Starting phenix.real_space_refine on Mon Jul 6 06:35:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdq_51275/07_2026/9gdq_51275.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdq_51275/07_2026/9gdq_51275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gdq_51275/07_2026/9gdq_51275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdq_51275/07_2026/9gdq_51275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gdq_51275/07_2026/9gdq_51275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdq_51275/07_2026/9gdq_51275.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 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 136 5.49 5 Mg 1 5.21 5 S 119 5.16 5 C 20057 2.51 5 N 5768 2.21 5 O 6536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32619 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 10187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1300, 10187 Classifications: {'peptide': 1300} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1244} Chain breaks: 3 Chain: "D" Number of atoms: 9408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1202, 9408 Classifications: {'peptide': 1202} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 1153} Chain breaks: 4 Chain: "E" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 545 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "A" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1704 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Chain: "F" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3810 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "G" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 557 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 67} Chain: "K" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "T" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1403 Classifications: {'DNA': 69} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 68} Chain: "N" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1422 Classifications: {'DNA': 69} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 68} Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} 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 10635 SG CYS D 70 52.715 93.239 117.263 1.00 95.70 S ATOM 10649 SG CYS D 72 53.278 92.189 120.425 1.00 69.94 S ATOM 10757 SG CYS D 85 49.503 92.644 119.070 1.00 95.41 S ATOM 10781 SG CYS D 88 51.677 95.645 120.100 1.00 93.60 S ATOM 16491 SG CYS D 814 26.440 145.778 84.646 1.00 74.98 S ATOM 17051 SG CYS D 888 29.903 144.704 85.706 1.00 78.95 S ATOM 17100 SG CYS D 895 28.452 143.421 82.407 1.00 74.74 S ATOM 17120 SG CYS D 898 29.466 146.928 82.607 1.00 70.11 S Time building chain proxies: 7.12, per 1000 atoms: 0.22 Number of scatterers: 32619 At special positions: 0 Unit cell: (156.18, 212.076, 197.28, 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 119 16.00 P 136 15.00 Mg 1 11.99 O 6536 8.00 N 5768 7.00 C 20057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " Number of angles added : 12 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 48 sheets defined 45.3% alpha, 15.2% beta 45 base pairs and 107 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.567A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.900A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.512A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.067A pdb=" N LEU C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 247' Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 274 through 279 removed outlier: 3.618A pdb=" N LYS C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.716A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.710A pdb=" N LEU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 3.639A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.572A pdb=" N ILE C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.973A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.384A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.607A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.703A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 713 removed outlier: 4.066A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 859 through 863 Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 979 removed outlier: 4.175A pdb=" N LYS C 958 " --> pdb=" O LYS C 954 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP C 959 " --> pdb=" O GLU C 955 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.267A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1159 through 1163 Processing helix chain 'C' and resid 1164 through 1175 Processing helix chain 'C' and resid 1190 through 1201 Processing helix chain 'C' and resid 1270 through 1281 Processing helix chain 'C' and resid 1282 through 1291 Processing helix chain 'C' and resid 1296 through 1310 removed outlier: 3.723A pdb=" N THR C1301 " --> pdb=" O VAL C1297 " (cutoff:3.500A) Processing helix chain 'C' and resid 1319 through 1332 removed outlier: 3.628A pdb=" N ASN C1323 " --> pdb=" O PRO C1319 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.687A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 208 removed outlier: 4.103A pdb=" N ASP D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.922A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 4.044A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.788A pdb=" N GLN D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.667A pdb=" N LEU D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.770A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 666 removed outlier: 4.236A pdb=" N THR D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 removed outlier: 3.657A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.683A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.640A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1215 through 1223 removed outlier: 3.666A pdb=" N ILE D1219 " --> pdb=" O SER D1215 " (cutoff:3.500A) Processing helix chain 'D' and resid 1224 through 1243 removed outlier: 4.222A pdb=" N VAL D1239 " --> pdb=" O GLU D1235 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D1243 " --> pdb=" O VAL D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1260 removed outlier: 4.285A pdb=" N ILE D1252 " --> pdb=" O ASN D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1295 Processing helix chain 'D' and resid 1309 through 1314 Processing helix chain 'D' and resid 1317 through 1325 removed outlier: 3.673A pdb=" N ALA D1321 " --> pdb=" O SER D1317 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D1325 " --> pdb=" O ALA D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1326 through 1338 Processing helix chain 'D' and resid 1345 through 1353 Processing helix chain 'D' and resid 1358 through 1360 No H-bonds generated for 'chain 'D' and resid 1358 through 1360' Processing helix chain 'D' and resid 1361 through 1374 removed outlier: 3.535A pdb=" N HIS D1365 " --> pdb=" O GLY D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 74 Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.536A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.785A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 235 Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.589A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.610A pdb=" N GLN B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 109 Processing helix chain 'F' and resid 114 through 138 removed outlier: 3.580A pdb=" N GLU F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.558A pdb=" N ALA F 155 " --> pdb=" O ASP F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.519A pdb=" N LEU F 163 " --> pdb=" O ARG F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 224 through 243 removed outlier: 3.788A pdb=" N LEU F 241 " --> pdb=" O GLN F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 266 removed outlier: 3.881A pdb=" N GLU F 266 " --> pdb=" O ASP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 300 removed outlier: 3.576A pdb=" N LEU F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER F 284 " --> pdb=" O THR F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 313 Processing helix chain 'F' and resid 320 through 330 removed outlier: 4.010A pdb=" N LEU F 324 " --> pdb=" O ASN F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 347 removed outlier: 4.076A pdb=" N GLU F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU F 344 " --> pdb=" O GLU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 360 removed outlier: 4.028A pdb=" N MET F 354 " --> pdb=" O LYS F 351 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU F 356 " --> pdb=" O GLN F 353 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN F 357 " --> pdb=" O MET F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 400 removed outlier: 4.013A pdb=" N ARG F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS F 367 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARG F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 408 through 426 Processing helix chain 'F' and resid 428 through 432 removed outlier: 3.549A pdb=" N ARG F 431 " --> pdb=" O GLU F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 455 removed outlier: 4.435A pdb=" N TYR F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 483 Processing helix chain 'F' and resid 489 through 494 removed outlier: 4.026A pdb=" N GLU F 493 " --> pdb=" O GLU F 489 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG F 494 " --> pdb=" O GLU F 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 489 through 494' Processing helix chain 'F' and resid 498 through 507 Processing helix chain 'F' and resid 526 through 531 removed outlier: 3.983A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 557 Processing helix chain 'F' and resid 560 through 572 Processing helix chain 'F' and resid 580 through 588 Processing helix chain 'F' and resid 591 through 607 Processing helix chain 'F' and resid 608 through 611 Processing helix