Starting phenix.real_space_refine on Mon Jul 6 07:45:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jke_36370/07_2026/8jke_36370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jke_36370/07_2026/8jke_36370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jke_36370/07_2026/8jke_36370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jke_36370/07_2026/8jke_36370.map" model { file = "/net/cci-nas-00/data/ceres_data/8jke_36370/07_2026/8jke_36370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jke_36370/07_2026/8jke_36370.cif" } resolution = 3.67 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 122 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 20877 2.51 5 N 6065 2.21 5 O 6760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33932 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: 8675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8675 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 58, 'TRANS': 1055} 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: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2398 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "G" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 734 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 6, 'TRANS': 85} Chain: "H" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1241 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 4, 'TRANS': 153} Chain: "I" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1934 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain: "J" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1934 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain: "K" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 545 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "O" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1233 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "P" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1258 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12656 SG CYS D 60 86.026 84.039 73.248 1.00 69.67 S ATOM 12674 SG CYS D 62 84.780 82.478 70.239 1.00 74.67 S ATOM 12783 SG CYS D 75 88.337 83.734 70.245 1.00 86.84 S ATOM 12809 SG CYS D 78 85.593 86.364 70.302 1.00 73.68 S ATOM 19208 SG CYS D 886 107.649 136.997 106.794 1.00 68.87 S ATOM 19772 SG CYS D 962 103.931 137.575 106.346 1.00 56.26 S ATOM 19820 SG CYS D 969 105.755 135.742 109.381 1.00 50.31 S ATOM 19839 SG CYS D 972 105.379 139.210 109.430 1.00 46.62 S Time building chain proxies: 7.26, per 1000 atoms: 0.21 Number of scatterers: 33932 At special positions: 0 Unit cell: (129.15, 184.8, 194.25, 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 2 29.99 S 105 16.00 P 122 15.00 Mg 1 11.99 O 6760 8.00 N 6065 7.00 C 20877 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: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " Number of angles added : 12 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7450 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 49 sheets defined 46.3% alpha, 13.9% beta 32 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.663A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.754A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 203 through 225 removed outlier: 4.005A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 removed outlier: 4.259A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.023A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 removed outlier: 4.402A 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 72 through 81 removed outlier: 3.773A pdb=" N ILE C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 240 removed outlier: 3.520A pdb=" N ILE C 236 " --> pdb=" O THR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.504A pdb=" N ARG C 247 " --> pdb=" O TYR C 243 " (cutoff:3.500A) 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 308 Processing helix chain 'C' and resid 320 through 337 removed outlier: 3.834A pdb=" N VAL C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 392 removed outlier: 3.583A pdb=" N THR C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 removed outlier: 4.281A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 Processing helix chain 'C' and resid 430 through 439 Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.705A pdb=" N ARG C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 4.081A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 553 removed outlier: 4.089A pdb=" N GLU C 553 " --> pdb=" O ARG C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 removed outlier: 4.390A pdb=" N MET C 572 " --> pdb=" O PRO C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 580 Processing helix chain 'C' and resid 582 through 586 removed outlier: 3.553A pdb=" N HIS C 585 " --> pdb=" O PHE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 598 Processing helix chain 'C' and resid 616 through 623 removed outlier: 3.643A pdb=" N ALA C 621 " --> pdb=" O GLU C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 removed outlier: 3.575A pdb=" N ASP C 730 " --> pdb=" O ARG C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 770 removed outlier: 4.490A pdb=" N ASP C 769 " --> pdb=" O VAL C 766 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 770 " --> pdb=" O LEU C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 906 through 912 removed outlier: 4.176A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 removed outlier: 3.668A 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 1054 through 1065 Processing helix chain 'C' and resid 1066 through 1075 Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 4.287A pdb=" N VAL C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS C1086 " --> pdb=" O THR C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1114 removed outlier: 3.637A pdb=" N LYS C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.649A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.551A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 removed outlier: 3.697A pdb=" N ASP D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 188 removed outlier: 3.710A pdb=" N GLY D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 228 removed outlier: 3.570A pdb=" N LYS D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN D 228 " --> pdb=" O ASN D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.846A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER D 267 " --> pdb=" O LYS D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.005A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.973A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 338 through 360 removed outlier: 3.850A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 407 through 410 removed outlier: 4.037A pdb=" N GLN D 410 " --> pdb=" O LYS D 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 407 through 410' Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 444 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: 4.317A 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 526 through 529 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 590 Processing helix chain 'D' and resid 606 through 617 Processing helix chain 'D' and resid 662 through 672 removed outlier: 3.545A pdb=" N ALA D 666 " --> pdb=" O THR D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 721 removed outlier: 3.744A pdb=" N ARG D 721 " --> pdb=" O PHE D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 removed outlier: 3.854A 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 799 Processing helix chain 'D' and resid 805 through 814 removed outlier: 3.508A pdb=" N MET D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 877 removed outlier: 3.550A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 970 through 974 Processing helix chain 'D' and resid 988 through 999 removed outlier: 3.593A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1002 No H-bonds generated for 'chain 'D' and resid 1000 through 1002' Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1109 Processing helix chain 'D' and resid 1109 through 1126 Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 3.948A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1179 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1208 removed outlier: 3.607A pdb=" N ALA D1206 " --> pdb=" O SER D1202 " (cutoff:3.500A) Processing helix chain 'D' and resid 1213 through 1223 Processing helix chain 'D' and resid 1231 through 1238 removed outlier: 3.968A pdb=" N ILE D1237 " --> pdb=" O GLU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1243 through 1246 removed outlier: 3.779A pdb=" N GLY D1246 " --> pdb=" O ALA D1243 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1243 through 1246' Processing helix chain 'D' and resid 1247 through 1252 Processing helix chain 'D' and resid 1258 through 1265 Processing helix chain 'E' and resid 15 through 24 removed outlier: 3.516A pdb=" N LEU E 19 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 45 Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.835A pdb=" N ILE E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 223 removed outlier: 3.626A pdb=" N ASP F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 252 removed outlier: 3.561A pdb=" N ASN F 252 " --> pdb=" O ASP F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 291 removed outlier: 4.992A pdb=" N ARG F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 294 No H-bonds generated for 'chain 'F' and resid 292 through 294' Processing helix chain 'F' and resid 299 through 317 removed outlier: 3.699A pdb=" N GLU F 316 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS F 317 " --> pdb=" O ARG F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 346 removed outlier: 4.026A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 4.138A 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 removed outlier: 3.729A pdb=" N ASP F 420 " --> pdb=" O GLU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 450 Processing helix chain 'F' and resid 451 through 462 removed outlier: 3.755A pdb=" N PHE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 498 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 removed outlier: 4.331A pdb=" N ASP F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 91 through 110 Processing helix chain 'H' and resid 53 through 58 Processing helix chain 'H' and resid 64 through 76 removed outlier: 4.120A pdb=" N LEU H 68 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP H 69 " --> pdb=" O GLN H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 100 removed outlier: 3.989A pdb=" N ARG H 89 " --> pdb=" O ASN H 85 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU H 95 " --> pdb=" O LYS H 91 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'H' and resid 125 through 144 removed outlier: 4.334A pdb=" N LEU H 142 " --> pdb=" O SER H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 156 removed outlier: 3.648A pdb=" N LEU H 155 " --> pdb=" O ALA H 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 removed outlier: 3.807A pdb=" N ARG I 59 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 74 Processing helix chain 'I' and resid 82 through 97 Processing helix chain 'I' and resid 119 through 138 Processing helix chain 'I' and resid 140 through 152 removed outlier: 3.550A pdb=" N ASP I 152 " --> pdb=" O ARG I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 193 Processing helix chain 'I' and resid 195 through 209 Processing helix chain 'I' and resid 212 through 227 removed outlier: 3.573A pdb=" N ARG I 216 " --> pdb=" O ARG I 212 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG I 225 " --> pdb=" O LEU I 221 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY I 227 " --> pdb=" O LEU I 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 247 Processing helix chain 'I' and resid 252 through 265 removed outlier: 3.539A pdb=" N GLN I 256 " --> pdb=" O ARG I 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 58 Processing helix chain 'J' and resid 65 through 74 Processing helix chain 'J' and resid 81 through 97 Processing helix chain 'J' and resid 119 through 137 Processing helix chain 'J' and resid 139 through 152 Processing helix chain 'J' and resid 164 through 193 Processing helix chain 'J' and resid 194 through 209 removed outlier: 3.962A pdb=" N ALA J 198 " --> pdb=" O CYS J 194 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 227 removed outlier: 3.926A pdb=" N ARG J 216 " --> pdb=" O ARG J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 246 Processing helix chain 'J' and resid 252 through 264 Processing helix chain 'K' and resid 240 through 249 Processing helix chain 'K' and resid 250 through 255 removed outlier: 3.646A pdb=" N GLU K 253 " --> pdb=" O PRO K 250 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU K 255 " --> pdb=" O GLU K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 267 removed outlier: 3.634A pdb=" N GLU K 267 " --> pdb=" O CYS K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 278 Processing helix chain 'K' and resid 279 through 285 removed outlier: 3.740A pdb=" N LEU K 283 " --> pdb=" O SER K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 305 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.801A 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 94 removed outlier: 3.748A pdb=" N SER A 53 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N SER A 87 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 49 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 85 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.748A pdb=" N SER A 53 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.641A pdb=" N LEU A 134 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.641A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.592A pdb=" N VAL A 147 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 13 removed outlier: 3.934A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 13 removed outlier: 3.934A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AB3, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.799A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.801A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 22 through 24 removed outlier: 6.347A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 100 removed outlier: 6.547A pdb=" N THR C 124 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N HIS C 98 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE C 122 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N PHE C 100 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 37 " --> pdb=" O ALA H 22 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA H 22 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS H 39 " --> pdb=" O ILE H 20 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE H 20 " --> pdb=" O LYS H 39 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG H 60 " --> pdb=" O VAL H 11 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB8, first strand: chain 'C' and resid 362 through 365 removed outlier: 6.550A pdb=" N SER C 165 " --> pdb=" O ASN C 442 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.626A pdb=" N ASP C 180 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 340 through 342 removed outlier: 3.581A pdb=" N THR C 341 " --> pdb=" O ILE C 349 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 491 through 492 removed outlier: 7.164A pdb=" N ILE C 498 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU C 517 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR C 500 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR C 502 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP C 513 " --> pdb=" O TYR C 502 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS C 504 " --> pdb=" O THR C 511 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 506 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AC4, first strand: chain 'C' and resid 544 through 545 removed outlier: 3.644A pdb=" N VAL C 545 " --> pdb=" O VAL C 557 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 628 through 629 removed outlier: 6.885A pdb=" N VAL C 628 " --> pdb=" O LEU C 688 