: 0.1119 (mpp) cc_final: -0.0012 (mmt) REVERT: D 1191 MET cc_start: 0.8719 (pmm) cc_final: 0.8338 (ptp) REVERT: F 245 PHE cc_start: 0.8471 (m-10) cc_final: 0.8252 (m-10) REVERT: F 283 LEU cc_start: 0.9290 (mt) cc_final: 0.9066 (mt) REVERT: F 298 MET cc_start: 0.5538 (tpp) cc_final: 0.5212 (tpp) REVERT: F 324 TYR cc_start: 0.8242 (m-80) cc_final: 0.7870 (m-80) REVERT: F 479 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6859 (t80) REVERT: N 79 CYS cc_start: 0.5342 (OUTLIER) cc_final: 0.4931 (m) outliers start: 84 outliers final: 61 residues processed: 369 average time/residue: 0.1970 time to fit residues: 119.6562 Evaluate side-chains 351 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 284 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 79 CYS Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 262 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 218 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 234 optimal weight: 0.0970 chunk 238 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.155631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.112453 restraints weight = 78110.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.110685 restraints weight = 51725.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.112213 restraints weight = 51101.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.112080 restraints weight = 40810.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.112743 restraints weight = 38024.819| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 31803 Z= 0.146 Angle : 0.681 14.600 43723 Z= 0.344 Chirality : 0.043 0.290 4969 Planarity : 0.004 0.052 5138 Dihedral : 20.875 179.716 5651 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.71 % Allowed : 24.49 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3513 helix: 1.32 (0.14), residues: 1431 sheet: -0.46 (0.27), residues: 414 loop : -0.52 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG D 242 TYR 0.029 0.001 TYR E 32 PHE 0.039 0.001 PHE D1209 TRP 0.030 0.002 TRP C 199 HIS 0.005 0.001 HIS D1133 Details of bonding type rmsd covalent geometry : bond 0.00339 (31775) covalent geometry : angle 0.66902 (43699) hydrogen bonds : bond 0.03661 ( 1443) hydrogen bonds : angle 4.21317 ( 3941) metal coordination : bond 0.01420 ( 28) metal coordination : angle 5.51551 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 293 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.7077 (ttm) cc_final: 0.6690 (mtm) REVERT: B 152 ASN cc_start: 0.8793 (m-40) cc_final: 0.8441 (p0) REVERT: C 52 ASP cc_start: 0.7202 (p0) cc_final: 0.6972 (p0) REVERT: C 359 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.6208 (t80) REVERT: C 442 ASN cc_start: 0.8807 (t0) cc_final: 0.8470 (t0) REVERT: C 499 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: C 517 LEU cc_start: 0.8582 (mp) cc_final: 0.8110 (mp) REVERT: C 648 ASN cc_start: 0.6074 (t0) cc_final: 0.4865 (t0) REVERT: C 710 MET cc_start: 0.8291 (ptm) cc_final: 0.7988 (ptp) REVERT: C 749 LYS cc_start: 0.8787 (tptt) cc_final: 0.8536 (mttt) REVERT: C 806 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9119 (mt) REVERT: C 819 ARG cc_start: 0.8196 (tmm-80) cc_final: 0.7913 (tmm-80) REVERT: C 999 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7276 (mtm180) REVERT: C 1015 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8777 (tp) REVERT: D 69 ARG cc_start: 0.8171 (ptm160) cc_final: 0.7849 (ptm160) REVERT: D 242 ARG cc_start: 0.8530 (ptp90) cc_final: 0.8226 (ptp90) REVERT: D 256 MET cc_start: 0.8131 (tpp) cc_final: 0.7844 (tpp) REVERT: D 344 TYR cc_start: 0.8729 (m-80) cc_final: 0.8124 (m-80) REVERT: D 670 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7793 (tm-30) REVERT: D 828 PRO cc_start: 0.8669 (Cg_endo) cc_final: 0.8434 (Cg_exo) REVERT: D 1006 MET cc_start: 0.0970 (mpp) cc_final: -0.0106 (mmt) REVERT: D 1191 MET cc_start: 0.8711 (pmm) cc_final: 0.8312 (ptp) REVERT: F 245 PHE cc_start: 0.8353 (m-10) cc_final: 0.8119 (m-10) REVERT: F 283 LEU cc_start: 0.9294 (mt) cc_final: 0.9076 (mt) REVERT: F 298 MET cc_start: 0.5398 (tpp) cc_final: 0.5037 (tpp) REVERT: F 324 TYR cc_start: 0.8147 (m-80) cc_final: 0.7935 (m-80) REVERT: F 479 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.6755 (t80) outliers start: 80 outliers final: 69 residues processed: 349 average time/residue: 0.1967 time to fit residues: 112.6323 Evaluate side-chains 350 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 276 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 962 CYS Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain S residue 304 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 126 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 329 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 218 optimal weight: 0.0040 chunk 196 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 ASN ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.155259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.111918 restraints weight = 77656.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110335 restraints weight = 52446.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.111279 restraints weight = 49794.