chain 'F' and resid 612 through 617 removed outlier: 3.655A pdb=" N SER F 617 " --> pdb=" O GLU F 613 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 274 removed outlier: 3.539A pdb=" N GLU G 274 " --> pdb=" O CYS G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 292 Processing helix chain 'G' and resid 297 through 312 Processing helix chain 'K' and resid 36 through 49 removed outlier: 3.591A pdb=" N ARG K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 65 Processing helix chain 'K' and resid 73 through 87 removed outlier: 3.582A pdb=" N THR K 77 " --> pdb=" O ASP K 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 Processing helix chain 'H' and resid 55 through 65 Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.903A pdb=" N THR H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.428A pdb=" N LYS C 13 " --> pdb=" O ALA C1182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.605A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.505A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 154 through 159 removed outlier: 4.902A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 236 through 238 Processing sheet with id=AA7, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.978A pdb=" N ILE C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.085A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR C 589 " --> pdb=" O ASP C 604 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB1, first strand: chain 'C' and resid 633 through 638 Processing sheet with id=AB2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.388A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.628A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'C' and resid 1208 through 1209 removed outlier: 7.074A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR C1225 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.117A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AB9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.829A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1243 through 1245 removed outlier: 6.117A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1268 through 1269 Processing sheet with id=AC3, first strand: chain 'C' and resid 1334 through 1339 removed outlier: 4.400A pdb=" N ALA D 19 " --> pdb=" O GLU C1339 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.791A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 159 through 160 removed outlier: 6.827A pdb=" N THR D 177 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 253 through 254 removed outlier: 6.540A pdb=" N PHE D 260 " --> pdb=" O ILE F 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AC8, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AC9, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AD1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD2, first strand: chain 'D' and resid 825 through 826 removed outlier: 4.066A pdb=" N VAL D 833 " --> pdb=" O HIS D 825 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 848 through 849 Processing sheet with id=AD4, first strand: chain 'D' and resid 957 through 959 Processing sheet with id=AD5, first strand: chain 'D' and resid 1184 through 1189 Processing sheet with id=AD6, first strand: chain 'D' and resid 1278 through 1280 removed outlier: 4.325A pdb=" N LYS D1262 " --> pdb=" O GLU D1304 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG D1300 " --> pdb=" O THR D1266 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 12 through 17 removed outlier: 5.147A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N HIS A 23 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR A 208 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS A 25 " --> pdb=" O MET A 206 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N MET A 206 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THR A 27 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE A 204 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLU A 29 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU A 202 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.754A pdb=" N GLU A 58 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU A 148 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL A 56 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY A 150 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N CYS A 54 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AE1, first strand: chain 'A' and resid 109 through 112 Processing sheet with id=AE2, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'B' and resid 13 through 17 removed outlier: 6.218A pdb=" N ASP B 200 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N THR B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 193 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.720A pdb=" N GLU B 58 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU B 148 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL B 56 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY B 150 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N CYS B 54 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AE6, first strand: chain 'B' and resid 109 through 112 removed outlier: 4.241A pdb=" N CYS B 132 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AE8, first strand: chain 'F' and resid 164 through 166 removed outlier: 3.765A pdb=" N ARG F 268 " --> pdb=" O GLY F 166 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 32 through 33 Processing sheet with id=AF1, first strand: chain 'K' and resid 97 through 100 Processing sheet with id=AF2, first strand: chain 'H' and resid 32 through 34 Processing sheet with id=AF3, first strand: chain 'H' and resid 97 through 100 1394 hydrogen bonds defined for protein. 3930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 107 stacking parallelities Total time for adding SS restraints: 10.99 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10430 1.34 - 1.46: 6244 1.46 - 1.58: 16238 1.58 - 1.70: 272 1.70 - 1.82: 213 Bond restraints: 33397 Sorted by residual: bond pdb=" C3' DC N 0 " pdb=" C2' DC N 0 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.41e+01 bond pdb=" C3' DT T 33 " pdb=" C2' DT T 33 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.37e+01 bond pdb=" C3' DT T 29 " pdb=" C2' DT T 29 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.35e+01 bond pdb=" C3' DG T 43 " pdb=" O3' DG T 43 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.19e+01 bond pdb=" C3' DT N -41 " pdb=" O3' DT N -41 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.19e+01 ... (remaining 33392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 45079 2.66 - 5.32: 513 5.32 - 7.97: 66 7.97 - 10.63: 6 10.63 - 13.29: 3 Bond angle restraints: 45667 Sorted by residual: angle pdb=" CA ARG F 372 " pdb=" CB ARG F 372 " pdb=" CG ARG F 372 " ideal model delta sigma weight residual 114.10 123.57 -9.47 2.00e+00 2.50e-01 2.24e+01 angle pdb=" N3 DT T -7 " pdb=" C4 DT T -7 " pdb=" O4 DT T -7 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT N -11 " pdb=" C4 DT N -11 " pdb=" O4 DT N -11 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT T 37 " pdb=" C4 DT T 37 " pdb=" O4 DT T 37 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT T 27 " pdb=" C4 DT T 27 " pdb=" O4 DT T 27 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 45662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 19028 34.03 - 68.07: 1162 68.07 - 102.10: 40 102.10 - 136.14: 0 136.14 - 170.17: 4 Dihedral angle restraints: 20234 sinusoidal: 9333 harmonic: 10901 Sorted by residual: dihedral pdb=" C4' DA T -9 " pdb=" C3' DA T -9 " pdb=" O3' DA T -9 " pdb=" P DT T -8 " ideal model delta sinusoidal sigma weight residual -140.00 30.17 -170.17 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA T 10 " pdb=" C3' DA T 10 " pdb=" O3' DA T 10 " pdb=" P DA T 11 " ideal model delta sinusoidal sigma weight residual -140.00 28.33 -168.33 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA N -8 " pdb=" C3' DA N -8 " pdb=" O3' DA N -8 " pdb=" P DA N -7 " ideal model delta sinusoidal sigma weight residual 220.00 55.48 164.52 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 20231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3997 0.051 - 0.102: 1005 0.102 - 0.153: 195 0.153 - 0.204: 13 0.204 - 0.255: 2 Chirality restraints: 5212 Sorted by residual: chirality pdb=" CG LEU C 901 " pdb=" CB LEU C 901 " pdb=" CD1 LEU C 901 " pdb=" CD2 LEU C 901 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB VAL C 261 " pdb=" CA VAL C 261 " pdb=" CG1 VAL C 261 " pdb=" CG2 VAL C 261 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL C 212 " pdb=" N VAL C 212 " pdb=" C VAL C 212 " pdb=" CB VAL C 212 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 5209 not shown) Planarity restraints: 5466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 211 " -0.458 9.50e-02 1.11e+02 2.05e-01 2.59e+01 pdb=" NE ARG C 211 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG C 211 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 211 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 211 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 204 " -0.063 5.00e-02 4.00e+02 9.37e-02 1.41e+01 pdb=" N PRO C 205 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO C 205 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 205 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 98 " -0.060 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO F 99 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO F 99 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 99 " -0.049 5.00e-02 4.00e+02 ... (remaining 5463 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 258 2.59 - 3.17: 26751 3.17 - 3.75: 51296 3.75 - 4.32: 70907 4.32 - 4.90: 115441 Nonbonded interactions: 264653 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.014 2.170 nonbonded pdb=" OE2 GLU C 562 " pdb=" OG SER C 662 " model vdw 2.080 3.040 nonbonded pdb=" O PRO D 149 " pdb=" OG1 THR D 152 " model vdw 2.138 3.040 nonbonded pdb=" OH TYR C 591 " pdb=" OE2 GLU C 611 " model vdw 2.165 3.040 nonbonded pdb=" O THR F 283 " pdb=" NE ARG F 287 " model vdw 2.172 3.120 ... (remaining 264648 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' and (resid 4 through 160 or resid 168 through 233)) selection = chain 'B' } ncs_group { reference = chain 'H' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 42.570 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 0.062 33405 Z= 0.291 Angle : 0.729 15.812 45679 Z= 0.446 Chirality : 0.046 0.255 5212 Planarity : 0.006 0.205 5466 Dihedral : 18.771 170.169 13184 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.14 % Allowed : 20.99 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 3744 helix: 0.64 (0.13), residues: 1561 sheet: 0.24 (0.25), residues: 416 loop : -0.19 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 372 TYR 0.034 0.002 TYR D 626 PHE 0.026 0.002 PHE D 116 TRP 0.026 0.002 TRP F 323 HIS 0.012 0.001 HIS K 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.29 (33397) covalent geometry : angle 0.72241 / 0.45 (45667) hydrogen bonds : bond 0.12977 / 8.76 ( 1500) hydrogen bonds : angle 5.74467 / 3.99 ( 4146) metal coordination : bond 0.00903 / 0.47 ( 8) metal coordination : angle 5.99144 / 3.