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 653 through 657 removed outlier: 6.722A pdb=" N TYR C 643 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL C 639 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C 645 " --> pdb=" O GLN C 637 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC8, first strand: chain 'C' and resid 992 through 993 removed outlier: 7.653A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ILE C 901 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU C 706 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU C 903 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA C 708 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 734 through 746 removed outlier: 3.878A pdb=" N HIS C 741 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C 857 " --> pdb=" O HIS C 741 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 835 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 860 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL C 833 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LYS C 862 " --> pdb=" O GLY C 831 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N GLY C 831 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 831 " --> pdb=" O VAL C 782 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 754 through 755 removed outlier: 3.675A pdb=" N GLU C 754 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 787 through 789 removed outlier: 7.258A pdb=" N LEU C 823 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 3.732A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL D 431 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1052 through 1053 Processing sheet with id=AD5, first strand: chain 'C' and resid 1128 through 1129 removed outlier: 8.194A pdb=" N VAL C1122 " --> pdb=" O SER C1129 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU D 10 " --> pdb=" O ASP D1226 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP D1226 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.103A pdb=" N SER D 24 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS D 94 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY D 26 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU D 96 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N ALA D 99 " --> pdb=" O CYS D 316 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 233 through 235 removed outlier: 4.311A pdb=" N ASP D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.282A pdb=" N PHE D 335 " --> pdb=" O ILE F 404 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 603 through 604 removed outlier: 3.765A pdb=" N PHE D 657 " --> pdb=" O PHE D 629 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 881 through 883 Processing sheet with id=AE2, first strand: chain 'D' and resid 892 through 895 Processing sheet with id=AE3, first strand: chain 'D' and resid 924 through 925 removed outlier: 7.388A pdb=" N VAL D 924 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1038 through 1039 Processing sheet with id=AE5, first strand: chain 'D' and resid 1070 through 1073 removed outlier: 3.566A pdb=" N VAL D1088 " --> pdb=" O GLY D1046 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D1048 " --> pdb=" O ASP D1086 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP D1086 " --> pdb=" O VAL D1048 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1163 through 1165 removed outlier: 3.554A pdb=" N SER D1185 " --> pdb=" O ILE D1151 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1253 through 1257 removed outlier: 3.599A pdb=" N GLU E 83 " --> pdb=" O ARG D1254 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D1256 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR E 81 " --> pdb=" O GLU D1256 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 39 through 45 removed outlier: 3.643A pdb=" N PHE G 40 " --> pdb=" O TYR G 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR G 32 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET G 42 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL G 30 " --> pdb=" O MET G 42 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 27 through 28 Processing sheet with id=AF1, first strand: chain 'I' and resid 25 through 28 removed outlier: 3.897A pdb=" N GLY I 28 " --> pdb=" O ARG I 34 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG I 34 " --> pdb=" O GLY I 28 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 102 through 105 Processing sheet with id=AF3, first strand: chain 'J' and resid 25 through 28 removed outlier: 3.535A pdb=" N GLY J 28 " --> pdb=" O ARG J 34 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG J 34 " --> pdb=" O GLY J 28 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 102 through 105 1492 hydrogen bonds defined for protein. 4299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 9.60 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7259 1.33 - 1.45: 7859 1.45 - 1.58: 19173 1.58 - 1.70: 242 1.70 - 1.83: 187 Bond restraints: 34720 Sorted by residual: bond pdb=" N GLU C1006 " pdb=" CA GLU C1006 " ideal model delta sigma weight residual 1.453 1.491 -0.038 8.30e-03 1.45e+04 2.04e+01 bond pdb=" N GLU C 312 " pdb=" CA GLU C 312 " ideal model delta sigma weight residual 1.457 1.489 -0.032 9.10e-03 1.21e+04 1.24e+01 bond pdb=" C3' DA P 40 " pdb=" C2' DA P 40 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" N VAL D1082 " pdb=" CA VAL D1082 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.13e+01 bond pdb=" N GLU D 640 " pdb=" CA GLU D 640 " ideal model delta sigma weight residual 1.462 1.488 -0.026 7.70e-03 1.69e+04 1.11e+01 ... (remaining 34715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 45930 2.09 - 4.18: 1354 4.18 - 6.27: 154 6.27 - 8.37: 38 8.37 - 10.46: 9 Bond angle restraints: 47485 Sorted by residual: angle pdb=" N ASN D 533 " pdb=" CA ASN D 533 " pdb=" C ASN D 533 " ideal model delta sigma weight residual 113.56 104.28 9.28 1.39e+00 5.18e-01 4.46e+01 angle pdb=" N ALA D1078 " pdb=" CA ALA D1078 " pdb=" C ALA D1078 " ideal model delta sigma weight residual 111.36 117.51 -6.15 1.09e+00 8.42e-01 3.18e+01 angle pdb=" N ARG D1079 " pdb=" CA ARG D1079 " pdb=" C ARG D1079 " ideal model delta sigma weight residual 108.52 117.55 -9.03 1.63e+00 3.76e-01 3.07e+01 angle pdb=" N GLU H 107 " pdb=" CA GLU H 107 " pdb=" CB GLU H 107 " ideal model delta sigma weight residual 110.28 118.04 -7.76 1.55e+00 4.16e-01 2.50e+01 angle pdb=" CA GLU C 312 " pdb=" C GLU C 312 " pdb=" N PRO C 313 " ideal model delta sigma weight residual 118.16 121.66 -3.50 7.00e-01 2.04e+00 2.49e+01 ... (remaining 47480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 20210 35.69 - 71.38: 732 71.38 - 107.07: 26 107.07 - 142.76: 2 142.76 - 178.45: 3 Dihedral angle restraints: 20973 sinusoidal: 9405 harmonic: 11568 Sorted by residual: dihedral pdb=" CA ARG I 62 " pdb=" C ARG I 62 " pdb=" N THR I 63 " pdb=" CA THR I 63 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASN F 229 " pdb=" C ASN F 229 " pdb=" N ALA F 230 " pdb=" CA ALA F 230 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA VAL D 726 " pdb=" C VAL D 726 " pdb=" N ALA D 727 " pdb=" CA ALA D 727 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 20970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4595 0.071 - 0.141: 736 0.141 - 0.212: 61 0.212 - 0.283: 8 0.283 - 0.353: 4 Chirality restraints: 5404 Sorted by residual: chirality pdb=" CA ARG D1079 " pdb=" N ARG D1079 " pdb=" C ARG D1079 " pdb=" CB ARG D1079 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA LEU D1080 " pdb=" N LEU D1080 " pdb=" C LEU D1080 " pdb=" CB LEU D1080 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CG LEU H 68 " pdb=" CB LEU H 68 " pdb=" CD1 LEU H 68 " pdb=" CD2 LEU H 68 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 5401 not shown) Planarity restraints: 5820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D1076 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C LYS D1076 " -0.060 2.00e-02 2.50e+03 pdb=" O LYS D1076 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG D1077 