Starting phenix.real_space_refine on Sat Feb 7 12:42:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdq_51275/02_2026/9gdq_51275.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdq_51275/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gdq_51275/02_2026/9gdq_51275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdq_51275/02_2026/9gdq_51275.map" model { file = "/net/cci-nas-00/data/ceres_data/9gdq_51275/02_2026/9gdq_51275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdq_51275/02_2026/9gdq_51275.cif" } 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-2.0-5952/lib/python3.9/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: 6.18, per 1000 atoms: 0.19 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 1.1 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: 3.95 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: 7.17 Time building geometry restraints manager: 3.86 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=" N VAL C 212 " pdb=" CA VAL C 212 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.38e-02 5.25e+03 6.48e+00 bond pdb=" C GLU C 386 " pdb=" O GLU C 386 " ideal model delta sigma weight residual 1.236 1.267 -0.031 1.26e-02 6.30e+03 5.96e+00 bond pdb=" C ALA C 381 " pdb=" O ALA C 381 " ideal model delta sigma weight residual 1.236 1.262 -0.026 1.15e-02 7.56e+03 5.11e+00 bond pdb=" CA SER C 383 " pdb=" CB SER C 383 " ideal model delta sigma weight residual 1.529 1.492 0.037 1.64e-02 3.72e+03 5.04e+00 bond pdb=" N LEU C 213 " pdb=" CA LEU C 213 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.14e-02 7.69e+03 4.45e+00 ... (remaining 33392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 45092 2.66 - 5.32: 500 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=" CA MET D1188 " pdb=" CB MET D1188 " pdb=" CG MET D1188 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CB MET F 373 " pdb=" CG MET F 373 " pdb=" SD MET F 373 " ideal model delta sigma weight residual 112.70 124.24 -11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" N GLN F 240 " pdb=" CA GLN F 240 " pdb=" C GLN F 240 " ideal model delta sigma weight residual 113.01 108.41 4.60 1.20e+00 6.94e-01 1.47e+01 angle pdb=" CB MET C 403 " pdb=" CG MET C 403 " pdb=" SD MET C 403 " ideal model delta sigma weight residual 112.70 123.82 -11.12 3.00e+00 1.11e-01 1.37e+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: 4121 0.051 - 0.102: 908 0.102 - 0.153: 169 0.153 - 0.204: 12 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: 7.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.050 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.004 0.062 33405 Z= 0.182 Angle : 0.701 15.812 45679 Z= 0.370 Chirality : 0.044 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 covalent geometry : bond 0.00417 (33397) covalent geometry : angle 0.69398 (45667) hydrogen bonds : bond 0.12977 ( 1500) hydrogen bonds : angle 5.74467 ( 4146) metal coordination : bond 0.00903 ( 8) metal coordination : angle 5.99144 ( 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 : 1.337 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: 0.2414 time to fit residues: 285.7899 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 : 1.162 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 638 GLN C1010 GLN C1013 GLN D 430 HIS D 680 ASN D 861 ASN D1226 HIS D1243 GLN 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.148606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121850 restraints weight = 52783.845| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.19 r_work: 0.3408 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33405 Z= 0.171 Angle : 0.601 12.193 45679 Z= 0.319 Chirality : 0.042 0.173 5212 Planarity : 0.005 0.073 5466 Dihedral : 18.150 174.536 5748 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % Rotamer: Outliers : 3.11 % Allowed : 16.59 % Favored : 80.30 % 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: 0.53 (0.14), residues: 3744 helix: 0.97 (0.13), residues: 1578 sheet: 0.30 (0.25), residues: 427 loop : -0.10 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1340 TYR 0.027 0.001 TYR D 626 PHE 0.016 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 covalent geometry : bond 0.00394 (33397) covalent geometry : angle 0.59546 (45667) hydrogen bonds : bond 0.04705 ( 1500) hydrogen bonds : angle 4.69584 ( 4146) metal coordination : bond 0.00842 ( 8) metal coordination : angle 5.25532 ( 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 877 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 776 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.7502 (pp20) cc_final: 0.7182 (pp20) REVERT: C 151 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7722 (mtm-85) REVERT: C 354 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.5097 (p0) REVERT: C 476 LYS cc_start: 0.7965 (tttt) cc_final: 0.7764 (ttmm) REVERT: C 515 