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 765 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 354 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.5351 (p0) REVERT: C 515 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.6634 (tmm) REVERT: C 772 MET cc_start: 0.7829 (mmp) cc_final: 0.7575 (mmp) REVERT: C 805 MET cc_start: 0.8774 (ptm) cc_final: 0.8570 (ptm) REVERT: C 1339 GLU cc_start: 0.7303 (mp0) cc_final: 0.6951 (mt-10) REVERT: D 126 LEU cc_start: 0.8517 (tt) cc_final: 0.8264 (tt) REVERT: D 192 MET cc_start: 0.7830 (mtm) cc_final: 0.7594 (mtt) REVERT: D 204 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7141 (tm-30) REVERT: D 339 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7455 (mtm-85) REVERT: D 578 MET cc_start: 0.8500 (mtt) cc_final: 0.8089 (mtt) REVERT: D 738 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7878 (ptp90) REVERT: D 785 ASP cc_start: 0.7788 (t0) cc_final: 0.7399 (t0) REVERT: B 104 ASN cc_start: 0.8559 (m-40) cc_final: 0.8345 (m-40) REVERT: F 285 MET cc_start: 0.7590 (tpt) cc_final: 0.7327 (tpt) REVERT: F 372 ARG cc_start: 0.7382 (mmp80) cc_final: 0.7109 (mmp80) REVERT: F 389 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7525 (mt-10) REVERT: F 401 LYS cc_start: 0.7827 (mppt) cc_final: 0.7536 (mppt) REVERT: G 292 LYS cc_start: 0.8603 (mtmp) cc_final: 0.8284 (mtmm) REVERT: K 15 THR cc_start: 0.7259 (t) cc_final: 0.6996 (m) REVERT: H 7 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6484 (ptmm) outliers start: 37 outliers final: 23 residues processed: 779 average time/residue: 0.2470 time to fit residues: 293.8085 Evaluate side-chains 787 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 759 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 622 LYS Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 1085 MET Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 496 GLN Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 318 ARG Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 61 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 638 GLN C1013 GLN D 430 HIS D 488 ASN D 680 ASN D 861 ASN D1226 HIS A 18 GLN A 104 ASN F 317 ASN F 496 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN K 60 HIS K 95 GLN H 57 ASN H 67 GLN H 78 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.148818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121992 restraints weight = 52843.884| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.19 r_work: 0.3411 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33405 Z= 0.169 Angle : 0.622 11.527 45679 Z= 0.335 Chirality : 0.044 0.382 5212 Planarity : 0.005 0.075 5466 Dihedral : 18.284 171.139 5748 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.89 % Allowed : 17.02 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3744 helix: 0.93 (0.13), residues: 1576 sheet: 0.31 (0.25), residues: 411 loop : -0.13 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1340 TYR 0.025 0.001 TYR D 626 PHE 0.019 0.001 PHE D 116 TRP 0.013 0.001 TRP F 323 HIS 0.012 0.001 HIS K 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (33397) covalent geometry : angle 0.61699 / 0.34 (45667) hydrogen bonds : bond 0.04909 / 3.30 ( 1500) hydrogen bonds : angle 4.78829 / 3.31 ( 4146) metal coordination : bond 0.00848 / 0.44 ( 8) metal coordination : angle 4.99667 / 2.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 767 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.7499 (pp20) cc_final: 0.7167 (pp20) REVERT: C 151 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7710 (mtm-85) REVERT: C 354 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.5172 (p0) REVERT: C 476 LYS cc_start: 0.7985 (tttt) cc_final: 0.7769 (ttmm) REVERT: C 515 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7226 (ttm) REVERT: C 593 ARG cc_start: 0.8406 (ptp90) cc_final: 0.8150 (ptp90) REVERT: C 599 VAL cc_start: 0.7920 (t) cc_final: 0.7539 (m) REVERT: C 731 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7710 (ttp-110) REVERT: C 772 MET cc_start: 0.7887 (mmp) cc_final: 0.7626 (mmp) REVERT: C 849 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7705 (mt-10) REVERT: C 899 GLU cc_start: 0.7825 (tp30) cc_final: 0.7490 (tp30) REVERT: C 903 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7932 (mtp85) REVERT: D 126 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8304 (tt) REVERT: D 134 ASP cc_start: 0.7259 (m-30) cc_final: 0.6911 (m-30) REVERT: D 159 MET cc_start: 0.7735 (mmt) cc_final: 0.7414 (mmt) REVERT: D 204 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7055 (tm-30) REVERT: D 644 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7667 (mtp) REVERT: D 662 ARG cc_start: 0.7517 (mtm180) cc_final: 0.7151 (mtm-85) REVERT: D 705 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: D 785 ASP cc_start: 0.7851 (t0) cc_final: 0.7417 (t0) REVERT: D 1243 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8423 (mp10) REVERT: D 1281 TYR cc_start: 0.8480 (t80) cc_final: 0.8100 (t80) REVERT: D 1348 GLU cc_start: 0.7951 (pm20) cc_final: 0.7726 (mp0) REVERT: B 104 ASN cc_start: 0.8656 (m-40) cc_final: 0.8440 (m-40) REVERT: B 149 ARG cc_start: 0.8646 (ttm-80) cc_final: 0.8440 (ttm-80) REVERT: B 220 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7878 (mtm-85) REVERT: F 343 GLU cc_start: 0.6019 (mp0) cc_final: 0.5451 (mp0) REVERT: F 347 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.5879 (tpp-160) REVERT: F 356 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.6039 (tp30) REVERT: F 385 LYS cc_start: 0.8297 (ttpt) cc_final: 0.7627 (ptmm) REVERT: F 389 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7728 (mt-10) REVERT: F 401 LYS cc_start: 0.7840 (mppt) cc_final: 0.7491 (mppt) REVERT: F 464 MET cc_start: 0.8542 (tpp) cc_final: 0.8217 (tpp) REVERT: F 478 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8152 (mtp) REVERT: F 485 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7438 (mm-30) REVERT: K 15 THR cc_start: 0.7263 (t) cc_final: 0.7000 (m) outliers start: 94 outliers final: 58 residues processed: 798 average time/residue: 0.2395 time to fit residues: 291.1088 Evaluate side-chains 831 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 761 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain C residue 1192 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 881 LYS Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 1243 GLN Chi-restraints excluded: chain D residue 1279 VAL Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 478 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 306 ASP Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 99 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 191 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 364 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 287 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 335 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 HIS D1234 ASN A 104 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.148548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121770 restraints weight = 52643.558| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.19 r_work: 0.3406 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33405 Z= 0.164 Angle : 0.580 11.429 45679 Z= 0.314 Chirality : 0.043 0.369 5212 Planarity : 0.005 0.063 5466 Dihedral : 18.196 173.429 5704 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.70 % Rotamer: Outliers : 3.35 % Allowed : 16.96 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3744 helix: 1.06 (0.13), residues: 1580 sheet: 0.43 (0.25), residues: 411 loop : -0.11 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1340 TYR 0.022 0.001 TYR D 144 PHE 0.013 0.001 PHE D 116 TRP 0.024 0.001 TRP F 323 HIS 0.008 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (33397) covalent geometry : angle 0.57567 / 0.31 (45667) hydrogen bonds : bond 0.04593 / 3.08 ( 1500) hydrogen bonds : angle 4.60397 / 3.18 ( 4146) metal coordination : bond 0.00991 / 0.52 ( 8) metal coordination : angle 4.55172 / 2.