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS J 209 " -0.039 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO J 210 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO J 210 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO J 210 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 32 " 0.023 2.00e-02 2.50e+03 1.67e-02 5.61e+00 pdb=" CG TYR E 32 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR E 32 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR E 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 32 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR E 32 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 32 " 0.004 2.00e-02 2.50e+03 ... (remaining 5817 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4325 2.75 - 3.29: 33142 3.29 - 3.83: 58438 3.83 - 4.36: 66694 4.36 - 4.90: 110540 Nonbonded interactions: 273139 Sorted by model distance: nonbonded pdb=" O LEU D 381 " pdb=" OG SER D 401 " model vdw 2.217 3.040 nonbonded pdb=" O PHE D 845 " pdb=" OG1 THR D 848 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR D 867 " pdb=" OE1 GLN D1210 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR C 502 " pdb=" OE2 GLU C 522 " model vdw 2.225 3.040 nonbonded pdb=" O MET C 246 " pdb=" OG1 THR C 249 " model vdw 2.248 3.040 ... (remaining 273134 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 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 7.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 40.020 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 0.053 34728 Z= 0.320 Angle : 0.802 15.896 47497 Z= 0.497 Chirality : 0.051 0.353 5404 Planarity : 0.005 0.080 5820 Dihedral : 16.834 178.450 13523 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.24 % Allowed : 0.92 % Favored : 98.84 % Cbeta Deviations : 0.03 % 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: -0.87 (0.13), residues: 4019 helix: -0.05 (0.12), residues: 1725 sheet: -0.62 (0.26), residues: 409 loop : -0.97 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 69 TYR 0.040 0.002 TYR E 32 PHE 0.033 0.002 PHE F 245 TRP 0.028 0.002 TRP C 231 HIS 0.011 0.001 HIS D 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.32 (34720) covalent geometry : angle 0.79244 / 0.50 (47485) hydrogen bonds : bond 0.18403 / 12.08 ( 1558) hydrogen bonds : angle 7.15955 / 4.91 ( 4459) metal coordination : bond 0.01160 / 0.46 ( 8) metal coordination : angle 7.99187 / 3.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 400 time to evaluate : 1.328 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: B 136 MET cc_start: 0.7304 (pmm) cc_final: 0.7003 (pmm) REVERT: C 243 TYR cc_start: 0.7298 (m-80) cc_final: 0.6959 (m-80) REVERT: C 328 ILE cc_start: 0.8185 (mm) cc_final: 0.7951 (mm) REVERT: C 329 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8936 (mmtt) REVERT: C 339 THR cc_start: 0.8410 (p) cc_final: 0.8171 (p) REVERT: C 643 TYR cc_start: 0.8299 (p90) cc_final: 0.7933 (p90) REVERT: C 852 ASN cc_start: 0.8586 (m110) cc_final: 0.8375 (m110) REVERT: D 92 MET cc_start: 0.9077 (ptp) cc_final: 0.8831 (ptp) REVERT: D 205 MET cc_start: 0.5389 (mmm) cc_final: 0.4597 (mmm) REVERT: D 428 SER cc_start: 0.8790 (p) cc_final: 0.8406 (m) REVERT: E 65 GLU cc_start: 0.8133 (pm20) cc_final: 0.7916 (pm20) REVERT: F 245 PHE cc_start: 0.8153 (m-80) cc_final: 0.7766 (m-80) REVERT: F 394 ILE cc_start: 0.9443 (mm) cc_final: 0.9235 (mm) REVERT: F 444 HIS cc_start: 0.8737 (t-90) cc_final: 0.8398 (t-90) REVERT: G 83 TRP cc_start: 0.9128 (t-100) cc_final: 0.8855 (t-100) REVERT: G 85 MET cc_start: 0.8284 (mtp) cc_final: 0.8048 (mmm) REVERT: I 105 GLU cc_start: 0.7882 (mp0) cc_final: 0.7508 (pm20) outliers start: 8 outliers final: 2 residues processed: 407 average time/residue: 0.2252 time to fit residues: 148.1691 Evaluate side-chains 312 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 154 GLN C 281 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 HIS ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN D 799 ASN ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN H 15 HIS ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.182707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123534 restraints weight = 64234.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123055 restraints weight = 44212.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122136 restraints weight = 37750.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122935 restraints weight = 42051.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123131 restraints weight = 34559.132| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34728 Z= 0.158 Angle : 0.659 14.003 47497 Z= 0.345 Chirality : 0.044 0.295 5404 Planarity : 0.005 0.079 5820 Dihedral : 16.269 178.419 5749 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.72 % Allowed : 9.22 % Favored : 90.07 % 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: -0.42 (0.13), residues: 4019 helix: 0.47 (0.12), residues: 1735 sheet: -0.37 (0.27), residues: 382 loop : -0.90 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 60 TYR 0.034 0.001 TYR E 32 PHE 0.028 0.002 PHE C 141 TRP 0.018 0.001 TRP J 74 HIS 0.008 0.001 HIS C1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (34720) covalent geometry : angle 0.65027 / 0.34 (47485) hydrogen bonds : bond 0.05303 / 3.42 ( 1558) hydrogen bonds : angle 5.22042 / 3.60 ( 4459) metal coordination : bond 0.00851 / 0.34 ( 8) metal coordination : angle 6.88948 / 3.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 350 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.8100 (mtp) cc_final: 0.7889 (ttp) REVERT: B 1 MET cc_start: 0.5136 (tmm) cc_final: 0.4848 (tmm) REVERT: C 91 MET cc_start: 0.7154 (pmm) cc_final: 0.6469 (pmm) REVERT: C 289 PHE cc_start: 0.8352 (m-80) cc_final: 0.8051 (m-80) REVERT: C 329 LYS cc_start: 0.9144 (mmtt) cc_final: 0.8803 (mmmt) REVERT: C 339 THR cc_start: 0.8314 (p) cc_final: 0.8058 (p) REVERT: C 538 MET cc_start: 0.8428 (mpp) cc_final: 0.7822 (mtp) REVERT: C 643 TYR cc_start: 0.8320 (p90) cc_final: 0.8003 (p90) REVERT: C 852 ASN cc_start: 0.8627 (m110) cc_final: 0.8401 (m110) REVERT: D 92 MET cc_start: 0.9143 (ptp) cc_final: 0.8906 (ptp) REVERT: D 113 ARG cc_start: 0.5431 (tpp-160) cc_final: 0.5221 (tpp-160) REVERT: D 335 PHE cc_start: 0.7980 (m-80) cc_final: 0.7714 (m-10) REVERT: F 245 PHE cc_start: 0.8265 (m-80) cc_final: 0.7881 (m-80) REVERT: F 444 HIS cc_start: 0.8660 (t-90) cc_final: 0.8337 (t-90) REVERT: F 460 MET cc_start: 0.6135 (mmm) cc_final: 0.5824 (mmp) REVERT: H 142 LEU cc_start: 0.7976 (tt) cc_final: 0.7534 (pt) REVERT: I 105 GLU cc_start: 0.7940 (mp0) cc_final: 0.7541 (pm20) REVERT: J 87 ARG cc_start: 0.8059 (mmt-90) cc_final: 0.7702 (mtt-85) outliers start: 24 outliers final: 15 residues processed: 364 average time/residue: 0.2192 time to fit residues: 130.4482 Evaluate side-chains 305 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 290 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 1031 THR Chi-restraints excluded: chain C residue 1037 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 387 optimal weight: 50.0000 chunk 86 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 381 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 408 optimal weight: 20.0000 chunk 198 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 ASN ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1027 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.181337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121905 restraints weight = 63615.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120167 restraints weight = 46176.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120294 restraints weight = 40371.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120916 restraints weight = 41653.