Starting phenix.real_space_refine on Sun Jun 29 02:20:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jke_36370/06_2025/8jke_36370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jke_36370/06_2025/8jke_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_36370/06_2025/8jke_36370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jke_36370/06_2025/8jke_36370.map" model { file = "/net/cci-nas-00/data/ceres_data/8jke_36370/06_2025/8jke_36370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jke_36370/06_2025/8jke_36370.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 2.42s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.98, per 1000 atoms: 0.62 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: 8.90 Conformation dependent library (CDL) restraints added in 4.5 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: 13.17 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: 18.40 Time building geometry restraints manager: 10.42 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=" 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 bond pdb=" N VAL C 818 " pdb=" CA VAL C 818 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.14e-02 7.69e+03 1.02e+01 ... (remaining 34715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 46051 2.09 - 4.18: 1233 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: 4677 0.071 - 0.141: 657 0.141 - 0.212: 58 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: 10.270 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: 0.030 Extract box with map and model: 1.500 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 98.040 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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= 0.256 Angle : 0.779 15.896 47497 Z= 0.443 Chirality : 0.049 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (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 TRP 0.028 0.002 TRP C 231 HIS 0.011 0.001 HIS D 25 PHE 0.033 0.002 PHE F 245 TYR 0.040 0.002 TYR E 32 ARG 0.012 0.000 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.18403 ( 1558) hydrogen bonds : angle 7.15955 ( 4459) metal coordination : bond 0.01160 ( 8) metal coordination : angle 7.99187 ( 12) covalent geometry : bond 0.00454 (34720) covalent geometry : angle 0.76913 (47485) *********************** 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 : 3.314 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: 0.4733 time to fit residues: 310.7854 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 : 3.395 ------------------------------------------------------------------------------- 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 347 optimal weight: 4.9990 chunk 311 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 322 optimal weight: 50.0000 chunk 124 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 chunk 373 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 154 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 ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.181243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119909 restraints weight = 63258.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120975 restraints weight = 46642.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120640 restraints weight = 36428.471| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34728 Z= 0.192 Angle : 0.660 15.230 47497 Z= 0.340 Chirality : 0.043 0.207 5404 Planarity : 0.005 0.061 5820 Dihedral : 16.224 176.832 5749 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.89 % Allowed : 9.43 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 4019 helix: 0.57 (0.12), residues: 1721 sheet: -0.47 (0.26), residues: 409 loop : -0.90 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 74 HIS 0.009 0.001 HIS D 25 PHE 0.026 0.002 PHE C 141 TYR 0.033 0.002 TYR E 32 ARG 0.007 0.000 ARG C 911 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 1558) hydrogen bonds : angle 5.08573 ( 4459) metal coordination : bond 0.01184 ( 8) metal coordination : angle 7.33237 ( 12) covalent geometry : bond 0.00441 (34720) covalent geometry : angle 0.64991 (47485) *********************** 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 377 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 347 time to evaluate : 3.806 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 6 ARG cc_start: 0.7890 (mmp80) cc_final: 0.7519 (mmp80) REVERT: B 1 MET cc_start: 0.5052 (tmm) cc_final: 0.4716 (tmm) REVERT: C 91 MET cc_start: 0.7094 (pmm) cc_final: 0.6423 (pmm) REVERT: C 289 PHE cc_start: 0.8475 (m-80) cc_final: 0.8152 (m-80) REVERT: C 339 THR cc_start: 0.8382 (p) cc_final: 0.8142 (p) REVERT: C 538 MET cc_start: 0.8563 (mpp) cc_final: 0.7918 (mtp) REVERT: C 643 TYR cc_start: 0.8385 (p90) cc_final: 0.8030 (p90) REVERT: C 852 ASN cc_start: 0.8719 (m110) cc_final: 0.8439 (m110) REVERT: D 113 ARG cc_start: 0.5631 (tpp-160) cc_final: 0.5353 (tpp-160) REVERT: D 335 PHE cc_start: 0.8029 (m-80) cc_final: 0.7771 (m-10) REVERT: F 245 PHE cc_start: 0.8399 (m-80) cc_final: 0.7960 (m-80) REVERT: F 444 HIS cc_start: 0.8749 (t-90) cc_final: 0.8417 (t-90) REVERT: G 83 TRP cc_start: 0.9352 (t-100) cc_final: 0.9120 (t-100) REVERT: H 117 ARG cc_start: 0.4935 (mmm160) cc_final: 0.4627 (mmm160) REVERT: H 155 LEU cc_start: 0.7591 (tp) cc_final: 0.6620 (mt) REVERT: I 105 GLU cc_start: 0.8048 (mp0) cc_final: 0.7639 (pm20) REVERT: J 87 ARG cc_start: 0.8088 (mmt-90) cc_final: 0.7706 (mtt-85) outliers start: 30 outliers final: 20 residues processed: 364 average time/residue: 0.5042 time to fit residues: 300.2524 Evaluate side-chains 313 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 293 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 469 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 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 95 LEU 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 J residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 333 optimal weight: 30.0000 chunk 321 optimal weight: 0.3980 chunk 164 optimal weight: 3.9990 chunk 379 optimal weight: 50.0000 chunk 205 optimal weight: 0.7980 chunk 362 optimal weight: 40.0000 chunk 15 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 chunk 207 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 ASN ** C 877 ASN ** 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 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 = 0.4402 r_free = 0.4402 target = 0.182693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122450 restraints weight = 63798.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122959 restraints weight = 44309.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122053 restraints weight = 36661.310| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- 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: 11 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1556 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= 0.148 Angle : 0.602 13.441 47497 Z= 0.309 Chirality : 0.042 0.216 5404 Planarity : 0.004 0.048 5820 Dihedral : 16.336 179.671 5749 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.58 % Allowed : 12.23 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 4019 helix: 0.81 (0.12), residues: 1727 sheet: -0.44 (0.26), residues: 400 loop : -0.81 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 74 HIS 0.008 0.001 HIS C1027 PHE 0.016 0.001 PHE F 245 TYR 0.020 0.001 TYR E 54 ARG 0.006 0.000 ARG F 453 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 1558) hydrogen bonds : angle 4.76388 ( 4459) metal coordination : bond 0.00876 ( 8) metal coordination : angle 6.73922 ( 12) covalent geometry : bond 0.00337 (34720) covalent geometry : angle 0.59221 (47485) *********************** 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 374 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 321 time to evaluate : 3.613 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: B 1 MET cc_start: 0.5073 (tmm) cc_final: 0.4816 (tmm) REVERT: B 136 MET cc_start: 0.7273 (pmm) cc_final: 0.6880 (pmm) REVERT: C 91 MET cc_start: 0.7063 (pmm) cc_final: 0.6403 (pmm) REVERT: C 203 GLU cc_start: 0.7866 (pt0) cc_final: 0.7659 (pt0) REVERT: C 289 PHE cc_start: 0.8506 (m-80) cc_final: 0.8153 (m-80) REVERT: C 598 MET cc_start: 0.8491 (mtm) cc_final: 0.8288 (mtm) REVERT: C 643 TYR cc_start: 0.8364 (p90) cc_final: 0.7999 (p90) REVERT: C 852 ASN cc_start: 0.8638 (m110) cc_final: 0.8242 (m110) REVERT: D 37 ARG cc_start: 0.7891 (ptp-170) cc_final: 0.7686 (ptp-170) REVERT: D 113 ARG cc_start: 0.5679 (tpp-160) cc_final: 0.5448 (tpp-160) REVERT: D 125 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6357 (tp) REVERT: F 245 PHE cc_start: 0.8421 (m-80) cc_final: 0.7919 (m-80) REVERT: F 280 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: F 326 PHE cc_start: 0.5510 (OUTLIER) cc_final: 0.3852 (t80) REVERT: F 444 HIS cc_start: 0.8767 (t-90) cc_final: 0.8431 (t-90) REVERT: G 87 MET cc_start: 0.9043 (mtm) cc_final: 0.8512 (mtm) REVERT: H 142 LEU cc_start: 0.8136 (tp) cc_final: 0.7519 (pt) REVERT: H 155 LEU cc_start: 0.7669 (tp) cc_final: 0.6881 (mt) REVERT: I 105 GLU cc_start: 0.8115 (mp0) cc_final: 0.7735 (pm20) outliers start: 53 outliers final: 31 residues processed: 345 average time/residue: 0.5754 time to fit residues: 326.4719 Evaluate side-chains 329 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 295 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 433 SER 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 820 ASP Chi-restraints excluded: chain C residue 1031 THR Chi-restraints excluded: chain C residue 1037 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 405 MET 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 242 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 212 optimal weight: 0.0010 chunk 362 optimal weight: 30.0000 chunk 158 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 405 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 332 optimal weight: 0.4980 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 944 GLN ** C1027 HIS ** 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** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.181747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121298 restraints weight = 63724.