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 787 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 GLU cc_start: 0.7757 (pm20) cc_final: 0.7529 (pm20) REVERT: C 119 GLU cc_start: 0.7551 (pp20) cc_final: 0.7145 (pp20) REVERT: C 354 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.5251 (t0) REVERT: C 476 LYS cc_start: 0.7964 (tttt) cc_final: 0.7763 (ttmm) REVERT: C 515 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7375 (ttp) REVERT: C 593 ARG cc_start: 0.8428 (ptp90) cc_final: 0.8061 (ptp90) REVERT: C 599 VAL cc_start: 0.7979 (t) cc_final: 0.7659 (m) REVERT: C 731 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7713 (ttp-110) REVERT: C 739 GLU cc_start: 0.7671 (mp0) cc_final: 0.7318 (mp0) REVERT: C 758 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8010 (ttt-90) REVERT: C 772 MET cc_start: 0.7991 (mmp) cc_final: 0.7710 (mmp) REVERT: C 849 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7746 (mt-10) REVERT: C 899 GLU cc_start: 0.7949 (tp30) cc_final: 0.7689 (tp30) REVERT: D 60 ARG cc_start: 0.8119 (ttt180) cc_final: 0.7839 (ttt180) REVERT: D 126 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8334 (tt) REVERT: D 134 ASP cc_start: 0.7279 (m-30) cc_final: 0.6934 (m-30) REVERT: D 140 TYR cc_start: 0.8480 (m-10) cc_final: 0.8173 (m-10) REVERT: D 159 MET cc_start: 0.7751 (mmt) cc_final: 0.7486 (mmt) REVERT: D 201 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6288 (mpp) REVERT: D 235 GLU cc_start: 0.6397 (mm-30) cc_final: 0.6191 (mp0) REVERT: D 301 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7488 (tp30) REVERT: D 579 LEU cc_start: 0.8690 (tp) cc_final: 0.8397 (tt) REVERT: D 644 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7720 (mtp) REVERT: D 662 ARG cc_start: 0.7554 (mtm180) cc_final: 0.7181 (mtm-85) REVERT: D 705 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8076 (mp10) REVERT: D 738 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7968 (ptp90) REVERT: D 785 ASP cc_start: 0.7884 (t0) cc_final: 0.7427 (t0) REVERT: D 832 LYS cc_start: 0.8238 (mmpt) cc_final: 0.7917 (mmpt) REVERT: D 907 HIS cc_start: 0.7472 (p90) cc_final: 0.7214 (p-80) REVERT: D 1015 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6825 (mt-10) REVERT: D 1146 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7662 (mt-10) REVERT: D 1155 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8726 (mm) REVERT: D 1243 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8493 (mp10) REVERT: D 1281 TYR cc_start: 0.8511 (t80) cc_final: 0.8101 (t80) REVERT: D 1348 GLU cc_start: 0.7967 (pm20) cc_final: 0.7746 (mp0) REVERT: B 104 ASN cc_start: 0.8643 (m-40) cc_final: 0.8429 (m-40) REVERT: B 105 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8354 (ttmt) REVERT: B 220 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7929 (mtm-85) REVERT: F 343 GLU cc_start: 0.6034 (mp0) cc_final: 0.5578 (mp0) REVERT: F 347 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.5871 (tpp-160) REVERT: F 356 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6181 (tp30) REVERT: F 385 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7638 (ptmm) REVERT: F 389 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7747 (mt-10) REVERT: F 401 LYS cc_start: 0.7859 (mppt) cc_final: 0.7487 (mppt) REVERT: F 478 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8087 (mtp) REVERT: F 485 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7416 (mm-30) REVERT: F 563 GLU cc_start: 0.6798 (tt0) cc_final: 0.6450 (tt0) REVERT: G 292 LYS cc_start: 0.8784 (mtmm) cc_final: 0.8479 (mtmm) REVERT: K 15 THR cc_start: 0.7273 (t) cc_final: 0.7031 (m) outliers start: 109 outliers final: 66 residues processed: 828 average time/residue: 0.2330 time to fit residues: 295.0243 Evaluate side-chains 853 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 771 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain C residue 1134 GLU Chi-restraints excluded: chain C residue 1192 SER Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 871 VAL Chi-restraints excluded: chain D residue 881 LYS Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1243 GLN Chi-restraints excluded: chain D residue 1279 VAL Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1350 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 385 LYS Chi-restraints excluded: chain F residue 422 LYS Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain F residue 478 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 298 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 283 optimal weight: 0.7980 chunk 339 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN D 777 HIS A 104 ASN F 291 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.147660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120902 restraints weight = 52483.395| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.18 r_work: 0.3397 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33405 Z= 0.186 Angle : 0.588 11.622 45679 Z= 0.315 Chirality : 0.044 0.374 5212 Planarity : 0.005 0.057 5466 Dihedral : 18.173 172.996 5701 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.19 % Favored : 97.78 % Rotamer: Outliers : 3.54 % Allowed : 17.54 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.13), residues: 3744 helix: 1.15 (0.13), residues: 1575 sheet: 0.46 (0.25), residues: 412 loop : -0.16 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1340 TYR 0.021 0.002 TYR C 73 PHE 0.013 0.001 PHE D 116 TRP 0.014 0.001 TRP F 323 HIS 0.010 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (33397) covalent geometry : angle 0.58315 / 0.32 (45667) hydrogen bonds : bond 0.04593 / 3.09 ( 1500) hydrogen bonds : angle 4.53389 / 3.13 ( 4146) metal coordination : bond 0.01258 / 0.67 ( 8) metal coordination : angle 4.49795 / 2.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 785 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.7551 (pp20) cc_final: 0.7116 (pp20) REVERT: C 337 PHE cc_start: 0.8369 (t80) cc_final: 0.8032 (t80) REVERT: C 339 ASN cc_start: 0.8382 (m-40) cc_final: 0.8147 (m-40) REVERT: C 354 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.5401 (p0) REVERT: C 382 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7306 (tm-30) REVERT: C 461 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7538 (tp30) REVERT: C 593 ARG cc_start: 0.8437 (ptp90) cc_final: 0.7985 (ptp90) REVERT: C 599 VAL cc_start: 0.8061 (t) cc_final: 0.7796 (m) REVERT: C 681 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8281 (mtp) REVERT: C 731 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7779 (ttp-110) REVERT: C 739 GLU cc_start: 0.7744 (mp0) cc_final: 0.7365 (mp0) REVERT: C 758 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7998 (ttt-90) REVERT: C 772 MET cc_start: 0.7977 (mmp) cc_final: 0.6705 (mmp) REVERT: C 775 GLU cc_start: 0.8037 (pm20) cc_final: 0.7346 (pm20) REVERT: C 849 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7751 (mt-10) REVERT: C 899 GLU cc_start: 0.7978 (tp30) cc_final: 0.7600 (tp30) REVERT: C 903 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8146 (mtp85) REVERT: D 53 ARG cc_start: 0.8523 (ttt180) cc_final: 0.8283 (ttt180) REVERT: D 60 ARG cc_start: 0.8172 (ttt180) cc_final: 0.7892 (ttt90) REVERT: D 126 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8365 (tt) REVERT: D 134 ASP cc_start: 0.7300 (m-30) cc_final: 0.6970 (m-30) REVERT: D 197 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6674 (tm-30) REVERT: D 201 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.6162 (mpp) REVERT: D 281 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7781 (mtp-110) REVERT: D 301 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7464 (tp30) REVERT: D 387 THR cc_start: 0.8674 (t) cc_final: 0.8413 (p) REVERT: D 404 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7298 (mm-30) REVERT: D 579 LEU cc_start: 0.8741 (tp) cc_final: 0.8442 (tt) REVERT: D 644 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7754 (mtp) REVERT: D 662 ARG cc_start: 0.7579 (mtm180) cc_final: 0.7235 (mtm-85) REVERT: D 705 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: D 738 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7976 (ptp90) REVERT: D 785 ASP cc_start: 0.7874 (t0) cc_final: 0.7409 (t0) REVERT: D 832 LYS cc_start: 0.8257 (mmpt) cc_final: 0.7947 (mmpt) REVERT: D 905 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8429 (mmt180) REVERT: D 907 HIS cc_start: 0.7486 (p90) cc_final: 0.7247 (p-80) REVERT: D 1146 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7738 (mt-10) REVERT: D 1155 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8722 (mm) REVERT: D 1281 TYR cc_start: 0.8598 (t80) cc_final: 0.8197 (t80) REVERT: D 1348 GLU cc_start: 0.7985 (pm20) cc_final: 0.7760 (mp0) REVERT: A 182 ASP cc_start: 0.8108 (t0) cc_final: 0.7878 (t0) REVERT: A 215 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7184 (mm-30) REVERT: B 104 ASN cc_start: 0.8659 (m-40) cc_final: 0.8443 (m-40) REVERT: B 220 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7989 (mtm-85) REVERT: F 261 LEU cc_start: 0.7472 (mm) cc_final: 0.7244 (mt) REVERT: F 343 GLU cc_start: 0.5966 (mp0) cc_final: 0.5601 (mp0) REVERT: F 347 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.5875 (tpp-160) REVERT: F 356 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6201 (tp30) REVERT: F 372 ARG cc_start: 0.7792 (mmp80) cc_final: 0.7210 (mmt180) REVERT: F 382 ARG cc_start: 0.7373 (mmp80) cc_final: 0.7103 (mmp80) REVERT: F 385 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7624 (ptmm) REVERT: F 389 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7755 (mt-10) REVERT: F 401 LYS cc_start: 0.7863 (mppt) cc_final: 0.7484 (mppt) REVERT: F 478 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8121 (mtp) REVERT: F 485 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7424 (mm-30) REVERT: G 292 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8431 (mtmm) REVERT: K 15 THR cc_start: 0.7287 (OUTLIER) cc_final: 0.7052 (m) outliers start: 115 outliers final: 78 residues processed: 824 average time/residue: 0.2262 time to fit residues: 285.0838 Evaluate side-chains 868 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 772 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain C residue 1134 GLU Chi-restraints excluded: chain C residue 1192 SER Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 871 VAL Chi-restraints excluded: chain