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7328 (ttt) REVERT: C 593 ARG cc_start: 0.8403 (ptp90) cc_final: 0.8092 (ptp90) REVERT: C 599 VAL cc_start: 0.7961 (t) cc_final: 0.7633 (m) REVERT: C 731 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8372 (ttp80) REVERT: C 758 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8000 (ttt-90) REVERT: C 772 MET cc_start: 0.7936 (mmp) cc_final: 0.7667 (mmp) REVERT: C 849 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7725 (mt-10) REVERT: C 899 GLU cc_start: 0.7910 (tp30) cc_final: 0.7654 (tp30) REVERT: D 60 ARG cc_start: 0.8060 (ttt180) cc_final: 0.7774 (ttt180) REVERT: D 76 LYS cc_start: 0.8288 (ttpp) cc_final: 0.8065 (ttpp) REVERT: D 126 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8332 (tt) REVERT: D 134 ASP cc_start: 0.7274 (m-30) cc_final: 0.6931 (m-30) REVERT: D 140 TYR cc_start: 0.8478 (m-10) cc_final: 0.8278 (m-10) REVERT: D 159 MET cc_start: 0.7762 (mmt) cc_final: 0.7506 (mmt) REVERT: D 201 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6283 (mpp) REVERT: D 204 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7040 (tm-30) REVERT: D 579 LEU cc_start: 0.8680 (tp) cc_final: 0.8376 (tt) REVERT: D 644 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7674 (mtp) REVERT: D 662 ARG cc_start: 0.7532 (mtm180) cc_final: 0.7149 (mtm-85) REVERT: D 705 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8055 (mp10) REVERT: D 785 ASP cc_start: 0.7873 (t0) cc_final: 0.7431 (t0) REVERT: D 1015 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6815 (mt-10) REVERT: D 1281 TYR cc_start: 0.8506 (t80) cc_final: 0.8164 (t80) REVERT: D 1348 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: B 104 ASN cc_start: 0.8653 (m-40) cc_final: 0.8429 (m-40) REVERT: B 149 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8422 (ttm-80) REVERT: B 220 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7859 (mtm-85) REVERT: F 343 GLU cc_start: 0.5951 (mp0) cc_final: 0.5442 (mp0) REVERT: F 356 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6193 (tp30) REVERT: F 373 MET cc_start: 0.7366 (mmm) cc_final: 0.7053 (mmm) REVERT: F 385 LYS cc_start: 0.8303 (ttpt) cc_final: 0.7633 (ptmm) REVERT: F 389 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7727 (mt-10) REVERT: F 401 LYS cc_start: 0.7860 (mppt) cc_final: 0.7517 (mppt) REVERT: F 478 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8130 (mtp) REVERT: F 485 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7433 (mm-30) REVERT: K 15 THR cc_start: 0.7264 (t) cc_final: 0.7013 (m) outliers start: 101 outliers final: 59 residues processed: 809 average time/residue: 0.2344 time to fit residues: 287.6778 Evaluate side-chains 836 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 765 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 731 ARG Chi-restraints excluded: chain C residue 836 LEU 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 1134 GLU 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 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 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 D residue 1348 GLU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 20 SER 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 143 MET Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 SER 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 356 GLU Chi-restraints excluded: chain F residue 368 ASP 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 599 GLU Chi-restraints excluded: chain G residue 263 LEU 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 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 191 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 364 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 269 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 287 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 335 optimal weight: 5.9990 chunk 268 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 H 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.149037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122328 restraints weight = 52562.422| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.17 r_work: 0.3416 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33405 Z= 0.144 Angle : 0.556 11.613 45679 Z= 0.296 Chirality : 0.041 0.161 5212 Planarity : 0.004 0.063 5466 Dihedral : 17.977 174.784 5704 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.86 % Rotamer: Outliers : 3.17 % Allowed : 17.30 % Favored : 79.53 % 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: 0.74 (0.14), residues: 3744 helix: 1.23 (0.13), residues: 1568 sheet: 0.51 (0.25), residues: 405 loop : -0.10 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1340 TYR 0.020 0.001 TYR D 626 PHE 0.013 0.001 PHE D 116 TRP 0.015 0.001 TRP F 323 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00327 (33397) covalent geometry : angle 0.55120 (45667) hydrogen bonds : bond 0.04195 ( 1500) hydrogen bonds : angle 4.48726 ( 4146) metal coordination : bond 0.00763 ( 8) metal coordination : angle 4.41103 ( 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 891 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 788 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.7526 (pp20) cc_final: 0.7135 (pp20) REVERT: C 337 PHE cc_start: 0.8335 (t80) cc_final: 0.8083 (t80) REVERT: C 339 ASN cc_start: 0.8320 (m-40) cc_final: 0.8094 (m-40) REVERT: C 354 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.5471 (p0) REVERT: C 461 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: C 488 MET cc_start: 0.7833 (mmt) cc_final: 0.7628 (mmm) REVERT: C 515 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7366 (ttt) REVERT: C 565 GLU cc_start: 0.7055 (mp0) cc_final: 0.6826 (mp0) REVERT: C 593 ARG cc_start: 0.8417 (ptp90) cc_final: 0.8023 (ptp90) REVERT: C 599 VAL cc_start: 0.7960 (t) cc_final: 0.7682 (m) REVERT: C 731 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7729 (ttp-110) REVERT: C 739 GLU cc_start: 0.7723 (mp0) cc_final: 0.7376 (mp0) REVERT: C 758 ARG cc_start: 0.8379 (ttp80) cc_final: 0.8018 (ttt-90) REVERT: C 772 MET cc_start: 0.7967 (mmp) cc_final: 0.6643 (mmp) REVERT: C 775 GLU cc_start: 0.8021 (pm20) cc_final: 0.7324 (pm20) REVERT: C 849 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7726 (mt-10) REVERT: C 899 GLU cc_start: 0.7917 (tp30) cc_final: 0.7551 (tp30) REVERT: D 40 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8161 (mtpp) REVERT: D 53 ARG cc_start: 0.8481 (ttt180) cc_final: 0.8085 (tpt170) REVERT: D 60 ARG cc_start: 0.8089 (ttt180) cc_final: 0.7789 (ttt180) REVERT: D 126 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8380 (tt) REVERT: D 134 ASP cc_start: 0.7289 (m-30) cc_final: 0.6904 (m-30) REVERT: D 140 TYR cc_start: 0.8441 (m-10) cc_final: 0.8200 (m-10) REVERT: D 159 MET cc_start: 0.7720 (mmt) cc_final: 0.7467 (mmt) REVERT: D 201 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6296 (mpp) REVERT: D 301 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7486 (tp30) REVERT: D 579 LEU cc_start: 0.8674 (tp) cc_final: 0.8374 (tt) REVERT: D 644 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7717 (mtp) REVERT: D 662 ARG cc_start: 0.7566 (mtm180) cc_final: 0.7204 (mtm-85) REVERT: D 705 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8055 (mp10) REVERT: D 785 ASP cc_start: 0.7887 (t0) cc_final: 0.7427 (t0) REVERT: D 832 LYS cc_start: 0.8249 (mmpt) cc_final: 0.7934 (mmpt) REVERT: D 907 HIS cc_start: 0.7438 (p90) cc_final: 0.7148 (p-80) REVERT: D 1015 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6815 (mt-10) REVERT: D 1146 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7676 (mt-10) REVERT: D 1155 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8718 (mm) REVERT: D 1281 TYR cc_start: 0.8541 (t80) cc_final: 0.8175 (t80) REVERT: A 215 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6958 (tm-30) REVERT: B 104 ASN cc_start: 0.8651 (m-40) cc_final: 0.8442 (m-40) REVERT: B 105 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8368 (ttmt) REVERT: B 220 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7922 (mtm-85) REVERT: F 339 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7702 (tpt90) REVERT: F 343 GLU cc_start: 0.5914 (mp0) cc_final: 0.5712 (mp0) REVERT: F 356 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6212 (tp30) REVERT: F 382 ARG cc_start: 0.7345 (mmp80) cc_final: 0.7095 (mmp80) REVERT: F 385 LYS cc_start: 0.8267 (ttpt) cc_final: 0.7590 (ptmm) REVERT: F 389 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7745 (mt-10) REVERT: F 401 LYS cc_start: 0.7871 (mppt) cc_final: 0.7499 (mppt) REVERT: F 466 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8007 (mt-10) REVERT: F 478 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8121 (mtp) REVERT: F 485 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7413 (mm-30) REVERT: G 292 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8364 (mtmm) REVERT: K 15 THR cc_start: 0.7272 (OUTLIER) cc_final: 0.7032 (m) outliers start: 103 outliers final: 60 residues processed: 821 average time/residue: 0.2276 time to fit residues: 284.4442 Evaluate side-chains 842 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 767 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 CYS 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 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 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 40 LYS 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 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 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 713 GLN 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 1155 ILE 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 33 ARG 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 