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112003 restraints weight = 39540.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.112181 restraints weight = 35811.208| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31803 Z= 0.157 Angle : 0.696 15.098 43723 Z= 0.352 Chirality : 0.043 0.293 4969 Planarity : 0.004 0.060 5138 Dihedral : 20.855 179.514 5651 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.88 % Allowed : 24.63 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3513 helix: 1.28 (0.14), residues: 1428 sheet: -0.45 (0.27), residues: 408 loop : -0.53 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 242 TYR 0.029 0.001 TYR E 32 PHE 0.024 0.001 PHE D 226 TRP 0.025 0.002 TRP C 199 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00365 (31775) covalent geometry : angle 0.68517 (43699) hydrogen bonds : bond 0.03696 ( 1443) hydrogen bonds : angle 4.23983 ( 3941) metal coordination : bond 0.00654 ( 28) metal coordination : angle 5.18729 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 284 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.7108 (ttm) cc_final: 0.6719 (mtm) REVERT: A 213 LYS cc_start: 0.9204 (tptp) cc_final: 0.8832 (tmtt) REVERT: B 152 ASN cc_start: 0.8779 (m-40) cc_final: 0.8411 (p0) REVERT: C 52 ASP cc_start: 0.7171 (p0) cc_final: 0.6963 (p0) REVERT: C 359 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6463 (t80) REVERT: C 442 ASN cc_start: 0.8829 (t0) cc_final: 0.8502 (t0) REVERT: C 499 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: C 517 LEU cc_start: 0.8571 (mp) cc_final: 0.8112 (mp) REVERT: C 648 ASN cc_start: 0.5925 (t0) cc_final: 0.4629 (t0) REVERT: C 749 LYS cc_start: 0.8773 (tptt) cc_final: 0.8523 (mttt) REVERT: C 806 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9128 (mt) REVERT: C 819 ARG cc_start: 0.8192 (tmm-80) cc_final: 0.7899 (tmm-80) REVERT: C 999 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7198 (ttt180) REVERT: C 1015 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8773 (tp) REVERT: D 69 ARG cc_start: 0.8231 (ptm160) cc_final: 0.7918 (ptm160) REVERT: D 242 ARG cc_start: 0.8515 (ptp90) cc_final: 0.8228 (ptp90) REVERT: D 256 MET cc_start: 0.8148 (tpp) cc_final: 0.7873 (tpp) REVERT: D 373 MET cc_start: 0.7629 (mmm) cc_final: 0.7382 (tpt) REVERT: D 670 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7841 (tm-30) REVERT: D 1006 MET cc_start: 0.1315 (mpp) cc_final: 0.0185 (mmt) REVERT: D 1191 MET cc_start: 0.8681 (pmm) cc_final: 0.8274 (ptp) REVERT: F 245 PHE cc_start: 0.8340 (m-10) cc_final: 0.8114 (m-10) REVERT: F 283 LEU cc_start: 0.9301 (mt) cc_final: 0.9086 (mt) REVERT: F 298 MET cc_start: 0.5412 (tpp) cc_final: 0.5204 (tpp) REVERT: F 479 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.6674 (t80) outliers start: 85 outliers final: 72 residues processed: 346 average time/residue: 0.1874 time to fit residues: 107.1434 Evaluate side-chains 348 residues out of total 2957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 271 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1115 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 962 CYS Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1053 THR Chi-restraints excluded: chain D residue 1116 HIS Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 276 ASN Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain S residue 304 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 122 optimal weight: 0.6980 chunk 283 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 331 optimal weight: 50.0000 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 364 optimal weight: 50.0000 chunk 339 optimal weight: 50.0000 chunk 359 optimal weight: 50.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 HIS ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.154053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110343 restraints weight = 78210.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108688 restraints weight = 53447.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109914 restraints weight = 53641.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.109927 restraints weight = 43883.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110633 restraints weight = 39134.900| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31803 Z= 0.192 Angle : 0.724 16.867 43723 Z= 0.366 Chirality : 0.044 0.286 4969 Planarity : 0.005 0.059 5138 Dihedral : 20.890 179.431 5651 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.84 % Allowed : 24.86 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3513 helix: 1.22 (0.14), residues: 1434 sheet: -0.47 (0.28), residues: 396 loop : -0.60 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 218 TYR 0.033 0.001 TYR E 32 PHE 0.077 0.002 PHE D1209 TRP 0.028 0.002 TRP C 231 HIS 0.011 0.001 HIS D1133 Details of bonding type rmsd covalent geometry : bond 0.00449 (31775) covalent geometry : angle 0.71367 (43699) hydrogen bonds : bond 0.03909 ( 1443) hydrogen bonds : angle 4.33902 ( 3941) metal coordination : bond 0.00647 ( 28) metal coordination : angle 5.36675 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5418.41 seconds wall clock time: 94 minutes 42.96 seconds (5682.96 seconds total)