D residue 881 LYS Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1279 VAL Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1350 VAL Chi-restraints excluded: chain D residue 1360 THR Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 385 LYS Chi-restraints excluded: chain F residue 422 LYS Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 478 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 318 ARG Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 15 optimal weight: 3.9990 chunk 268 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 383 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 129 optimal weight: 0.0870 chunk 204 optimal weight: 1.9990 chunk 384 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN D 424 ASN A 104 ASN F 579 HIS ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.147627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120971 restraints weight = 52459.122| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.18 r_work: 0.3396 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33405 Z= 0.173 Angle : 0.581 12.820 45679 Z= 0.310 Chirality : 0.043 0.373 5212 Planarity : 0.004 0.054 5466 Dihedral : 18.141 172.844 5701 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.76 % Rotamer: Outliers : 4.06 % Allowed : 17.57 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3744 helix: 1.28 (0.13), residues: 1567 sheet: 0.47 (0.25), residues: 412 loop : -0.12 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1340 TYR 0.027 0.001 TYR D 144 PHE 0.014 0.001 PHE D 116 TRP 0.015 0.001 TRP F 323 HIS 0.009 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (33397) covalent geometry : angle 0.57493 / 0.31 (45667) hydrogen bonds : bond 0.04435 / 2.99 ( 1500) hydrogen bonds : angle 4.47165 / 3.09 ( 4146) metal coordination : bond 0.01080 / 0.57 ( 8) metal coordination : angle 5.16191 / 3.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 784 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7578 (mm-30) REVERT: C 70 TYR cc_start: 0.8305 (t80) cc_final: 0.8015 (t80) REVERT: C 119 GLU cc_start: 0.7562 (pp20) cc_final: 0.7083 (pp20) REVERT: C 337 PHE cc_start: 0.8345 (t80) cc_final: 0.8046 (t80) REVERT: C 339 ASN cc_start: 0.8386 (m-40) cc_final: 0.8100 (m-40) REVERT: C 354 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.5224 (p0) REVERT: C 382 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7218 (tm-30) REVERT: C 461 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7525 (tp30) REVERT: C 515 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7293 (ttt) REVERT: C 593 ARG cc_start: 0.8450 (ptp90) cc_final: 0.7961 (ptp90) REVERT: C 599 VAL cc_start: 0.8110 (t) cc_final: 0.7855 (m) REVERT: C 604 ASP cc_start: 0.8291 (m-30) cc_final: 0.8055 (m-30) REVERT: C 681 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8264 (mtp) REVERT: C 731 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8400 (ttp80) REVERT: C 739 GLU cc_start: 0.7745 (mp0) cc_final: 0.7349 (mp0) REVERT: C 758 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8008 (ttt-90) REVERT: C 772 MET cc_start: 0.8045 (mmp) cc_final: 0.6761 (mmp) REVERT: C 775 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7402 (pm20) REVERT: C 849 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7739 (mt-10) REVERT: C 899 GLU cc_start: 0.7986 (tp30) cc_final: 0.7515 (tp30) REVERT: C 903 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8126 (mtp85) REVERT: D 53 ARG cc_start: 0.8532 (ttt180) cc_final: 0.8225 (ttt180) REVERT: D 60 ARG cc_start: 0.8184 (ttt180) cc_final: 0.7885 (ttt90) REVERT: D 126 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8340 (tt) REVERT: D 134 ASP cc_start: 0.7357 (m-30) cc_final: 0.7032 (m-30) REVERT: D 140 TYR cc_start: 0.8447 (m-10) cc_final: 0.8176 (m-10) REVERT: D 159 MET cc_start: 0.7770 (mmt) cc_final: 0.7520 (mmt) REVERT: D 197 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6643 (tm-30) REVERT: D 201 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6147 (mpp) REVERT: D 281 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7778 (mtp-110) REVERT: D 301 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7453 (tp30) REVERT: D 387 THR cc_start: 0.8706 (t) cc_final: 0.8405 (p) REVERT: D 568 LYS cc_start: 0.8369 (ptmt) cc_final: 0.8061 (ptmt) REVERT: D 644 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7756 (mtp) REVERT: D 662 ARG cc_start: 0.7568 (mtm180) cc_final: 0.7193 (mtm-85) REVERT: D 705 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: D 738 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7983 (ptp90) REVERT: D 785 ASP cc_start: 0.7871 (t0) cc_final: 0.7398 (t0) REVERT: D 832 LYS cc_start: 0.8264 (mmpt) cc_final: 0.7932 (mmpt) REVERT: D 892 PHE cc_start: 0.7632 (t80) cc_final: 0.7244 (t80) REVERT: D 905 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8433 (mmt180) REVERT: D 907 HIS cc_start: 0.7479 (p90) cc_final: 0.7252 (p-80) REVERT: D 1146 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7752 (mt-10) REVERT: D 1281 TYR cc_start: 0.8614 (t80) cc_final: 0.8225 (t80) REVERT: D 1348 GLU cc_start: 0.7982 (pm20) cc_final: 0.7758 (mp0) REVERT: A 182 ASP cc_start: 0.8095 (t0) cc_final: 0.7871 (t0) REVERT: A 215 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7191 (mm-30) REVERT: B 104 ASN cc_start: 0.8659 (m-40) cc_final: 0.8441 (m-40) REVERT: B 105 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8324 (ttmt) REVERT: B 220 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8022 (mtm-85) REVERT: F 261 LEU cc_start: 0.7476 (mm) cc_final: 0.7251 (mt) REVERT: F 292 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: F 343 GLU cc_start: 0.5936 (mp0) cc_final: 0.5374 (mm-30) REVERT: F 347 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.5915 (tpp-160) REVERT: F 356 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6192 (tp30) REVERT: F 372 ARG cc_start: 0.7813 (mmp80) cc_final: 0.7374 (mmt180) REVERT: F 373 MET cc_start: 0.7568 (mmm) cc_final: 0.7261 (mmm) REVERT: F 385 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8071 (ptmm) REVERT: F 401 LYS cc_start: 0.7890 (mppt) cc_final: 0.7506 (mppt) REVERT: F 464 MET cc_start: 0.8529 (tpp) cc_final: 0.8232 (tpp) REVERT: F 478 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8164 (mtp) REVERT: F 485 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7437 (mm-30) REVERT: K 15 THR cc_start: 0.7272 (OUTLIER) cc_final: 0.7058 (m) outliers start: 132 outliers final: 90 residues processed: 831 average time/residue: 0.2421 time to fit residues: 307.3416 Evaluate side-chains 881 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 770 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain C residue 1134 GLU Chi-restraints excluded: chain C residue 1192 SER Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 871 VAL Chi-restraints excluded: chain D residue 881 LYS Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 1279 VAL Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1350 VAL Chi-restraints excluded: chain D residue 1360 THR Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 385 LYS Chi-restraints excluded: chain F residue 422 LYS Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 478 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 318 ARG Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 266 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 300 optimal weight: 0.7980 chunk 386 optimal weight: 0.0770 chunk 27 optimal weight: 0.6980 chunk 328 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1234 ASN A 104 ASN F 579 HIS ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.147819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121174 restraints weight = 52415.769| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.18 r_work: 0.3398 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33405 Z= 0.158 Angle : 0.573 12.264 45679 Z= 0.306 Chirality : 0.043 0.372 5212 Planarity : 0.004 0.055 5466 Dihedral : 18.118 172.802 5699 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 3.88 % Allowed : 17.94 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3744 helix: 1.35 (0.13), residues: 1561 sheet: 0.51 (0.25), residues: 405 loop : -0.13 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 34 TYR 0.026 0.001 TYR D 144 PHE 0.013 0.001 PHE D 116 TRP 0.016 0.001 TRP F 323 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (33397) covalent geometry : angle 0.56708 / 0.31 (45667) hydrogen bonds : bond 0.04306 / 2.90 ( 1500) hydrogen bonds : angle 4.44074 / 3.07 ( 4146) metal coordination : bond 0.00866 / 0.46 ( 8) metal coordination : angle 4.92239 / 2.