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122026 restraints weight = 45687.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121399 restraints weight = 36684.697| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34728 Z= 0.175 Angle : 0.610 14.121 47497 Z= 0.312 Chirality : 0.042 0.176 5404 Planarity : 0.004 0.045 5820 Dihedral : 16.459 178.338 5749 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.94 % Allowed : 14.29 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.13), residues: 4019 helix: 0.89 (0.12), residues: 1741 sheet: -0.48 (0.26), residues: 407 loop : -0.80 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 231 HIS 0.007 0.001 HIS D 25 PHE 0.025 0.001 PHE C 141 TYR 0.027 0.002 TYR C1014 ARG 0.007 0.000 ARG E 73 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 1558) hydrogen bonds : angle 4.57998 ( 4459) metal coordination : bond 0.01091 ( 8) metal coordination : angle 6.93474 ( 12) covalent geometry : bond 0.00409 (34720) covalent geometry : angle 0.59965 (47485) *********************** 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 387 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 322 time to evaluate : 3.356 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: 0.7554 (pmm) cc_final: 0.7180 (pmm) REVERT: C 91 MET cc_start: 0.7058 (pmm) cc_final: 0.6349 (pmm) REVERT: C 203 GLU cc_start: 0.8019 (pt0) cc_final: 0.7764 (pt0) REVERT: C 289 PHE cc_start: 0.8566 (m-80) cc_final: 0.8208 (m-80) REVERT: C 538 MET cc_start: 0.8579 (mpp) cc_final: 0.8010 (mtp) REVERT: C 643 TYR cc_start: 0.8387 (p90) cc_final: 0.8010 (p90) REVERT: C 806 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9133 (pp) REVERT: C 852 ASN cc_start: 0.8622 (m110) cc_final: 0.8335 (m110) REVERT: D 154 HIS cc_start: 0.8929 (p90) cc_final: 0.8709 (p90) REVERT: F 245 PHE cc_start: 0.8329 (m-80) cc_final: 0.7844 (m-80) REVERT: F 280 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7248 (pt0) REVERT: F 326 PHE cc_start: 0.5367 (OUTLIER) cc_final: 0.4005 (t80) REVERT: F 444 HIS cc_start: 0.8727 (t-90) cc_final: 0.8373 (t-90) REVERT: F 460 MET cc_start: 0.5915 (mmp) cc_final: 0.5416 (mmp) REVERT: H 142 LEU cc_start: 0.8061 (tp) cc_final: 0.7506 (pt) REVERT: H 155 LEU cc_start: 0.7638 (tp) cc_final: 0.6895 (mt) REVERT: I 105 GLU cc_start: 0.8115 (mp0) cc_final: 0.7564 (pm20) REVERT: I 229 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7911 (mm-40) outliers start: 65 outliers final: 41 residues processed: 355 average time/residue: 0.4604 time to fit residues: 270.3271 Evaluate side-chains 342 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 179 GLU 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 199 TRP 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 435 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 747 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 827 HIS 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 125 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 19 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 321 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 269 optimal weight: 0.4980 chunk 239 optimal weight: 1.9990 chunk 322 optimal weight: 30.0000 chunk 404 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 386 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN C 509 GLN C 529 GLN C 877 ASN D 329 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.183080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122186 restraints weight = 63671.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123536 restraints weight = 44448.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122874 restraints weight = 34722.325| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 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 = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34728 Z= 0.126 Angle : 0.579 12.728 47497 Z= 0.295 Chirality : 0.041 0.190 5404 Planarity : 0.004 0.051 5820 Dihedral : 16.474 178.327 5749 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.15 % Allowed : 15.33 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 4019 helix: 1.03 (0.13), residues: 1734 sheet: -0.37 (0.26), residues: 406 loop : -0.76 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 231 HIS 0.008 0.001 HIS C1027 PHE 0.015 0.001 PHE B 63 TYR 0.044 0.001 TYR E 32 ARG 0.014 0.000 ARG J 185 