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120968 restraints weight = 35700.500| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34728 Z= 0.173 Angle : 0.634 15.387 47497 Z= 0.329 Chirality : 0.044 0.306 5404 Planarity : 0.004 0.044 5820 Dihedral : 16.468 179.895 5749 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.40 % Allowed : 11.99 % Favored : 86.61 % 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: -0.23 (0.13), residues: 4019 helix: 0.72 (0.12), residues: 1723 sheet: -0.47 (0.26), residues: 401 loop : -0.84 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 293 TYR 0.022 0.002 TYR F 324 PHE 0.017 0.001 PHE C 240 TRP 0.018 0.001 TRP G 83 HIS 0.008 0.001 HIS D 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (34720) covalent geometry : angle 0.62431 / 0.33 (47485) hydrogen bonds : bond 0.04733 / 3.09 ( 1558) hydrogen bonds : angle 4.91750 / 3.39 ( 4459) metal coordination : bond 0.01075 / 0.45 ( 8) metal coordination : angle 6.93782 / 3.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 314 time to evaluate : 1.295 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: B 1 MET cc_start: 0.5198 (tmm) cc_final: 0.4976 (tmm) REVERT: C 91 MET cc_start: 0.7046 (pmm) cc_final: 0.6412 (pmm) REVERT: C 289 PHE cc_start: 0.8537 (m-80) cc_final: 0.8179 (m-80) REVERT: C 329 LYS cc_start: 0.9118 (mmtt) cc_final: 0.8838 (mmtt) REVERT: C 339 THR cc_start: 0.8227 (p) cc_final: 0.7975 (p) REVERT: C 598 MET cc_start: 0.8384 (mtm) cc_final: 0.8056 (mtm) REVERT: C 643 TYR cc_start: 0.8344 (p90) cc_final: 0.8015 (p90) REVERT: C 852 ASN cc_start: 0.8599 (m110) cc_final: 0.8388 (m110) REVERT: D 37 ARG cc_start: 0.7913 (ptp-170) cc_final: 0.7692 (ptp-170) REVERT: D 335 PHE cc_start: 0.8030 (m-80) cc_final: 0.7816 (m-10) REVERT: F 245 PHE cc_start: 0.8309 (m-80) cc_final: 0.7782 (m-80) REVERT: F 280 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7316 (pt0) REVERT: F 301 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7765 (tt) REVERT: F 326 PHE cc_start: 0.5493 (OUTLIER) cc_final: 0.3742 (t80) REVERT: F 444 HIS cc_start: 0.8672 (t-90) cc_final: 0.8336 (t-90) REVERT: F 460 MET cc_start: 0.6076 (mmm) cc_final: 0.5871 (mmp) REVERT: G 83 TRP cc_start: 0.9021 (t-100) cc_final: 0.8705 (t-100) REVERT: G 98 VAL cc_start: 0.7284 (t) cc_final: 0.7066 (m) REVERT: H 142 LEU cc_start: 0.7915 (tt) cc_final: 0.7565 (pt) REVERT: H 155 LEU cc_start: 0.7460 (tp) cc_final: 0.6648 (mt) REVERT: I 105 GLU cc_start: 0.8040 (mp0) cc_final: 0.7673 (pm20) REVERT: I 205 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8794 (mt) outliers start: 47 outliers final: 28 residues processed: 336 average time/residue: 0.2082 time to fit residues: 115.2960 Evaluate side-chains 325 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 293 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 1031 THR Chi-restraints excluded: chain C residue 1037 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 898 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 170 GLN Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 74 TRP Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 110 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 292 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 409 optimal weight: 30.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1027 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN ** D1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 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 = 0.4394 r_free = 0.4394 target = 0.182166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122617 restraints weight = 63499.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121936 restraints weight = 46300.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121478 restraints weight = 39650.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121799 restraints weight = 40165.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121952 restraints weight = 36896.027| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34728 Z= 0.170 Angle : 0.614 14.143 47497 Z= 0.318 Chirality : 0.043 0.315 5404 Planarity : 0.004 0.044 5820 Dihedral : 16.641 179.241 5749 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.64 % Allowed : 14.14 % Favored : 84.22 % 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: -0.11 (0.13), residues: 4019 helix: 0.82 (0.12), residues: 1730 sheet: -0.43 (0.26), residues: 409 loop : -0.79 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 293 TYR 0.027 0.002 TYR C1014 PHE 0.027 0.001 PHE C 141 TRP 0.025 0.001 TRP C 231 HIS 0.007 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (34720) covalent geometry : angle 0.60420 / 0.32 (47485) hydrogen bonds : bond 0.04308 / 2.81 ( 1558) hydrogen bonds : angle 4.74220 / 3.27 ( 4459) metal coordination : bond 0.01047 / 0.44 ( 8) metal coordination : angle 6.86326 / 3.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 319 time to evaluate : 1.586 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: C 91 MET cc_start: 0.7089 (pmm) cc_final: 0.6417 (pmm) REVERT: C 281 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8331 (tp-100) REVERT: C 289 PHE cc_start: 0.8573 (m-80) cc_final: 0.8218 (m-80) REVERT: C 329 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8870 (mmtt) REVERT: C 643 TYR cc_start: 0.8374 (p90) cc_final: 0.8007 (p90) REVERT: C 852 ASN cc_start: 0.8697 (m110) cc_final: 0.8245 (m110) REVERT: D 218 ARG cc_start: 0.8467 (ptp-170) cc_final: 0.8218 (ptt-90) REVERT: F 245 PHE cc_start: 0.8428 (m-80) cc_final: 0.7881 (m-80) REVERT: F 280 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7288 (pt0) REVERT: F 326 PHE cc_start: 0.5398 (OUTLIER) cc_final: 0.3868 (t80) REVERT: F 444 HIS cc_start: 0.8739 (t-90) cc_final: 0.8402 (t-90) REVERT: H 142 LEU cc_start: 0.8095 (tt) cc_final: 0.7750 (pt) REVERT: H 155 LEU cc_start: 0.7438 (tp) cc_final: 0.6679 (mt) REVERT: I 105 GLU cc_start: 0.8083 (mp0) cc_final: 0.7478 (pm20) outliers start: 55 outliers final: 38 residues processed: 348 average time/residue: 0.2156 time to fit residues: 123.8136 Evaluate side-chains 335 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 1031 THR Chi-restraints excluded: chain C residue 1037 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 898 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 170 GLN Chi-restraints excluded: chain J residue 74 TRP Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 408 optimal weight: 20.0000 chunk 388 optimal weight: 50.0000 chunk 391 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 250 optimal weight: 0.2980 chunk 251 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 326 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 ASN C 944 GLN ** C1027 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.182467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122406 restraints weight = 63792.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123034 restraints weight = 44040.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122266 restraints weight = 35879.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.122569 restraints weight = 37006.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122752 restraints weight = 34897.481| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34728 Z= 0.147 Angle : 0.604 13.231 47497 Z= 0.312 Chirality : 0.043 0.298 5404 Planarity : 0.004 0.060 5820 Dihedral : 16.691 179.266 5749 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.91 % Allowed : 15.30 % Favored : 82.79 % 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: -0.03 (0.13), residues: 4019 helix: 0.92 (0.12), residues: 1729 sheet: -0.42 (0.26), residues: 407 loop : -0.77 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 214 TYR 0.025 0.001 TYR E 32 PHE 0.023 0.001 PHE B 63 TRP 0.024 0.001 TRP C 231 HIS 0.008 0.001 HIS D 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (34720) covalent geometry : angle 0.59524 / 0.31 (47485) hydrogen bonds : bond 0.04113 / 2.69 ( 1558) hydrogen bonds : angle 4.59459 / 3.17 ( 4459) metal coordination : bond 0.00871 / 0.37 ( 8) metal coordination : angle 6.62528 / 3.