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 783 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.7588 (pp20) cc_final: 0.7113 (pp20) REVERT: C 238 MET cc_start: 0.1889 (mmm) cc_final: 0.0455 (mmm) REVERT: C 337 PHE cc_start: 0.8319 (t80) cc_final: 0.8007 (t80) REVERT: C 339 ASN cc_start: 0.8358 (m-40) cc_final: 0.8047 (m-40) REVERT: C 354 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.5309 (t0) REVERT: C 382 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7210 (tm-30) REVERT: C 461 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7498 (tp30) REVERT: C 515 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7364 (ttt) REVERT: C 599 VAL cc_start: 0.8145 (t) cc_final: 0.7896 (m) REVERT: C 681 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8256 (mtp) REVERT: C 731 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8407 (ttp80) REVERT: C 739 GLU cc_start: 0.7773 (mp0) cc_final: 0.7451 (mp0) REVERT: C 758 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8015 (ttt-90) REVERT: C 772 MET cc_start: 0.8074 (mmp) cc_final: 0.6749 (mmp) REVERT: C 775 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: C 849 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7734 (mt-10) REVERT: C 899 GLU cc_start: 0.7962 (tp30) cc_final: 0.7457 (tp30) REVERT: C 903 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8099 (mtp85) REVERT: D 126 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8404 (tt) REVERT: D 134 ASP cc_start: 0.7394 (m-30) cc_final: 0.7074 (m-30) REVERT: D 201 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.6368 (mpp) REVERT: D 281 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7778 (mtp-110) REVERT: D 301 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7451 (tp30) REVERT: D 387 THR cc_start: 0.8703 (t) cc_final: 0.8387 (p) REVERT: D 404 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7253 (mm-30) REVERT: D 568 LYS cc_start: 0.8363 (ptmt) cc_final: 0.8070 (ptmt) REVERT: D 644 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7770 (mtp) REVERT: D 662 ARG cc_start: 0.7565 (mtm180) cc_final: 0.7182 (mtm-85) REVERT: D 705 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: D 738 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7993 (ptp90) REVERT: D 785 ASP cc_start: 0.7889 (t0) cc_final: 0.7415 (t0) REVERT: D 832 LYS cc_start: 0.8266 (mmpt) cc_final: 0.7924 (mmpt) REVERT: D 892 PHE cc_start: 0.7636 (t80) cc_final: 0.7255 (t80) REVERT: D 907 HIS cc_start: 0.7473 (p90) cc_final: 0.7229 (p-80) REVERT: D 1146 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7776 (mt-10) REVERT: D 1188 MET cc_start: 0.6878 (tpt) cc_final: 0.6657 (tpt) REVERT: D 1281 TYR cc_start: 0.8616 (t80) cc_final: 0.8228 (t80) REVERT: A 182 ASP cc_start: 0.8130 (t0) cc_final: 0.7901 (t0) REVERT: A 215 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 104 ASN cc_start: 0.8629 (m-40) cc_final: 0.8400 (m-40) REVERT: B 105 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8320 (ttmt) REVERT: B 216 GLU cc_start: 0.8189 (tp30) cc_final: 0.7910 (tp30) REVERT: B 220 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8100 (mtm-85) REVERT: F 240 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6412 (pm20) REVERT: F 261 LEU cc_start: 0.7502 (mm) cc_final: 0.7278 (mt) REVERT: F 292 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: F 347 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.5850 (tpp-160) REVERT: F 356 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6216 (tp30) REVERT: F 372 ARG cc_start: 0.7839 (mmp80) cc_final: 0.7270 (mmt180) REVERT: F 385 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8080 (ptmm) REVERT: F 401 LYS cc_start: 0.7914 (mppt) cc_final: 0.7519 (mppt) REVERT: F 470 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8257 (ttmm) REVERT: F 478 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8196 (mtp) REVERT: F 485 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7429 (mm-30) REVERT: K 15 THR cc_start: 0.7290 (OUTLIER) cc_final: 0.7067 (m) outliers start: 126 outliers final: 91 residues processed: 827 average time/residue: 0.2410 time to fit residues: 303.9063 Evaluate side-chains 891 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 779 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain C residue 1134 GLU Chi-restraints excluded: chain C residue 1192 SER Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 871 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1350 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 385 LYS Chi-restraints excluded: chain F residue 422 LYS Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 478 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 318 ARG Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 345 optimal weight: 0.5980 chunk 382 optimal weight: 3.9990 chunk 370 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 134 optimal weight: 0.2980 chunk 200 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN F 579 HIS ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.146976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120290 restraints weight = 52662.862| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.19 r_work: 0.3383 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 33405 Z= 0.200 Angle : 0.603 13.244 45679 Z= 0.319 Chirality : 0.044 0.377 5212 Planarity : 0.005 0.052 5466 Dihedral : 18.114 171.635 5699 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.43 % Favored : 97.54 % Rotamer: Outliers : 4.03 % Allowed : 17.97 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 3744 helix: 1.31 (0.13), residues: 1562 sheet: 0.47 (0.25), residues: 421 loop : -0.14 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 34 TYR 0.031 0.002 TYR D 144 PHE 0.023 0.001 PHE F 310 TRP 0.016 0.001 TRP F 323 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (33397) covalent geometry : angle 0.59758 / 0.32 (45667) hydrogen bonds : bond 0.04567 / 3.07 ( 1500) hydrogen bonds : angle 4.46343 / 3.08 ( 4146) metal coordination : bond 0.01094 / 0.58 ( 8) metal coordination : angle 5.23312 / 3.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 782 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.7560 (pp20) cc_final: 0.7075 (pp20) REVERT: C 238 MET cc_start: 0.1990 (mmm) cc_final: 0.0555 (mmm) REVERT: C 337 PHE cc_start: 0.8334 (t80) cc_final: 0.7969 (t80) REVERT: C 339 ASN cc_start: 0.8411 (m-40) cc_final: 0.8065 (m-40) REVERT: C 354 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.5294 (t0) REVERT: C 382 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7233 (tm-30) REVERT: C 461 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: C 515 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7374 (ttt) REVERT: C 593 ARG cc_start: 0.8471 (ptp90) cc_final: 0.8261 (ptp90) REVERT: C 599 VAL cc_start: 0.8187 (t) cc_final: 0.7948 (m) REVERT: C 681 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8295 (mtp) REVERT: C 731 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8406 (ttp80) REVERT: C 739 GLU cc_start: 0.7786 (mp0) cc_final: 0.7378 (mp0) REVERT: C 758 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8022 (ttt-90) REVERT: C 772 MET cc_start: 0.8068 (mmp) cc_final: 0.6908 (mmm) REVERT: C 775 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: C 849 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7695 (mt-10) REVERT: C 899 GLU cc_start: 0.7980 (tp30) cc_final: 0.7570 (tp30) REVERT: D 76 LYS cc_start: 0.8362 (ttpp) cc_final: 0.8099 (ttpp) REVERT: D 126 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8409 (tt) REVERT: D 134 ASP cc_start: 0.7410 (m-30) cc_final: 0.7108 (m-30) REVERT: D 140 TYR cc_start: 0.8440 (m-10) cc_final: 0.8175 (m-10) REVERT: D 159 MET cc_start: 0.7809 (mmt) cc_final: 0.7567 (mmt) REVERT: D 281 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7783 (mtp-110) REVERT: D 404 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7227 (mm-30) REVERT: D 568 LYS cc_start: 0.8370 (ptmt) cc_final: 0.8077 (ptmt) REVERT: D 644 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7808 (mtp) REVERT: D 662 ARG cc_start: 0.7581 (mtm180) cc_final: 0.7194 (mtm-85) REVERT: D 705 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: D 738 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7984 (ptp90) REVERT: D 785 ASP cc_start: 0.7888 (t0) cc_final: 0.7431 (t0) REVERT: D 832 LYS cc_start: 0.8248 (mmpt) cc_final: 0.7895 (mmpt) REVERT: D 892 PHE cc_start: 0.7628 (t80) cc_final: 0.7250 (t80) REVERT: D 907 HIS cc_start: 0.7492 (p90) cc_final: 0.7251 (p-80) REVERT: D 1187 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: D 1188 MET cc_start: 0.6995 (tpt) cc_final: 0.6763 (tpt) REVERT: D 1281 TYR cc_start: 0.8633 (t80) cc_final: 0.8302 (t80) REVERT: D 1302 GLU cc_start: 0.7626 (pm20) cc_final: 0.7404 (pm20) REVERT: A 215 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7245 (mm-30) REVERT: B 104 ASN cc_start: 0.8624 (m-40) cc_final: 0.8401 (m-40) REVERT: B 216 GLU cc_start: 0.8204 (tp30) cc_final: 0.7858 (tp30) REVERT: B 220 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8082 (mtm-85) REVERT: F 240 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.6259 (pm20) REVERT: F 292 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: F 347 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.5855 (tpp-160) REVERT: F 372 ARG cc_start: 0.7866 (mmp80) cc_final: 0.7320 (mmt180) REVERT: F 385 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8081 (ptmm) REVERT: F 464 MET cc_start: 0.8557 (tpp) cc_final: 0.8272 (tpp) REVERT: F 478 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8166 (mtp) REVERT: K 15 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7069 (m) REVERT: K 56 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.6248 (ttm170) REVERT: H 90 SER cc_start: 0.6237 (OUTLIER) cc_final: 0.6029 (p) outliers start: 131 outliers final: 95 residues processed: 832 average time/residue: 0.2404 time to fit residues: 305.0933 Evaluate side-chains 888 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 773 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain C residue 1134 GLU Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 871 VAL Chi-restraints excluded: chain D residue 881 LYS Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1279 VAL Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1344 ARG Chi-restraints excluded: chain D residue 1348 GLU Chi-restraints excluded: chain D residue 1350 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 385 LYS Chi-restraints excluded: chain F residue 422 LYS Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 478 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 318 ARG Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 365 optimal weight: 10.0000 chunk 318 optimal weight: 0.7980 chunk 205 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 303 optimal weight: 0.7980 chunk 360 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 65 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS H 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.147346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120730 restraints weight = 52532.228| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.19 r_work: 0.3391 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33405 Z= 0.172 Angle : 0.593 12.706 45679 Z= 0.313 Chirality : 0.043 0.375 5212 Planarity : 0.004 0.051 5466 Dihedral : 18.077 171.432 5699 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.81 % Rotamer: Outliers : 3.76 % Allowed : 18.84 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3744 helix: 1.37 (0.13), residues: 1562 sheet: 0.48 (0.25), residues: 418 loop : -0.10 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 34 TYR 0.026 0.002 TYR D 144 PHE 0.018 0.001 PHE F 310 TRP 0.012 0.001 TRP G 322 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (33397) covalent geometry : angle 0.58695 / 0.31 (45667) hydrogen bonds : bond 0.04363 / 2.94 ( 1500) hydrogen bonds : angle 4.42407 / 3.06 ( 4146) metal coordination : bond 0.00967 / 0.51 ( 8) metal coordination : angle 5.02940 / 2.