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 1558) hydrogen bonds : angle 4.43013 ( 4459) metal coordination : bond 0.00702 ( 8) metal coordination : angle 6.37139 ( 12) covalent geometry : bond 0.00285 (34720) covalent geometry : angle 0.56991 (47485) *********************** 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 402 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 330 time to evaluate : 3.387 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: 0.7411 (pmm) cc_final: 0.7019 (pmm) REVERT: C 91 MET cc_start: 0.7071 (pmm) cc_final: 0.6398 (pmm) REVERT: C 203 GLU cc_start: 0.8018 (pt0) cc_final: 0.7702 (pt0) REVERT: C 289 PHE cc_start: 0.8622 (m-80) cc_final: 0.8229 (m-80) REVERT: C 538 MET cc_start: 0.8568 (mpp) cc_final: 0.8155 (mtt) REVERT: C 643 TYR cc_start: 0.8338 (p90) cc_final: 0.7955 (p90) REVERT: C 806 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9122 (pp) REVERT: C 852 ASN cc_start: 0.8562 (m110) cc_final: 0.8283 (m110) REVERT: D 125 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6302 (tp) REVERT: D 154 HIS cc_start: 0.8926 (p90) cc_final: 0.8712 (p90) REVERT: F 245 PHE cc_start: 0.8365 (m-80) cc_final: 0.7828 (m-80) REVERT: F 280 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7324 (pt0) REVERT: F 326 PHE cc_start: 0.5594 (OUTLIER) cc_final: 0.4264 (t80) REVERT: F 444 HIS cc_start: 0.8724 (t-90) cc_final: 0.8375 (t-90) REVERT: F 460 MET cc_start: 0.5806 (mmp) cc_final: 0.5377 (mmp) REVERT: F 509 TYR cc_start: 0.7467 (m-80) cc_final: 0.7080 (m-80) REVERT: H 117 ARG cc_start: 0.5683 (mmm160) cc_final: 0.5285 (mmm160) REVERT: H 142 LEU cc_start: 0.8243 (tp) cc_final: 0.7585 (pt) REVERT: H 155 LEU cc_start: 0.7704 (tp) cc_final: 0.6969 (mt) REVERT: I 36 TRP cc_start: 0.8576 (m100) cc_final: 0.7859 (m100) REVERT: I 105 GLU cc_start: 0.8124 (mp0) cc_final: 0.7569 (pm20) outliers start: 72 outliers final: 40 residues processed: 372 average time/residue: 0.4536 time to fit residues: 278.9079 Evaluate side-chains 349 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 305 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 179 GLU 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 433 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 469 MET 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 747 ASP 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 125 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 728 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 155 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 359 optimal weight: 7.9990 chunk 187 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 381 optimal weight: 0.0670 chunk 260 optimal weight: 8.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 200 GLN ** D 25 HIS ** 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** 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 = 0.4385 r_free = 0.4385 target = 0.180564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118429 restraints weight = 63486.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119900 restraints weight = 43983.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.119407 restraints weight = 34962.511| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34728 Z= 0.173 Angle : 0.621 16.540 47497 Z= 0.313 Chirality : 0.042 0.383 5404 Planarity : 0.004 0.048 5820 Dihedral : 16.499 177.368 5749 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.30 % Allowed : 16.29 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4019 helix: 1.01 (0.12), residues: 1747 sheet: -0.50 (0.26), residues: 417 loop : -0.73 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 231 HIS 0.007 0.001 HIS D 154 PHE 0.026 0.001 PHE B 63 TYR 0.033 0.002 TYR I 89 ARG 0.009 0.000 ARG C 270 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 1558) hydrogen bonds : angle 4.44085 ( 4459) metal coordination : bond 0.01076 ( 8) metal coordination : angle 6.79795 ( 12) covalent geometry : bond 0.00405 (34720) covalent geometry : angle 0.61147 (47485) *********************** 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 386 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 309 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.7477 (pmm) cc_final: 0.7206 (pmm) REVERT: C 91 MET cc_start: 0.7053 (pmm) cc_final: 0.6354 (pmm) REVERT: C 110 CYS cc_start: 0.8065 (m) cc_final: 0.7168 (m) REVERT: C 289 PHE cc_start: 0.8644 (m-80) cc_final: 0.8301 (m-80) REVERT: C 538 MET cc_start: 0.8688 (mpp) cc_final: 0.8000 (mtm) REVERT: C 643 TYR cc_start: 0.8399 (p90) cc_final: 0.8024 (p90) REVERT: C 806 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9138 (pp) REVERT: C 1076 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8892 (mt) REVERT: D 37 ARG cc_start: 0.7767 (ptp-170) cc_final: 0.7416 (ptp-170) REVERT: D 151 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8465 (pp) REVERT: D 154 HIS cc_start: 0.8965 (p90) cc_final: 0.8755 (p90) REVERT: D 548 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8699 (p) REVERT: E 73 ARG cc_start: 0.8290 (mtp85) cc_final: 0.8049 (mtm110) REVERT: F 280 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7308 (pt0) REVERT: F 326 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.4393 (t80) REVERT: F 460 MET cc_start: 0.5881 (mmp) cc_final: 0.5490 (mmp) REVERT: F 509 TYR cc_start: 0.7582 (m-80) cc_final: 0.7109 (m-80) REVERT: G 85 MET cc_start: 0.4670 (ptt) cc_final: 0.4009 (ptm) REVERT: H 142 LEU cc_start: 0.8185 (tp) cc_final: 0.7585 (pt) REVERT: H 155 LEU cc_start: 0.7722 (tp) cc_final: 0.6982 (mt) REVERT: I 36 TRP cc_start: 0.8658 (m100) cc_final: 0.7888 (m100) REVERT: I 105 GLU cc_start: 0.8183 (mp0) cc_final: 0.7900 (mp0) REVERT: J 166 TYR cc_start: 0.7906 (t80) cc_final: 0.7648 (t80) outliers start: 77 outliers final: 54 residues processed: 354 average time/residue: 0.4614 time to fit residues: 270.7053 Evaluate side-chains 348 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 288 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 179 GLU 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 199 TRP Chi-restraints excluded: chain C residue 255 THR 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 469 MET 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 C residue 1076 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 151 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 548 SER 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 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 354 optimal weight: 50.0000 chunk 373 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 396 optimal weight: 40.0000 chunk 203 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN ** D 25 HIS ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.181079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120554 restraints weight = 63335.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120906 restraints weight = 43674.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120025 restraints weight = 36872.771| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 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 = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2260 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= 0.143 Angle : 0.603 16.905 47497 Z= 0.305 Chirality : 0.042 0.371 5404 Planarity : 0.004 0.050 5820 Dihedral : 16.506 176.656 5749 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.18 % Allowed : 16.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.13), residues: 4019 helix: 1.03 (0.13), residues: 1749 sheet: -0.51 (0.25), residues: 428 loop : -0.73 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 231 HIS 0.008 0.001 HIS D 154 PHE 0.027 0.001 PHE B 63 TYR 0.040 0.001 TYR E 32 ARG 0.007 0.000 ARG C 270 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1558) hydrogen bonds : angle 4.36021 ( 4459) metal coordination : bond 0.00899 ( 8) metal coordination : angle 6.55749 ( 12) covalent geometry : bond 0.00332 (34720) covalent geometry : angle 0.59433 (47485) *********************** 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 381 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 308 time to evaluate : 4.403 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 136 MET cc_start: 0.7339 (pmm) cc_final: 0.7102 (pmm) REVERT: C 91 MET cc_start: 0.7048 (pmm) cc_final: 0.6357 (pmm) REVERT: C 110 CYS cc_start: 0.8067 (m) cc_final: 0.7182 (m) REVERT: C 289 PHE cc_start: 0.8707 (m-80) cc_final: 0.8330 (m-80) REVERT: C 643 TYR cc_start: 0.8326 (p90) cc_final: 0.7921 (p90) REVERT: C 806 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9093 (pp) REVERT: D 37 ARG cc_start: 0.7811 (ptp-170) cc_final: 0.7597 (ptp-170) REVERT: D 125 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6318 (tp) REVERT: D 151 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8541 (pp) REVERT: D 256 MET cc_start: 0.7700 (tpt) cc_final: 0.7467 (tpt) REVERT: D 747 GLN cc_start: 0.6406 (OUTLIER) cc_final: 0.5072 (pt0) REVERT: D 944 ASP cc_start: 0.8299 (m-30) cc_final: 0.8087 (m-30) REVERT: F 229 ASN cc_start: 0.8788 (p0) cc_final: 0.8335 (p0) REVERT: F 245 PHE cc_start: 0.8348 (m-80) cc_final: 0.7859 (m-80) REVERT: F 280 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7337 (pt0) REVERT: F 326 PHE cc_start: 0.5713 (OUTLIER) cc_final: 0.4453 (t80) REVERT: F 509 TYR cc_start: 0.7564 (m-80) cc_final: 0.7060 (m-80) REVERT: H 142 LEU cc_start: 0.8189 (tp) cc_final: 0.7631 (pt) REVERT: H 155 LEU cc_start: 0.7752 (tp) cc_final: 0.7020 (mt) REVERT: I 36 TRP cc_start: 0.8685 (m100) cc_final: 0.7899 (m100) REVERT: I 105 GLU cc_start: 0.8197 (mp0) cc_final: 0.7904 (mp0) outliers start: 73 outliers final: 50 residues processed: 355 average time/residue: 0.4838 time to fit residues: 284.5295 Evaluate side-chains 349 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 293 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 179 GLU 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 199 TRP Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 562 VAL 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 125 LEU Chi-restraints excluded: chain D residue 151 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 362 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 chunk 318 optimal weight: 0.7980 chunk 316 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 391 optimal weight: 0.6980 chunk 319 optimal weight: 50.0000 chunk 408 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 256 optimal weight: 40.