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 182 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 287 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 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 599 GLU Chi-restraints excluded: chain G residue 263 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 298 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 283 optimal weight: 0.5980 chunk 339 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 324 ASN D 488 ASN D 777 HIS A 104 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.147891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121104 restraints weight = 52483.753| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.19 r_work: 0.3398 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33405 Z= 0.178 Angle : 0.567 11.801 45679 Z= 0.300 Chirality : 0.042 0.167 5212 Planarity : 0.004 0.059 5466 Dihedral : 17.921 174.450 5701 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.76 % Rotamer: Outliers : 3.54 % Allowed : 17.33 % Favored : 79.13 % 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: 0.77 (0.14), residues: 3744 helix: 1.27 (0.13), residues: 1574 sheet: 0.54 (0.26), residues: 403 loop : -0.11 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1340 TYR 0.023 0.001 TYR D 144 PHE 0.014 0.001 PHE F 310 TRP 0.016 0.001 TRP F 323 HIS 0.009 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00416 (33397) covalent geometry : angle 0.56197 (45667) hydrogen bonds : bond 0.04329 ( 1500) hydrogen bonds : angle 4.43745 ( 4146) metal coordination : bond 0.01009 ( 8) metal coordination : angle 4.63319 ( 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 902 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 787 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 50 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7685 (mm-30) REVERT: C 98 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8170 (m) REVERT: C 119 GLU cc_start: 0.7558 (pp20) cc_final: 0.7122 (pp20) REVERT: C 337 PHE cc_start: 0.8314 (t80) cc_final: 0.8040 (t80) REVERT: C 339 ASN cc_start: 0.8361 (m-40) cc_final: 0.8068 (m-40) REVERT: C 354 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.5261 (p0) REVERT: C 382 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7333 (tm-30) REVERT: C 461 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7522 (tp30) REVERT: C 515 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7212 (ttt) REVERT: C 593 ARG cc_start: 0.8428 (ptp90) cc_final: 0.7961 (ptp90) REVERT: C 599 VAL cc_start: 0.8047 (t) cc_final: 0.7785 (m) REVERT: C 731 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8398 (ttp80) REVERT: C 739 GLU cc_start: 0.7762 (mp0) cc_final: 0.7219 (mp0) REVERT: C 758 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8016 (ttt-90) REVERT: C 772 MET cc_start: 0.8039 (mmp) cc_final: 0.6817 (mmp) REVERT: C 775 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7405 (pm20) REVERT: C 805 MET cc_start: 0.8842 (ptp) cc_final: 0.8630 (ptm) REVERT: C 849 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7724 (mt-10) REVERT: C 899 GLU cc_start: 0.7934 (tp30) cc_final: 0.7351 (tp30) REVERT: D 53 ARG cc_start: 0.8501 (ttt180) cc_final: 0.8221 (ttt180) REVERT: D 60 ARG cc_start: 0.8178 (ttt180) cc_final: 0.7893 (ttt90) REVERT: D 126 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8379 (tt) REVERT: D 134 ASP cc_start: 0.7320 (m-30) cc_final: 0.6991 (m-30) REVERT: D 140 TYR cc_start: 0.8443 (m-10) cc_final: 0.8170 (m-10) REVERT: D 159 MET cc_start: 0.7733 (mmt) cc_final: 0.7503 (mmt) REVERT: D 197 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6818 (tm-30) REVERT: D 201 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6087 (mpp) REVERT: D 204 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7108 (tm-30) REVERT: D 281 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7770 (mtp-110) REVERT: D 301 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7456 (tp30) REVERT: D 387 THR cc_start: 0.8667 (t) cc_final: 0.8414 (p) REVERT: D 579 LEU cc_start: 0.8736 (tp) cc_final: 0.8433 (tt) REVERT: D 644 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7765 (mtp) REVERT: D 662 ARG cc_start: 0.7552 (mtm180) cc_final: 0.7175 (mtm-85) REVERT: D 705 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: D 738 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7961 (ptp90) REVERT: D 785 ASP cc_start: 0.7871 (t0) cc_final: 0.7412 (t0) REVERT: D 832 LYS cc_start: 0.8266 (mmpt) cc_final: 0.7928 (mmpt) REVERT: D 892 PHE cc_start: 0.7629 (t80) cc_final: 0.7258 (t80) REVERT: D 905 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8419 (mmt180) REVERT: D 907 HIS cc_start: 0.7484 (p90) cc_final: 0.7227 (p-80) REVERT: D 1146 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7719 (mt-10) REVERT: D 1281 TYR cc_start: 0.8597 (t80) cc_final: 