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 777 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.7559 (pp20) cc_final: 0.7062 (pp20) REVERT: C 238 MET cc_start: 0.1941 (mmm) cc_final: 0.0557 (mmm) REVERT: C 337 PHE cc_start: 0.8311 (t80) cc_final: 0.8022 (t80) REVERT: C 339 ASN cc_start: 0.8405 (m-40) cc_final: 0.8030 (m-40) REVERT: C 354 ASP cc_start: 0.6875 (OUTLIER) cc_final: 0.5332 (t0) REVERT: C 382 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7369 (tm-30) REVERT: C 461 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7496 (tp30) REVERT: C 599 VAL cc_start: 0.8206 (t) cc_final: 0.7986 (m) REVERT: C 681 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8283 (mtp) REVERT: C 731 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8409 (ttp80) REVERT: C 739 GLU cc_start: 0.7797 (mp0) cc_final: 0.7384 (mp0) REVERT: C 758 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8006 (ttt-90) REVERT: C 772 MET cc_start: 0.8090 (mmp) cc_final: 0.6950 (mmm) REVERT: C 775 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: C 849 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 899 GLU cc_start: 0.7980 (tp30) cc_final: 0.7537 (tp30) REVERT: C 1318 MET cc_start: 0.8552 (tpp) cc_final: 0.8271 (tpp) REVERT: D 75 TYR cc_start: 0.8322 (m-10) cc_final: 0.8062 (m-10) REVERT: D 76 LYS cc_start: 0.8353 (ttpp) cc_final: 0.8083 (ttpp) REVERT: D 126 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8403 (tt) REVERT: D 134 ASP cc_start: 0.7384 (m-30) cc_final: 0.7064 (m-30) REVERT: D 140 TYR cc_start: 0.8435 (m-10) cc_final: 0.8138 (m-10) REVERT: D 159 MET cc_start: 0.7798 (mmt) cc_final: 0.7536 (mmt) REVERT: D 281 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7773 (mtp-110) REVERT: D 301 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7486 (tm-30) REVERT: D 404 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7257 (mm-30) REVERT: D 568 LYS cc_start: 0.8342 (ptmt) cc_final: 0.8042 (ptmt) REVERT: D 644 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7793 (mtp) REVERT: D 662 ARG cc_start: 0.7578 (mtm180) cc_final: 0.7174 (mtm-85) REVERT: D 705 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: D 738 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7986 (ptp90) REVERT: D 785 ASP cc_start: 0.7878 (t0) cc_final: 0.7420 (t0) REVERT: D 832 LYS cc_start: 0.8243 (mmpt) cc_final: 0.7893 (mmpt) REVERT: D 892 PHE cc_start: 0.7630 (t80) cc_final: 0.7246 (t80) REVERT: D 907 HIS cc_start: 0.7487 (p90) cc_final: 0.7273 (p-80) REVERT: D 1015 GLU cc_start: 0.7268 (tt0) cc_final: 0.6831 (tp30) REVERT: D 1187 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: D 1281 TYR cc_start: 0.8641 (t80) cc_final: 0.8309 (t80) REVERT: D 1329 ARG cc_start: 0.8448 (mtp85) cc_final: 0.7949 (mtp-110) REVERT: A 182 ASP cc_start: 0.8113 (t0) cc_final: 0.7883 (t0) REVERT: A 215 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7229 (mm-30) REVERT: B 58 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8061 (mt-10) REVERT: B 104 ASN cc_start: 0.8638 (m-40) cc_final: 0.8408 (m-40) REVERT: B 216 GLU cc_start: 0.8192 (tp30) cc_final: 0.7786 (tp30) REVERT: B 220 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8051 (mtm-85) REVERT: F 240 GLN cc_start: 0.6496 (OUTLIER) cc_final: 0.6277 (pm20) REVERT: F 292 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: F 347 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.5873 (tpp-160) REVERT: F 372 ARG cc_start: 0.7856 (mmp80) cc_final: 0.7414 (mmt180) REVERT: F 385 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8068 (ptmm) REVERT: F 464 MET cc_start: 0.8544 (tpp) cc_final: 0.8275 (tpp) REVERT: F 470 LYS cc_start: 0.8484 (ttmm) cc_final: 0.8234 (ttmm) REVERT: F 485 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7450 (mm-30) REVERT: F 532 GLU cc_start: 0.7837 (mp0) cc_final: 0.7583 (mp0) REVERT: K 15 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.7040 (m) REVERT: K 56 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.6151 (ttm170) outliers start: 122 outliers final: 87 residues processed: 820 average time/residue: 0.2218 time to fit residues: 278.4201 Evaluate side-chains 875 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 770 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain C residue 1134 GLU Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 871 VAL Chi-restraints excluded: chain D residue 881 LYS Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1279 VAL Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1344 ARG Chi-restraints excluded: chain D residue 1350 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 385 LYS Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 478 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 318 ARG Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 21 optimal weight: 0.4980 chunk 318 optimal weight: 1.9990 chunk 353 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 307 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 65 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS H 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.147090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120409 restraints weight = 52402.152| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.18 r_work: 0.3384 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33405 Z= 0.186 Angle : 0.615 13.152 45679 Z= 0.322 Chirality : 0.044 0.376 5212 Planarity : 0.004 0.053 5466 Dihedral : 18.014 171.104 5690 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.73 % Rotamer: Outliers : 3.63 % Allowed : 19.21 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3744 helix: 1.35 (0.13), residues: 1560 sheet: 0.48 (0.25), residues: 423 loop : -0.10 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 34 TYR 0.030 0.002 TYR D 144 PHE 0.013 0.001 PHE C1029 TRP 0.010 0.001 TRP F 323 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (33397) covalent geometry : angle 0.60904 / 0.32 (45667) hydrogen bonds : bond 0.04433 / 2.99 ( 1500) hydrogen bonds : angle 4.43600 / 3.07 ( 4146) metal coordination : bond 0.01006 / 0.53 ( 8) metal coordination : angle 5.12297 / 2.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 784 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.7571 (pp20) cc_final: 0.7056 (pp20) REVERT: C 238 MET cc_start: 0.1893 (mmm) cc_final: 0.0530 (mmm) REVERT: C 337 PHE cc_start: 0.8314 (t80) cc_final: 0.7955 (t80) REVERT: C 339 ASN cc_start: 0.8407 (m-40) cc_final: 0.8011 (m-40) REVERT: C 354 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.5185 (t0) REVERT: C 382 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 461 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: C 599 VAL cc_start: 0.8236 (t) cc_final: 0.8035 (m) REVERT: C 681 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8272 (mtp) REVERT: C 731 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8417 (ttp80) REVERT: C 739 GLU cc_start: 0.7824 (mp0) cc_final: 0.7407 (mp0) REVERT: C 758 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8019 (ttt-90) REVERT: C 772 MET cc_start: 0.8067 (mmp) cc_final: 0.6929 (mmm) REVERT: C 775 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: C 899 GLU cc_start: 0.7962 (tp30) cc_final: 0.7498 (tp30) REVERT: C 1221 GLU cc_start: 0.7284 (pm20) cc_final: 0.7052 (pm20) REVERT: C 1318 MET cc_start: 0.8559 (tpp) cc_final: 0.8273 (tpp) REVERT: D 75 TYR cc_start: 0.8328 (m-10) cc_final: 0.8073 (m-10) REVERT: D 76 LYS cc_start: 0.8349 (ttpp) cc_final: 0.8058 (ttpp) REVERT: D 126 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8405 (tt) REVERT: D 134 ASP cc_start: 0.7392 (m-30) cc_final: 0.7070 (m-30) REVERT: D 140 TYR cc_start: 0.8426 (m-10) cc_final: 0.8118 (m-10) REVERT: D 159 MET cc_start: 0.7804 (mmt) cc_final: 0.7542 (mmt) REVERT: D 281 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7786 (mtp-110) REVERT: D 404 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7269 (mm-30) REVERT: D 568 LYS cc_start: 0.8351 (ptmt) cc_final: 0.8055 (ptmt) REVERT: D 644 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7778 (mtp) REVERT: D 662 ARG cc_start: 0.7575 (mtm180) cc_final: 0.7165 (mtm-85) REVERT: D 705 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: D 738 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8000 (ptp90) REVERT: D 785 ASP cc_start: 0.7882 (t0) cc_final: 0.7424 (t0) REVERT: D 832 LYS cc_start: 0.8231 (mmpt) cc_final: 0.7880 (mmpt) REVERT: D 892 PHE cc_start: 0.7641 (t80) cc_final: 0.7253 (t80) REVERT: D 907 HIS cc_start: 0.7505 (p90) cc_final: 0.7286 (p-80) REVERT: D 1187 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6686 (pm20) REVERT: D 1281 TYR cc_start: 0.8643 (t80) cc_final: 0.8305 (t80) REVERT: D 1348 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: A 182 ASP cc_start: 0.8117 (t0) cc_final: 0.7880 (t0) REVERT: A 215 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7195 (mm-30) REVERT: B 58 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 104 ASN cc_start: 0.8647 (m-40) cc_final: 0.8413 (m-40) REVERT: B 216 GLU cc_start: 0.8211 (tp30) cc_final: 0.7801 (tp30) REVERT: B 220 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8056 (mtm-85) REVERT: F 240 GLN cc_start: 0.6491 (OUTLIER) cc_final: 0.6281 (pm20) REVERT: F 292 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: F 347 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.5838 (tpp-160) REVERT: F 356 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6268 (tp30) REVERT: F 372 ARG cc_start: 0.7901 (mmp80) cc_final: 0.7401 (mmt180) REVERT: F 385 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8085 (ptmm) REVERT: F 464 MET cc_start: 0.8530 (tpp) cc_final: 0.8248 (tpp) REVERT: F 470 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8216 (ttmm) REVERT: F 485 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7417 (mm-30) REVERT: F 532 GLU cc_start: 0.7869 (mp0) cc_final: 0.7602 (mp0) REVERT: G 292 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8415 (mtmm) REVERT: K 15 THR cc_start: 0.7297 (OUTLIER) cc_final: 0.7057 (m) REVERT: K 56 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.6148 (ttm170) outliers start: 118 outliers final: 86 residues processed: 826 average time/residue: 0.2279 time to fit residues: 287.9557 Evaluate side-chains 888 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 782 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain C residue 1134 GLU Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 871 VAL Chi-restraints excluded: chain D residue 881 LYS Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1279 VAL Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1344 ARG Chi-restraints excluded: chain D residue 1348 GLU Chi-restraints excluded: chain D residue 1350 VAL Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 385 LYS Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 478 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 318 ARG Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 276 optimal weight: 3.9990 chunk 371 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 214 optimal weight: 2.9990 chunk 321 optimal weight: 0.3980 chunk 256 optimal weight: 0.0670 chunk 68 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 65 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS H 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.147882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121231 restraints weight = 52568.648| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.15 r_work: 0.3402 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33405 Z= 0.146 Angle : 0.602 12.266 45679 Z= 0.317 Chirality : 0.043 0.371 5212 Planarity : 0.004 0.050 5466 Dihedral : 17.976 171.191 5688 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.08 % Favored : 97.89 % Rotamer: Outliers : 3.20 % Allowed : 19.73 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3744 helix: 1.44 (0.13), residues: 1560 sheet: 0.45 (0.25), residues: 418 loop : -0.04 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 604 TYR 0.035 0.001 TYR D 144 PHE 0.015 0.001 PHE K 69 TRP 0.014 0.001 TRP G 322 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (33397) covalent geometry : angle 0.59738 / 0.32 (45667) hydrogen bonds : bond 0.04162 / 2.80 ( 1500) hydrogen bonds : angle 4.38509 / 3.03 ( 4146) metal coordination : bond 0.00773 / 0.41 ( 8) metal coordination : angle 4.74466 / 2.78 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 783 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.7560 (pp20) cc_final: 0.7057 (pp20) REVERT: C 194 LEU cc_start: 0.7713 (tt) cc_final: 0.7330 (tp) REVERT: C 238 MET cc_start: 0.1859 (mmm) cc_final: 0.0510 (mmm) REVERT: C 337 PHE cc_start: 0.8286 (t80) cc_final: 0.7992 (t80) REVERT: C 339 ASN cc_start: 0.8365 (m-40) cc_final: 0.7969 (m-40) REVERT: C 354 ASP cc_start: 0.6860 (OUTLIER) cc_final: 0.5277 (t0) REVERT: C 461 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: C 472 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: C 599 VAL cc_start: 0.8240 (t) cc_final: 0.8023 (m) REVERT: C 681 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8289 (mtp) REVERT: C 731 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8403 (ttp80) REVERT: C 739 GLU cc_start: 0.7799 (mp0) cc_final: 0.7399 (mp0) REVERT: C 758 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8029 (ttt-90) REVERT: C 772 MET cc_start: 0.8063 (mmp) cc_final: 0.6927 (mmm) REVERT: C 775 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: C 899 GLU cc_start: 0.7933 (tp30) cc_final: 0.7478 (tp30) REVERT: C 1085 MET cc_start: 0.8566 (mmm) cc_final: 0.8353 (mmm) REVERT: C 1221 GLU cc_start: 0.7239 (pm20) cc_final: 0.7011 (pm20) REVERT: C 1318 MET cc_start: 0.8520 (tpp) cc_final: 0.8244 (tpp) REVERT: D 75 TYR cc_start: 0.8295 (m-10) cc_final: 0.8065 (m-10) REVERT: D 76 LYS cc_start: 0.8326 (ttpp) cc_final: 0.8039 (ttpp) REVERT: D 126 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8416 (tt) REVERT: D 134 ASP cc_start: 0.7389 (m-30) cc_final: 0.7065 (m-30) REVERT: D 140 TYR cc_start: 0.8430 (m-10) cc_final: 0.8114 (m-10) REVERT: D 159 MET cc_start: 0.7787 (mmt) cc_final: 0.7535 (mmt) REVERT: D 281 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7770 (mtp-110) REVERT: D 387 THR cc_start: 0.8649 (t) cc_final: 0.8424 (p) REVERT: D 404 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7281 (mm-30) REVERT: D 534 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: D 568 LYS cc_start: 0.8337 (ptmt) cc_final: 0.8061 (ptmt) REVERT: D 644 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7773 (mtp) REVERT: D 662 ARG cc_start: 0.7569 (mtm180) cc_final: 0.7154 (mtm-85) REVERT: D 705 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: D 738 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8001 (ptp90) REVERT: D 785 ASP cc_start: 0.7887 (t0) cc_final: 0.7436 (t0) REVERT: D 832 LYS cc_start: 0.8247 (mmpt) cc_final: 0.7897 (mmpt) REVERT: D 892 PHE cc_start: 0.7626 (t80) cc_final: 0.7242 (t80) REVERT: D 907 HIS cc_start: 0.7474 (p90) cc_final: 0.7249 (p-80) REVERT: D 1187 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: D 1281 TYR cc_start: 0.8642 (t80) cc_final: 0.8319 (t80) REVERT: D 1302 GLU cc_start: 0.7785 (pm20) cc_final: 0.7562 (pm20) REVERT: D 1329 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7988 (mtp-110) REVERT: A 182 ASP cc_start: 0.8133 (t0) cc_final: 0.7894 (t0) REVERT: A 215 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7210 (mm-30) REVERT: B 58 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8130 (mt-10) REVERT: B 104 ASN cc_start: 0.8610 (m-40) cc_final: 0.8380 (m-40) REVERT: B 216 GLU cc_start: 0.8209 (tp30) cc_final: 0.7795 (tp30) REVERT: B 220 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8078 (mtm-85) REVERT: F 240 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.6269 (pm20) REVERT: F 292 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: F 347 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.5782 (tpp-160) REVERT: F 356 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6284 (tp30) REVERT: F 372 ARG cc_start: 0.7851 (mmp80) cc_final: 0.7318 (mmt180) REVERT: F 385 LYS cc_start: 0.8271 (ttpt) cc_final: 0.8038 (ptmm) REVERT: F 464 MET cc_start: 0.8524 (tpp) cc_final: 0.8253 (tpp) REVERT: F 470 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8207 (ttmm) REVERT: F 485 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7400 (mm-30) REVERT: F 532 GLU cc_start: 0.7851 (mp0) cc_final: 0.7562 (mp0) REVERT: G 292 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8373 (mtmm) REVERT: K 15 THR cc_start: 0.7266 (OUTLIER) cc_final: 0.7021 (m) REVERT: K 56 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.6133 (ttm170) outliers start: 104 outliers final: 78 residues processed: 822 average time/residue: 0.2326 time to fit residues: 292.1990 Evaluate side-chains 874 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 776 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain C residue 1134 GLU Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 881 LYS Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1279 VAL Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1344 ARG Chi-restraints excluded: chain D residue 1350 VAL Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 478 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 318 ARG Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 91 optimal weight: 0.3980 chunk 223 optimal weight: 20.0000 chunk 254 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 341 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 329 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 65 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS H 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.147650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121132 restraints weight = 52449.825| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.14 r_work: 0.3399 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33405 Z= 0.158 Angle : 0.607 12.258 45679 Z= 0.319 Chirality : 0.043 0.371 5212 Planarity : 0.004 0.050 5466 Dihedral : 17.954 171.621 5687 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 3.29 % Allowed : 19.85 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3744 helix: 1.45 (0.13), residues: 1558 sheet: 0.48 (0.25), residues: 418 loop : -0.04 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 65 TYR 0.035 0.001 TYR D 144 PHE 0.014 0.001 PHE C1029 TRP 0.011 0.001 TRP F 323 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (33397) covalent geometry : angle 0.60180 / 0.32 (45667) hydrogen bonds : bond 0.04185 / 2.81 ( 1500) hydrogen bonds : angle 4.37893 / 3.03 ( 4146) metal coordination : bond 0.00848 / 0.45 ( 8) metal coordination : angle 4.76795 / 2.78 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11847.87 seconds wall clock time: 202 minutes 16.71 seconds (12136.71 seconds total)