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 321 time to evaluate : 0.991 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: C 91 MET cc_start: 0.6981 (pmm) cc_final: 0.6335 (pmm) REVERT: C 174 TYR cc_start: 0.7593 (m-10) cc_final: 0.7349 (m-10) REVERT: C 246 MET cc_start: 0.7728 (ttp) cc_final: 0.7461 (ttp) REVERT: C 281 GLN cc_start: 0.8841 (tp-100) cc_final: 0.8309 (tp-100) REVERT: C 289 PHE cc_start: 0.8549 (m-80) cc_final: 0.8221 (m-80) REVERT: C 329 LYS cc_start: 0.9112 (mmtt) cc_final: 0.8902 (mmtt) REVERT: C 643 TYR cc_start: 0.8340 (p90) cc_final: 0.7967 (p90) REVERT: C 806 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9114 (pp) REVERT: C 852 ASN cc_start: 0.8496 (m110) cc_final: 0.8266 (m110) REVERT: D 37 ARG cc_start: 0.7817 (ptp-170) cc_final: 0.7504 (ptp-170) REVERT: F 245 PHE cc_start: 0.8255 (m-80) cc_final: 0.7612 (m-80) REVERT: F 280 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7256 (pt0) REVERT: F 326 PHE cc_start: 0.5312 (OUTLIER) cc_final: 0.3949 (t80) REVERT: F 444 HIS cc_start: 0.8608 (t-90) cc_final: 0.8238 (t-90) REVERT: F 460 MET cc_start: 0.5853 (mmp) cc_final: 0.5327 (mmp) REVERT: G 87 MET cc_start: 0.8857 (mmt) cc_final: 0.8441 (mmt) REVERT: H 155 LEU cc_start: 0.7460 (tp) cc_final: 0.6705 (mt) REVERT: I 105 GLU cc_start: 0.8046 (mp0) cc_final: 0.7522 (pm20) outliers start: 64 outliers final: 41 residues processed: 360 average time/residue: 0.2022 time to fit residues: 120.6582 Evaluate side-chains 337 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 293 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 747 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 925 LEU Chi-restraints excluded: chain C residue 1031 THR Chi-restraints excluded: chain C residue 1037 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 898 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 170 GLN Chi-restraints excluded: chain J residue 74 TRP Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 283 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 69 optimal weight: 10.0000 chunk 380 optimal weight: 5.9990 chunk 320 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 404 optimal weight: 30.0000 chunk 370 optimal weight: 7.9990 chunk 112 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 HIS ** 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 = 0.4397 r_free = 0.4397 target = 0.182270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122459 restraints weight = 63561.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121949 restraints weight = 46044.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121457 restraints weight = 40263.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121670 restraints weight = 40406.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121811 restraints weight = 38159.428| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34728 Z= 0.148 Angle : 0.620 17.241 47497 Z= 0.316 Chirality : 0.043 0.429 5404 Planarity : 0.004 0.049 5820 Dihedral : 16.732 179.083 5749 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.18 % Allowed : 16.20 % Favored : 81.62 % 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: -0.00 (0.13), residues: 4019 helix: 0.96 (0.12), residues: 1740 sheet: -0.40 (0.26), residues: 399 loop : -0.78 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 185 TYR 0.023 0.001 TYR E 32 PHE 0.018 0.001 PHE F 300 TRP 0.027 0.001 TRP C 231 HIS 0.009 0.001 HIS C1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (34720) covalent geometry : angle 0.61169 / 0.32 (47485) hydrogen bonds : bond 0.04035 / 2.63 ( 1558) hydrogen bonds : angle 4.52658 / 3.13 ( 4459) metal coordination : bond 0.00894 / 0.38 ( 8) metal coordination : angle 6.56966 / 3.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 317 time to evaluate : 1.261 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: B 1 MET cc_start: 0.4592 (tpt) cc_final: 0.4328 (tpt) REVERT: C 91 MET cc_start: 0.7142 (pmm) cc_final: 0.6450 (pmm) REVERT: C 246 MET cc_start: 0.7732 (ttp) cc_final: 0.7419 (ttp) REVERT: C 281 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8292 (tp-100) REVERT: C 289 PHE cc_start: 0.8606 (m-80) cc_final: 0.8260 (m-80) REVERT: C 643 TYR cc_start: 0.8349 (p90) cc_final: 0.7990 (p90) REVERT: C 806 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9167 (pp) REVERT: C 852 ASN cc_start: 0.8504 (m110) cc_final: 0.8248 (m110) REVERT: D 37 ARG cc_start: 0.7691 (ptp-170) cc_final: 0.7389 (ptp-170) REVERT: E 73 ARG cc_start: 0.8620 (tpp80) cc_final: 0.8368 (mmm-85) REVERT: F 233 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: F 280 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7335 (pt0) REVERT: F 326 PHE cc_start: 0.5573 (OUTLIER) cc_final: 0.4272 (t80) REVERT: F 444 HIS cc_start: 0.8708 (t-90) cc_final: 0.8361 (t-90) REVERT: F 460 MET cc_start: 0.5841 (mmp) cc_final: 0.5347 (mmp) REVERT: F 509 TYR cc_start: 0.7533 (m-80) cc_final: 0.7130 (m-80) REVERT: G 87 MET cc_start: 0.8834 (mmt) cc_final: 0.8297 (mmt) REVERT: H 155 LEU cc_start: 0.7585 (tp) cc_final: 0.6827 (mt) REVERT: I 105 GLU cc_start: 0.8106 (mp0) cc_final: 0.7562 (pm20) outliers start: 73 outliers final: 49 residues processed: 362 average time/residue: 0.2128 time to fit residues: 126.6952 Evaluate side-chains 348 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 295 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 747 ASP Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 827 HIS Chi-restraints excluded: chain C residue 925 LEU Chi-restraints excluded: chain C residue 1031 THR Chi-restraints excluded: chain C residue 1037 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 170 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 74 TRP Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 283 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 45 optimal weight: 0.0020 chunk 115 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 394 optimal weight: 50.0000 chunk 314 optimal weight: 0.0030 chunk 296 optimal weight: 10.0000 chunk 238 optimal weight: 0.0000 chunk 367 optimal weight: 5.9990 overall best weight: 0.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN B 200 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 HIS ** 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 = 0.4415 r_free = 0.4415 target = 0.183996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121686 restraints weight = 64064.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123693 restraints weight = 45720.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123463 restraints weight = 33410.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123712 restraints weight = 35437.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123828 restraints weight = 33877.877| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 34728 Z= 0.116 Angle : 0.615 17.748 47497 Z= 0.311 Chirality : 0.043 0.407 5404 Planarity : 0.004 0.058 5820 Dihedral : 16.750 178.791 5749 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.00 % Allowed : 16.56 % Favored : 81.44 % 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: 0.09 (0.13), residues: 4019 helix: 1.05 (0.13), residues: 1729 sheet: -0.33 (0.27), residues: 404 loop : -0.74 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 214 TYR 0.028 0.001 TYR I 89 PHE 0.020 0.001 PHE B 63 TRP 0.021 0.001 TRP C 231 HIS 0.008 0.001 HIS C1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (34720) covalent geometry : angle 0.60725 / 0.31 (47485) hydrogen bonds : bond 0.03898 / 2.55 ( 1558) hydrogen bonds : angle 4.43357 / 3.07 ( 4459) metal coordination : bond 0.00503 / 0.21 ( 8) metal coordination : angle 6.14643 / 2.