0.8299 (t80) REVERT: D 1302 GLU cc_start: 0.7629 (pm20) cc_final: 0.7414 (pm20) REVERT: A 215 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7005 (tm-30) REVERT: B 58 GLU cc_start: 0.8357 (tt0) cc_final: 0.8128 (mt-10) REVERT: B 104 ASN cc_start: 0.8657 (m-40) cc_final: 0.8431 (m-40) REVERT: B 149 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8379 (ttm-80) REVERT: B 220 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7959 (mtm-85) REVERT: F 261 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7288 (mt) REVERT: F 296 MET cc_start: 0.7875 (mmm) cc_final: 0.7404 (mmm) REVERT: F 356 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6175 (tp30) REVERT: F 372 ARG cc_start: 0.7791 (mmp80) cc_final: 0.7234 (mmt180) REVERT: F 382 ARG cc_start: 0.7324 (mmp80) cc_final: 0.7046 (mmp80) REVERT: F 385 LYS cc_start: 0.8299 (ttpt) cc_final: 0.8072 (ptmm) REVERT: F 401 LYS cc_start: 0.7896 (mppt) cc_final: 0.7512 (mppt) REVERT: F 464 MET cc_start: 0.8515 (tpp) cc_final: 0.8228 (tpp) REVERT: F 466 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8018 (mt-10) REVERT: F 478 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8193 (mtp) REVERT: F 485 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7437 (mm-30) REVERT: G 292 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8396 (mtmm) REVERT: K 15 THR cc_start: 0.7284 (t) cc_final: 0.7055 (m) outliers start: 115 outliers final: 79 residues processed: 822 average time/residue: 0.2283 time to fit residues: 285.8789 Evaluate side-chains 863 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 768 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 CYS 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 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 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 607 SER Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 622 LYS Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 647 ARG 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 935 THR 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 96 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 192 MET 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 421 VAL 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 656 GLU 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 1279 VAL Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain D residue 1317 SER 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 136 SER 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 128 GLU 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 127 ASP Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 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 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 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 K residue 54 ILE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 97 VAL 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: 0.7980 chunk 192 optimal weight: 0.0020 chunk 383 optimal weight: 0.0570 chunk 5 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 204 optimal weight: 0.3980 chunk 384 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 overall best weight: 0.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 ASN D 424 ASN D1234 ASN A 104 ASN ** 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 = 0.3954 r_free = 0.3954 target = 0.149188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122527 restraints weight = 52496.698| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.18 r_work: 0.3420 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33405 Z= 0.125 Angle : 0.537 12.109 45679 Z= 0.285 Chirality : 0.040 0.177 5212 Planarity : 0.004 0.055 5466 Dihedral : 17.831 175.681 5699 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 3.23 % Allowed : 18.01 % Favored : 78.76 % 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: 0.97 (0.14), residues: 3744 helix: 1.49 (0.13), residues: 1568 sheet: 0.59 (0.26), residues: 401 loop : -0.03 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 65 TYR 0.024 0.001 TYR D 144 PHE 0.010 0.001 PHE D1301 TRP 0.018 0.001 TRP F 323 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00281 (33397) covalent geometry : angle 0.53337 (45667) hydrogen bonds : bond 0.03817 ( 1500) hydrogen bonds : angle 4.30036 ( 4146) metal coordination : bond 0.00653 ( 8) metal coordination : angle 3.93529 ( 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 888 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 783 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8105 (m) REVERT: C 119 GLU cc_start: 0.7538 (pp20) cc_final: 0.7070 (pp20) REVERT: C 238 MET cc_start: 0.1742 (mmm) cc_final: 0.0420 (mmm) REVERT: C 337 PHE cc_start: 0.8259 (t80) cc_final: 0.8007 (t80) REVERT: C 339 ASN cc_start: 0.8309 (m-40) cc_final: 0.7962 (m-40) REVERT: C 354 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.5331 (t0) REVERT: C 461 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7478 (tp30) REVERT: C 515 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7093 (ttp) REVERT: C 565 GLU cc_start: 0.7267 (mp0) cc_final: 0.7031 (mp0) REVERT: C 593 ARG cc_start: 0.8414 (ptp90) cc_final: 0.8051 (ptp90) REVERT: C 599 VAL cc_start: 0.8004 (t) cc_final: 0.7725 (m) REVERT: C 681 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8240 (mtp) REVERT: C 731 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8417 (ttp80) REVERT: C 739 GLU cc_start: 0.7766 (mp0) cc_final: 0.7440 (mp0) REVERT: C 758 ARG cc_start: 0.8377 (ttp80) cc_final: 0.8052 (ttt-90) REVERT: C 772 MET cc_start: 0.8046 (mmp) cc_final: 0.6816 (mmp) REVERT: C 775 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: C 805 MET cc_start: 0.8828 (ptp) cc_final: 0.8620 (ptm) REVERT: C 849 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7697 (mt-10) REVERT: C 899 GLU cc_start: 0.7902 (tp30) cc_final: 0.7307 (tp30) REVERT: D 126 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8413 (tt) REVERT: D 134 ASP cc_start: 0.7331 (m-30) cc_final: 0.7019 (m-30) REVERT: D 140 TYR cc_start: 0.8420 (m-10) cc_final: 0.8094 (m-10) REVERT: D 159 MET cc_start: 0.7704 (mmt) cc_final: 0.7468 (tpp) REVERT: D 201 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6185 (mpp) REVERT: D 204 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7158 (tm-30) REVERT: D 281 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7784 (mtp-110) REVERT: D 301 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7499 (tp30) REVERT: D 387 THR cc_start: 0.8669 (t) cc_final: 0.8384 (p) REVERT: D 534 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7657 (tp30) REVERT: D 579 LEU cc_start: 0.8676 (tp) cc_final: 0.8390 (tt) REVERT: D 644 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7731 (mtp) REVERT: D 662 ARG cc_start: 0.7542 (mtm180) cc_final: 0.7145 (mtm-85) REVERT: D 705 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: D 785 ASP cc_start: 0.7863 (t0) cc_final: 0.7413 (t0) REVERT: D 811 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7904 (mt-10) REVERT: D 832 LYS cc_start: 0.8246 (mmpt) cc_final: 0.7918 (mmpt) REVERT: D 892 PHE cc_start: 0.7592 (t80) cc_final: 0.7183 (t80) REVERT: D 905 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8391 (mmt180) REVERT: D 907 HIS cc_start: 0.7467 (p90) cc_final: 0.7234 (p-80) REVERT: D 1146 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7732 (mt-10) REVERT: D 1188 MET cc_start: 0.6906 (tpt) cc_final: 0.6631 (tpt) REVERT: D 1281 TYR cc_start: 0.8579 (t80) cc_final: 0.8244 (t80) REVERT: D 1302 GLU cc_start: 0.7711 (pm20) cc_final: 0.7498 (pm20) REVERT: A 32 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 215 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6987 (tm-30) REVERT: B 58 GLU cc_start: 0.8364 (tt0) cc_final: 0.8153 (mt-10) REVERT: B 104 ASN cc_start: 0.8643 (m-40) cc_final: 0.8423 (m-40) REVERT: B 105 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8370 (ttmt) REVERT: B 220 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8002 (mtm-85) REVERT: F 261 LEU cc_start: 0.7465 (mm) cc_final: 0.7260 (mt) REVERT: F 285 MET cc_start: 0.7675 (tpt) cc_final: 0.7469 (tpt) REVERT: F 372 ARG cc_start: 0.7812 (mmp80) cc_final: 0.7292 (mmt180) REVERT: F 385 LYS cc_start: 0.8229 (ttpt) cc_final: 0.8025 (ptmm) REVERT: F 401 LYS cc_start: 0.7901 (mppt) cc_final: 0.7509 (mppt) REVERT: F 464 MET cc_start: 0.8514 (tpp) cc_final: 0.8233 (tpp) REVERT: F 466 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7976 (mt-10) REVERT: F 478 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8095 (mtp) REVERT: F 485 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7430 (mm-30) REVERT: F 530 PHE cc_start: 0.8601 (m-10) cc_final: 0.8362 (m-80) REVERT: G 292 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8313 (mtmm) REVERT: K 15 THR cc_start: 0.7286 (OUTLIER) cc_final: 0.7058 (m) outliers start: 105 outliers final: 66 residues processed: 818 average time/residue: 0.2231 time to fit residues: 278.1972 Evaluate side-chains 852 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 770 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 151 ARG Chi-restraints excluded: chain C residue 354 ASP 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 622 LYS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 647 ARG Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 935 THR 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 96 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 192 MET 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 421 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 853 THR 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 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 91 ARG Chi-restraints excluded: chain A residue 136 SER 