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 HIS ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 787 ASN ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.179295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118414 restraints weight = 63664.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118685 restraints weight = 46908.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118242 restraints weight = 38996.102| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 34728 Z= 0.255 Angle : 0.687 16.593 47497 Z= 0.348 Chirality : 0.044 0.405 5404 Planarity : 0.004 0.054 5820 Dihedral : 16.567 175.280 5749 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.27 % Allowed : 17.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 4019 helix: 0.91 (0.12), residues: 1745 sheet: -0.60 (0.25), residues: 423 loop : -0.79 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 231 HIS 0.008 0.001 HIS D 103 PHE 0.027 0.002 PHE B 63 TYR 0.035 0.002 TYR E 32 ARG 0.008 0.000 ARG C 270 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 1558) hydrogen bonds : angle 4.56615 ( 4459) metal coordination : bond 0.01688 ( 8) metal coordination : angle 7.68848 ( 12) covalent geometry : bond 0.00605 (34720) covalent geometry : angle 0.67629 (47485) *********************** 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 377 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 301 time to evaluate : 3.924 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 136 MET cc_start: 0.7581 (pmm) cc_final: 0.7266 (pmm) REVERT: C 91 MET cc_start: 0.7101 (pmm) cc_final: 0.6405 (pmm) REVERT: C 110 CYS cc_start: 0.8175 (m) cc_final: 0.7213 (m) REVERT: C 289 PHE cc_start: 0.8659 (m-80) cc_final: 0.8318 (m-80) REVERT: C 643 TYR cc_start: 0.8555 (p90) cc_final: 0.8129 (p90) REVERT: C 806 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9137 (pp) REVERT: C 1076 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9064 (mt) REVERT: D 36 TYR cc_start: 0.8224 (p90) cc_final: 0.7958 (p90) REVERT: D 37 ARG cc_start: 0.7792 (ptp-170) cc_final: 0.7247 (ptp-170) REVERT: D 944 ASP cc_start: 0.8424 (m-30) cc_final: 0.8177 (m-30) REVERT: F 229 ASN cc_start: 0.8926 (p0) cc_final: 0.8460 (p0) REVERT: F 245 PHE cc_start: 0.8370 (m-80) cc_final: 0.7855 (m-80) REVERT: F 280 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7335 (pt0) REVERT: F 326 PHE cc_start: 0.5807 (OUTLIER) cc_final: 0.4597 (t80) REVERT: H 142 LEU cc_start: 0.8241 (tp) cc_final: 0.7791 (pt) REVERT: H 155 LEU cc_start: 0.7833 (tp) cc_final: 0.7113 (mt) REVERT: I 105 GLU cc_start: 0.8269 (mp0) cc_final: 0.7953 (mp0) outliers start: 76 outliers final: 56 residues processed: 347 average time/residue: 0.4800 time to fit residues: 274.9866 Evaluate side-chains 351 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 291 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 187 ILE 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 469 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 562 VAL 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 747 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 827 HIS 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 C residue 1076 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 125 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 475 MET 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 280 GLU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 428 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 68 optimal weight: 4.9990 chunk 248 optimal weight: 0.3980 chunk 356 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 323 optimal weight: 0.0870 chunk 160 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 chunk 281 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 331 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** C1027 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 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 = 0.4394 r_free = 0.4394 target = 0.182226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120926 restraints weight = 64334.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121319 restraints weight = 46190.