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 337 time to evaluate : 1.225 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: A 208 MET cc_start: 0.8034 (mtp) cc_final: 0.7756 (ttp) REVERT: B 1 MET cc_start: 0.4479 (tpt) cc_final: 0.4150 (tpt) REVERT: B 41 THR cc_start: 0.9295 (t) cc_final: 0.9040 (m) REVERT: B 136 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6680 (pmm) REVERT: C 91 MET cc_start: 0.7107 (pmm) cc_final: 0.6430 (pmm) REVERT: C 110 CYS cc_start: 0.7986 (m) cc_final: 0.7164 (m) REVERT: C 246 MET cc_start: 0.7682 (ttp) cc_final: 0.7427 (ttp) REVERT: C 266 TYR cc_start: 0.8980 (t80) cc_final: 0.8742 (t80) REVERT: C 281 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8232 (tp-100) REVERT: C 289 PHE cc_start: 0.8634 (m-80) cc_final: 0.8277 (m-80) REVERT: C 643 TYR cc_start: 0.8304 (p90) cc_final: 0.7936 (p90) REVERT: C 806 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9156 (pp) REVERT: C 852 ASN cc_start: 0.8530 (m110) cc_final: 0.8265 (m110) REVERT: D 37 ARG cc_start: 0.7763 (ptp-170) cc_final: 0.7369 (ptp-170) REVERT: D 214 ARG cc_start: 0.8877 (ptt-90) cc_final: 0.8571 (ptp90) REVERT: D 682 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7312 (tm-30) REVERT: E 73 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8343 (mmm-85) REVERT: F 233 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: F 245 PHE cc_start: 0.8318 (m-80) cc_final: 0.7729 (m-80) REVERT: F 280 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: F 326 PHE cc_start: 0.5575 (OUTLIER) cc_final: 0.4277 (t80) REVERT: F 355 MET cc_start: 0.8374 (mmm) cc_final: 0.8152 (mmm) REVERT: F 460 MET cc_start: 0.5753 (mmp) cc_final: 0.5361 (mmp) REVERT: F 509 TYR cc_start: 0.7398 (m-80) cc_final: 0.6973 (m-80) REVERT: G 87 MET cc_start: 0.8851 (mmt) cc_final: 0.8476 (mmm) REVERT: H 155 LEU cc_start: 0.7698 (tp) cc_final: 0.6927 (mt) REVERT: I 36 TRP cc_start: 0.8711 (m100) cc_final: 0.7941 (m100) REVERT: I 105 GLU cc_start: 0.8130 (mp0) cc_final: 0.7563 (pm20) outliers start: 67 outliers final: 44 residues processed: 371 average time/residue: 0.2145 time to fit residues: 131.0258 Evaluate side-chains 358 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 309 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 747 ASP Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 827 HIS Chi-restraints excluded: chain C residue 925 LEU Chi-restraints excluded: chain C residue 1031 THR Chi-restraints excluded: chain C residue 1037 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain I residue 170 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 74 TRP Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 283 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 204 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 293 optimal weight: 7.9990 chunk 375 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 152 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 199 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 HIS ** 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 = 0.4390 r_free = 0.4390 target = 0.181049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120006 restraints weight = 62988.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119592 restraints weight = 41898.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120106 restraints weight = 34894.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120252 restraints weight = 37153.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120378 restraints weight = 33573.274| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34728 Z= 0.163 Angle : 0.635 17.484 47497 Z= 0.321 Chirality : 0.043 0.422 5404 Planarity : 0.004 0.071 5820 Dihedral : 16.787 178.995 5749 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.91 % Allowed : 17.12 % Favored : 80.97 % 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: 0.07 (0.13), residues: 4019 helix: 1.03 (0.13), residues: 1740 sheet: -0.44 (0.26), residues: 420 loop : -0.73 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 185 TYR 0.031 0.001 TYR E 32 PHE 0.017 0.001 PHE C 141 TRP 0.040 0.001 TRP C 231 HIS 0.007 0.001 HIS C1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (34720) covalent geometry : angle 0.62609 / 0.32 (47485) hydrogen bonds : bond 0.03937 / 2.58 ( 1558) hydrogen bonds : angle 4.46316 / 3.10 ( 4459) metal coordination : bond 0.01018 / 0.43 ( 8) metal coordination : angle 6.59189 / 3.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 306 time to evaluate : 1.238 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: B 1 MET cc_start: 0.4568 (tpt) cc_final: 0.4261 (tpt) REVERT: C 91 MET cc_start: 0.6999 (pmm) cc_final: 0.6306 (pmm) REVERT: C 110 CYS cc_start: 0.8020 (m) cc_final: 0.7197 (m) REVERT: C 266 TYR cc_start: 0.8942 (t80) cc_final: 0.8718 (t80) REVERT: C 281 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8355 (tp-100) REVERT: C 289 PHE cc_start: 0.8617 (m-80) cc_final: 0.8273 (m-80) REVERT: C 643 TYR cc_start: 0.8377 (p90) cc_final: 0.8009 (p90) REVERT: C 806 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9153 (pp) REVERT: D 37 ARG cc_start: 0.7772 (ptp-170) cc_final: 0.7438 (ptp-170) REVERT: D 91 ARG cc_start: 0.8373 (tpp80) cc_final: 0.8021 (tpt-90) REVERT: E 73 ARG cc_start: 0.8657 (tpp80) cc_final: 0.8380 (mmm-85) REVERT: F 233 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7795 (pm20) REVERT: F 280 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7319 (pt0) REVERT: F 326 PHE cc_start: 0.5790 (OUTLIER) cc_final: 0.4416 (t80) REVERT: F 444 HIS cc_start: 0.8659 (t-90) cc_final: 0.8281 (t-90) REVERT: F 460 MET cc_start: 0.5865 (mmp) cc_final: 0.5429 (mmp) REVERT: F 509 TYR cc_start: 0.7501 (m-80) cc_final: 0.7152 (m-80) REVERT: G 87 MET cc_start: 0.8752 (mmt) cc_final: 0.8412 (mmm) REVERT: H 155 LEU cc_start: 0.7647 (tp) cc_final: 0.6896 (mt) REVERT: I 36 TRP cc_start: 0.8631 (m100) cc_final: 0.7929 (m100) REVERT: I 105 GLU cc_start: 0.8147 (mp0) cc_final: 0.7591 (pm20) REVERT: J 166 TYR cc_start: 0.7906 (t80) cc_final: 0.7671 (t80) outliers start: 64 outliers final: 48 residues processed: 345 average time/residue: 0.2084 time to fit residues: 119.3672 Evaluate side-chains 347 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 747 ASP Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 827 HIS Chi-restraints excluded: chain C residue 925 LEU Chi-restraints excluded: chain C residue 1031 THR Chi-restraints excluded: chain C residue 1037 ILE Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 170 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 74 TRP Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 240 optimal weight: 2.9990 chunk 391 optimal weight: 0.1980 chunk 123 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 362 optimal weight: 30.0000 chunk 279 optimal weight: 0.9980 chunk 370 optimal weight: 40.0000 chunk 257 optimal weight: 0.0870 chunk 264 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.0070 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 HIS ** 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 = 0.4412 r_free = 0.4412 target = 0.183690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122994 restraints weight = 63815.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123889 restraints weight = 45263.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123378 restraints weight = 35471.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123593 restraints weight = 37312.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123609 restraints weight = 35705.117| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34728 Z= 0.122 Angle : 0.634 18.504 47497 Z= 0.319 Chirality : 0.043 0.445 5404 Planarity : 0.004 0.066 5820 Dihedral : 16.800 179.228 5749 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.67 % Allowed : 17.72 % Favored : 80.61 % 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: 0.09 (0.13), residues: 4019 helix: 1.03 (0.13), residues: 1739 sheet: -0.32 (0.26), residues: 409 loop : -0.72 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 185 TYR 0.026 0.001 TYR E 32 PHE 0.015 0.001 PHE B 63 TRP 0.043 0.001 TRP C 231 HIS 0.007 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (34720) covalent geometry : angle 0.62611 / 0.32 (47485) hydrogen bonds : bond 0.03790 / 2.48 ( 1558) hydrogen bonds : angle 4.40023 / 3.06 ( 4459) metal coordination : bond 0.00583 / 0.25 ( 8) metal coordination : angle 6.23313 / 3.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 309 time to evaluate : 1.303 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: A 208 MET cc_start: 0.8070 (mtp) cc_final: 0.7788 (ttp) REVERT: B 41 THR cc_start: 0.9293 (t) cc_final: 0.9054 (m) REVERT: B 136 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6755 (pmm) REVERT: C 91 MET cc_start: 0.7061 (pmm) cc_final: 0.6367 (pmm) REVERT: C 110 CYS cc_start: 0.8097 (m) cc_final: 0.7248 (m) REVERT: C 266 TYR cc_start: 0.8924 (t80) cc_final: 0.8530 (t80) REVERT: C 281 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8347 (tp-100) REVERT: C 289 PHE cc_start: 0.8641 (m-80) cc_final: 0.8297 (m-80) REVERT: C 643 TYR cc_start: 0.8329 (p90) cc_final: 0.7923 (p90) REVERT: C 806 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9153 (pp) REVERT: C 852 ASN cc_start: 0.8491 (m110) cc_final: 0.8233 (m110) REVERT: D 37 ARG cc_start: 0.7809 (ptp-170) cc_final: 0.7435 (ptp-170) REVERT: D 214 ARG cc_start: 0.9041 (ptp90) cc_final: 0.8768 (ptp90) REVERT: D 747 GLN cc_start: 0.6378 (OUTLIER) cc_final: 0.4840 (pt0) REVERT: E 73 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8345 (mmm-85) REVERT: F 233 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: F 280 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: F 326 PHE cc_start: 0.5819 (OUTLIER) cc_final: 0.4476 (t80) REVERT: F 509 TYR cc_start: 0.7528 (m-80) cc_final: 0.7138 (m-80) REVERT: G 87 MET cc_start: 0.8709 (mmt) cc_final: 0.8409 (mmm) REVERT: H 155 LEU cc_start: 0.7691 (tp) cc_final: 0.6951 (mt) REVERT: I 36 TRP cc_start: 0.8689 (m100) cc_final: 0.7979 (m100) REVERT: I 105 GLU cc_start: 0.8148 (mp0) cc_final: 0.7573 (pm20) outliers start: 56 outliers final: 43 residues processed: 340 average time/residue: 0.2210 time to fit residues: 123.6976 Evaluate side-chains 350 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 747 ASP Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 827 HIS Chi-restraints excluded: chain C residue 925 LEU Chi-restraints excluded: chain C residue 1031 THR Chi-restraints excluded: chain C residue 1037 ILE Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 170 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 74 TRP Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 214 optimal weight: 0.0370 chunk 387 optimal weight: 20.0000 chunk 153 optimal weight: 0.0070 chunk 114 optimal weight: 0.0870 chunk 194 optimal weight: 0.0770 chunk 169 optimal weight: 2.9990 chunk 391 optimal weight: 9.9990 chunk 327 optimal weight: 50.0000 chunk 351 optimal weight: 0.0040 chunk 59 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 overall best weight: 0.0424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1021 GLN ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 HIS ** 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 = 0.4413 r_free = 0.4413 target = 0.183687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123245 restraints weight = 64406.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124043 restraints weight = 45742.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123573 restraints weight = 37173.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123726 restraints weight = 36220.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123774 restraints weight = 34863.566| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.166 34728 Z= 0.153 Angle : 0.739 59.199 47497 Z= 0.390 Chirality : 0.044 0.430 5404 Planarity : 0.004 0.065 5820 Dihedral : 16.798 179.221 5749 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.49 % Allowed : 17.87 % Favored : 80.64 % Cbeta Deviations : 0.03 % 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: 0.11 (0.13), residues: 4019 helix: 1.05 (0.13), residues: 1739 sheet: -0.32 (0.26), residues: 409 loop : -0.72 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG I 261 TYR 0.044 0.001 TYR I 224 PHE 0.016 0.001 PHE B 63 TRP 0.046 0.002 TRP C 231 HIS 0.019 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (34720) covalent geometry : angle 0.73219 / 0.39 (47485) hydrogen bonds : bond 0.03791 / 2.48 ( 1558) hydrogen bonds : angle 4.40873 / 3.07 ( 4459) metal coordination : bond 0.00514 / 0.22 ( 8) metal coordination : angle 6.22679 / 3.01 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 301 time to evaluate : 1.365 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: A 208 MET cc_start: 0.8052 (mtp) cc_final: 0.7776 (ttp) REVERT: B 41 THR cc_start: 0.9288 (t) cc_final: 0.9044 (m) REVERT: B 136 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6771 (pmm) REVERT: C 91 MET cc_start: 0.7011 (pmm) cc_final: 0.6340 (pmm) REVERT: C 110 CYS cc_start: 0.8092 (m) cc_final: 0.7232 (m) REVERT: C 266 TYR cc_start: 0.8847 (t80) cc_final: 0.8443 (t80) REVERT: C 281 GLN cc_start: 0.8781 (tp-100) cc_final: 0.8311 (tp-100) REVERT: C 289 PHE cc_start: 0.8602 (m-80) cc_final: 0.8276 (m-80) REVERT: C 643 TYR cc_start: 0.8315 (p90) cc_final: 0.7958 (p90) REVERT: C 806 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9131 (pp) REVERT: C 852 ASN cc_start: 0.8437 (m110) cc_final: 0.8203 (m110) REVERT: D 37 ARG cc_start: 0.7765 (ptp-170) cc_final: 0.7403 (ptp-170) REVERT: E 73 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8322 (mmm-85) REVERT: F 233 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: F 280 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7304 (pt0) REVERT: F 326 PHE cc_start: 0.5787 (OUTLIER) cc_final: 0.4446 (t80) REVERT: F 509 TYR cc_start: 0.7475 (m-80) cc_final: 0.7110 (m-80) REVERT: G 87 MET cc_start: 0.8656 (mmt) cc_final: 0.8408 (mmm) REVERT: H 155 LEU cc_start: 0.7583 (tp) cc_final: 0.6868 (mt) REVERT: I 36 TRP cc_start: 0.8480 (m100) cc_final: 0.7854 (m100) REVERT: I 105 GLU cc_start: 0.8108 (mp0) cc_final: 0.7568 (pm20) outliers start: 50 outliers final: 44 residues processed: 329 average time/residue: 0.2157 time to fit residues: 118.0809 Evaluate side-chains 347 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 298 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 747 ASP Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 827 HIS Chi-restraints excluded: chain C residue 925 LEU Chi-restraints excluded: chain C residue 1031 THR Chi-restraints excluded: chain C residue 1037 ILE Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 170 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 74 TRP Chi-restraints excluded: chain J residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 259 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 chunk 279 optimal weight: 0.0010 chunk 340 optimal weight: 50.0000 chunk 168 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 299 optimal weight: 4.9990 chunk 344 optimal weight: 8.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.183745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122717 restraints weight = 63925.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123666 restraints weight = 44049.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122983 restraints weight = 37226.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123056 restraints weight = 37346.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123435 restraints weight = 35825.658| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.166 34728 Z= 0.153 Angle : 0.739 59.189 47497 Z= 0.390 Chirality : 0.044 0.429 5404 Planarity : 0.004 0.065 5820 Dihedral : 16.798 179.221 5749 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.46 % Allowed : 17.99 % Favored : 80.55 % Cbeta Deviations : 0.03 % 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: 0.11 (0.13), residues: 4019 helix: 1.05 (0.13), residues: 1739 sheet: -0.32 (0.26), residues: 409 loop : -0.72 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG I 261 TYR 0.044 0.001 TYR I 224 PHE 0.016 0.001 PHE B 63 TRP 0.046 0.002 TRP C 231 HIS 0.019 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (34720) covalent geometry : angle 0.73214 / 0.39 (47485) hydrogen bonds : bond 0.03791 / 2.48 ( 1558) hydrogen bonds : angle 4.40873 / 3.07 ( 4459) metal coordination : bond 0.00514 / 0.22 ( 8) metal coordination : angle 6.22678 / 3.01 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.38 seconds wall clock time: 112 minutes 14.60 seconds (6734.60 seconds total)