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121001 restraints weight = 37660.009| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2466 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= 0.137 Angle : 0.627 17.881 47497 Z= 0.315 Chirality : 0.042 0.386 5404 Planarity : 0.004 0.095 5820 Dihedral : 16.576 175.213 5749 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.94 % Allowed : 17.75 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 4019 helix: 1.02 (0.13), residues: 1738 sheet: -0.49 (0.26), residues: 407 loop : -0.79 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 231 HIS 0.007 0.001 HIS F 354 PHE 0.028 0.001 PHE B 63 TYR 0.034 0.001 TYR E 32 ARG 0.011 0.000 ARG J 185 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 1558) hydrogen bonds : angle 4.40227 ( 4459) metal coordination : bond 0.00810 ( 8) metal coordination : angle 6.65533 ( 12) covalent geometry : bond 0.00315 (34720) covalent geometry : angle 0.61857 (47485) *********************** 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 373 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 308 time to evaluate : 5.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.7485 (pmm) cc_final: 0.7208 (pmm) REVERT: C 91 MET cc_start: 0.7047 (pmm) cc_final: 0.6366 (pmm) REVERT: C 110 CYS cc_start: 0.8030 (m) cc_final: 0.7152 (m) REVERT: C 289 PHE cc_start: 0.8689 (m-80) cc_final: 0.8389 (m-80) REVERT: C 617 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7838 (mt-10) REVERT: C 643 TYR cc_start: 0.8315 (p90) cc_final: 0.7871 (p90) REVERT: C 707 VAL cc_start: 0.9409 (t) cc_final: 0.9161 (p) REVERT: C 806 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9105 (pp) REVERT: C 1076 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8892 (mt) REVERT: D 36 TYR cc_start: 0.8137 (p90) cc_final: 0.7861 (p90) REVERT: D 37 ARG cc_start: 0.7732 (ptp-170) cc_final: 0.7192 (ptp-170) REVERT: D 125 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6300 (tp) REVERT: D 245 ARG cc_start: 0.7975 (mmm160) cc_final: 0.7494 (tpm170) REVERT: D 248 PHE cc_start: 0.6789 (m-10) cc_final: 0.6425 (m-10) REVERT: D 944 ASP cc_start: 0.8247 (m-30) cc_final: 0.8038 (m-30) REVERT: D 1164 VAL cc_start: 0.8755 (t) cc_final: 0.8516 (t) REVERT: E 73 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7893 (mtm110) REVERT: F 229 ASN cc_start: 0.8769 (p0) cc_final: 0.8299 (p0) REVERT: F 245 PHE cc_start: 0.8144 (m-80) cc_final: 0.7668 (m-80) REVERT: F 280 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7356 (pt0) REVERT: F 326 PHE cc_start: 0.5984 (OUTLIER) cc_final: 0.4906 (t80) REVERT: F 509 TYR cc_start: 0.7405 (m-80) cc_final: 0.6945 (m-80) REVERT: H 142 LEU cc_start: 0.8160 (tp) cc_final: 0.7735 (pt) REVERT: H 155 LEU cc_start: 0.7746 (tp) cc_final: 0.7058 (mt) REVERT: I 36 TRP cc_start: 0.8605 (m100) cc_final: 0.7894 (m100) REVERT: I 74 TRP cc_start: 0.7888 (m-10) cc_final: 0.7049 (m-10) REVERT: I 105 GLU cc_start: 0.8247 (mp0) cc_final: 0.7953 (mp0) outliers start: 65 outliers final: 52 residues processed: 346 average time/residue: 0.6032 time to fit residues: 353.4905 Evaluate side-chains 356 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 298 time to evaluate : 5.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 179 GLU 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 199 TRP Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 747 ASP 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 1076 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 125 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 475 MET 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 280 GLU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 428 VAL 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 I residue 188 MET 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 290 optimal weight: 8.9990 chunk 376 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 258 optimal weight: 0.2980 chunk 206 optimal weight: 0.1980 chunk 283 optimal weight: 1.9990 chunk 350 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 181 optimal weight: 0.0020 chunk 299 optimal weight: 4.9990 chunk 16 optimal weight: 0.0040 overall best weight: 0.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 154 GLN ** C1027 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 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 = 0.4411 r_free = 0.4411 target = 0.183436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124676 restraints weight = 63782.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123714 restraints weight = 43474.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123866 restraints weight = 36672.694| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34728 Z= 0.115 Angle : 0.621 18.967 47497 Z= 0.309 Chirality : 0.041 0.404 5404 Planarity : 0.004 0.084 5820 Dihedral : 16.562 175.121 5749 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.67 % Allowed : 18.41 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.13), residues: 4019 helix: 1.08 (0.13), residues: 1740 sheet: -0.30 (0.26), residues: 399 loop : -0.74 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP G 83 HIS 0.009 0.001 HIS F 354 PHE 0.030 0.001 PHE B 63 TYR 0.029 0.001 TYR E 32 ARG 0.010 0.000 ARG C 746 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 1558) hydrogen bonds : angle 4.27303 ( 4459) metal coordination : bond 0.00510 ( 8) metal coordination : angle 6.22390 ( 12) covalent geometry : bond 0.00258 (34720) covalent geometry : angle 0.61357 (47485) ********************** 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 389 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 333 time to evaluate : 3.525 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: 0.7430 (pmm) cc_final: 0.7147 (pmm) REVERT: C 91 MET cc_start: 0.6904 (pmm) cc_final: 0.6272 (pmm) REVERT: C 110 CYS cc_start: 0.8005 (m) cc_final: 0.7178 (m) REVERT: C 289 PHE cc_start: 0.8659 (m-80) cc_final: 0.8352 (m-80) REVERT: C 442 ASN cc_start: 0.8595 (t0) cc_final: 0.8156 (t0) REVERT: C 643 TYR cc_start: 0.8251 (p90) cc_final: 0.7843 (p90) REVERT: C 707 VAL cc_start: 0.9463 (t) cc_final: 0.9201 (p) REVERT: C 806 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9108 (pp) REVERT: D 36 TYR cc_start: 0.8102 (p90) cc_final: 0.7824 (p90) REVERT: D 37 ARG cc_start: 0.7729 (ptp-170) cc_final: 0.7228 (ptp-170) REVERT: D 125 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6338 (tp) REVERT: D 245 ARG cc_start: 0.7935 (mmm160) cc_final: 0.7542 (tpm170) REVERT: D 944 ASP cc_start: 0.8211 (m-30) cc_final: 0.7997 (m-30) REVERT: D 1164 VAL cc_start: 0.8702 (t) cc_final: 0.8479 (t) REVERT: E 65 GLU cc_start: 0.8151 (pm20) cc_final: 0.7831 (pm20) REVERT: E 73 ARG cc_start: 0.8257 (mtp85) cc_final: 0.8056 (mtm110) REVERT: F 229 ASN cc_start: 0.8759 (p0) cc_final: 0.8296 (p0) REVERT: F 245 PHE cc_start: 0.8149 (m-80) cc_final: 0.7649 (m-80) REVERT: F 280 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: F 326 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.5024 (t80) REVERT: F 509 TYR cc_start: 0.7268 (m-80) cc_final: 0.6945 (m-80) REVERT: G 44 PHE cc_start: 0.0741 (OUTLIER) cc_final: -0.1053 (m-80) REVERT: G 87 MET cc_start: 0.8980 (mmm) cc_final: 0.8759 (mmm) REVERT: H 142 LEU cc_start: 0.8130 (tp) cc_final: 0.7657 (pt) REVERT: H 155 LEU cc_start: 0.7787 (tp) cc_final: 0.7113 (mt) REVERT: I 36 TRP cc_start: 0.8572 (m100) cc_final: 0.7874 (m100) REVERT: I 74 TRP cc_start: 0.7862 (m-10) cc_final: 0.7023 (m-10) REVERT: I 89 TYR cc_start: 0.7861 (m-80) cc_final: 0.7612 (m-80) REVERT: I 105 GLU cc_start: 0.8226 (mp0) cc_final: 0.7934 (mp0) outliers start: 56 outliers final: 41 residues processed: 360 average time/residue: 0.4675 time to fit residues: 276.6357 Evaluate side-chains 359 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 747 ASP 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 1037 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 329 GLN 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 280 GLU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain G residue 44 PHE 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 I residue 188 MET Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 74 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 69 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 294 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 ASN ** 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** 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 = 0.180988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120252 restraints weight = 63705.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121005 restraints weight = 43486.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120302 restraints weight = 34385.998| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34728 Z= 0.151 Angle : 0.639 19.150 47497 Z= 0.319 Chirality : 0.042 0.390 5404 Planarity : 0.004 0.082 5820 Dihedral : 16.559 174.082 5749 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.55 % Allowed : 18.68 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.13), residues: 4019 helix: 1.09 (0.13), residues: 1737 sheet: -0.36 (0.26), residues: 404 loop : -0.73 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 231 HIS 0.009 0.001 HIS F 354 PHE 0.030 0.001 PHE B 63 TYR 0.029 0.001 TYR E 32 ARG 0.010 0.000 ARG C 746 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 1558) hydrogen bonds : angle 4.30211 ( 4459) metal coordination : bond 0.00879 ( 8) metal coordination : angle 6.56065 ( 12) covalent geometry : bond 0.00356 (34720) covalent geometry : angle 0.63053 (47485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12680.88 seconds wall clock time: 225 minutes 2.73 seconds (13502.73 seconds total)