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 105 LYS Chi-restraints excluded: chain B residue 128 GLU 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 127 ASP Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 355 ILE 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 502 ILE Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain H residue 43 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 266 optimal weight: 3.9990 chunk 251 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 311 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 300 optimal weight: 0.7980 chunk 386 optimal weight: 0.0270 chunk 27 optimal weight: 0.4980 chunk 328 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS A 104 ASN F 579 HIS ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN K 60 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.147077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120318 restraints weight = 52390.548| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.18 r_work: 0.3384 rms_B_bonded: 2.90 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: 0.7789 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33405 Z= 0.204 Angle : 0.591 14.048 45679 Z= 0.311 Chirality : 0.043 0.225 5212 Planarity : 0.004 0.053 5466 Dihedral : 17.813 174.114 5696 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.62 % Rotamer: Outliers : 3.54 % Allowed : 18.10 % 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: 0.83 (0.14), residues: 3744 helix: 1.37 (0.13), residues: 1568 sheet: 0.51 (0.25), residues: 411 loop : -0.11 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 248 TYR 0.028 0.002 TYR D 144 PHE 0.011 0.001 PHE D1301 TRP 0.017 0.001 TRP F 323 HIS 0.010 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00480 (33397) covalent geometry : angle 0.58419 (45667) hydrogen bonds : bond 0.04477 ( 1500) hydrogen bonds : angle 4.41001 ( 4146) metal coordination : bond 0.01100 ( 8) metal coordination : angle 5.66173 ( 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 902 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 787 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8188 (m) REVERT: C 119 GLU cc_start: 0.7564 (pp20) cc_final: 0.7087 (pp20) REVERT: C 238 MET cc_start: 0.1867 (mmm) cc_final: 0.0479 (mmm) REVERT: C 273 HIS cc_start: 0.6922 (OUTLIER) cc_final: 0.6509 (m90) REVERT: C 337 PHE cc_start: 0.8289 (t80) cc_final: 0.7944 (t80) REVERT: C 339 ASN cc_start: 0.8386 (m-40) cc_final: 0.8006 (m-40) REVERT: C 354 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.5317 (t0) REVERT: C 461 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: C 565 GLU cc_start: 0.7310 (mp0) cc_final: 0.6926 (mp0) REVERT: C 593 ARG cc_start: 0.8483 (ptp90) cc_final: 0.7911 (ptp90) REVERT: C 599 VAL cc_start: 0.8175 (t) cc_final: 0.7914 (m) REVERT: C 604 ASP cc_start: 0.8308 (m-30) cc_final: 0.8046 (m-30) REVERT: C 681 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8277 (mtp) REVERT: C 731 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8403 (ttp80) REVERT: C 739 GLU cc_start: 0.7811 (mp0) cc_final: 0.7405 (mp0) REVERT: C 758 ARG cc_start: 0.8368 (ttp80) cc_final: 0.8033 (ttt-90) REVERT: C 772 MET cc_start: 0.8093 (mmp) cc_final: 0.6994 (mmm) REVERT: C 775 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: C 805 MET cc_start: 0.8851 (ptp) cc_final: 0.8637 (ptm) REVERT: C 849 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7723 (mt-10) REVERT: C 859 GLU cc_start: 0.5640 (tm-30) cc_final: 0.5369 (tp30) REVERT: C 899 GLU cc_start: 0.7925 (tp30) cc_final: 0.7351 (tp30) REVERT: C 1318 MET cc_start: 0.8519 (tpp) cc_final: 0.8246 (tpp) REVERT: D 126 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8425 (tt) REVERT: D 134 ASP cc_start: 0.7390 (m-30) cc_final: 0.7142 (m-30) REVERT: D 140 TYR cc_start: 0.8429 (m-10) cc_final: 0.8101 (m-10) REVERT: D 204 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7064 (tm-30) REVERT: D 281 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7779 (mtp-110) REVERT: D 301 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7437 (tp30) REVERT: D 387 THR cc_start: 0.8703 (t) cc_final: 0.8393 (p) REVERT: D 644 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7787 (mtp) REVERT: D 662 ARG cc_start: 0.7605 (mtm180) cc_final: 0.7197 (mtm-85) REVERT: D 705 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: D 738 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7977 (ptp90) REVERT: D 785 ASP cc_start: 0.7872 (t0) cc_final: 0.7419 (t0) REVERT: D 811 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7924 (mt-10) REVERT: D 832 LYS cc_start: 0.8251 (mmpt) cc_final: 0.7894 (mmpt) REVERT: D 892 PHE cc_start: 0.7618 (t80) cc_final: 0.7219 (t80) REVERT: D 905 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8392 (mmt180) REVERT: D 907 HIS cc_start: 0.7484 (p90) cc_final: 0.7256 (p-80) REVERT: D 1187 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6871 (pm20) REVERT: D 1281 TYR cc_start: 0.8682 (t80) cc_final: 0.8364 (t80) REVERT: D 1302 GLU cc_start: 0.7733 (pm20) cc_final: 0.7471 (pm20) REVERT: A 215 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7052 (tm-30) REVERT: B 58 GLU cc_start: 0.8383 (tt0) cc_final: 0.7828 (mt-10) REVERT: B 104 ASN cc_start: 0.8671 (m-40) cc_final: 0.8437 (m-40) REVERT: B 216 GLU cc_start: 0.8198 (tp30) cc_final: 0.7777 (tp30) REVERT: B 220 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8056 (mtm-85) REVERT: F 285 MET cc_start: 0.7747 (tpt) cc_final: 0.7511 (tpt) REVERT: F 356 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6333 (tp30) REVERT: F 372 ARG cc_start: 0.7883 (mmp80) cc_final: 0.7521 (mmt180) REVERT: F 373 MET cc_start: 0.7594 (mmm) cc_final: 0.7263 (mmm) REVERT: F 385 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8093 (ptmm) REVERT: F 464 MET cc_start: 0.8535 (tpp) cc_final: 0.8260 (tpp) REVERT: F 466 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8024 (mt-10) REVERT: F 530 PHE cc_start: 0.8733 (m-10) cc_final: 0.8466 (m-80) REVERT: F 532 GLU cc_start: 0.7810 (mp0) cc_final: 0.7580 (mp0) REVERT: K 15 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.7077 (m) outliers start: 115 outliers final: 80 residues processed: 830 average time/residue: 0.2364 time to fit residues: 298.9052 Evaluate side-chains 868 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 771 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 151 ARG Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 273 HIS 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 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP 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 622 LYS 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 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 935 THR 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 192 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 421 VAL Chi-restraints excluded: chain D residue 553 THR 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 656 GLU 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 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 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 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 80 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 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 128 GLU 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 102 MET Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 287 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 502 ILE Chi-restraints excluded: chain F residue 560 THR 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 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: 0.5980 chunk 345 optimal weight: 0.9990 chunk 382 optimal weight: 0.9980 chunk 370 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 134 optimal weight: 0.0000 chunk 200 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN F 496 GLN F 579 HIS ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS H 78 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121410 restraints weight = 52666.250| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.18 r_work: 0.3401 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1622 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= 0.153 Angle : 0.570 12.314 45679 Z= 0.299 Chirality : 0.041 0.179 5212 Planarity : 0.004 0.052 5466 Dihedral : 17.761 174.877 5693 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 3.60 % Allowed : 18.31 % Favored : 78.09 % 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: 0.96 (0.14), residues: 3744 helix: 1.52 (0.13), residues: 1559 sheet: 0.54 (0.26), residues: 410 loop : -0.06 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1340 TYR 0.025 0.001 TYR D 144 PHE 0.010 0.001 PHE C 284 TRP 0.012 0.001 TRP F 323 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00355 (33397) covalent geometry : angle 0.56414 (45667) hydrogen bonds : bond 0.04020 ( 1500) hydrogen bonds : angle 4.33038 ( 4146) metal coordination : bond 0.00815 ( 8) metal coordination : angle 5.06374 ( 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 891 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 774 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8136 (m) REVERT: C 119 GLU cc_start: 0.7545 (pp20) cc_final: 0.7049 (pp20) REVERT: C 238 MET cc_start: 0.1724 (mmm) cc_final: 0.0449 (mmm) REVERT: C 273 HIS cc_start: 0.6947 (OUTLIER) cc_final: 0.6549 (m90) REVERT: C 337 PHE cc_start: 0.8258 (t80) cc_final: 0.7966 (t80) REVERT: C 339 ASN cc_start: 0.8329 (m-40) cc_final: 0.7909 (m-40) REVERT: C 354 ASP cc_start: 0.6820 (OUTLIER) cc_final: 0.5253 (t0) REVERT: C 461 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: C 565 GLU cc_start: 0.7304 (mp0) cc_final: 0.6938 (mp0) REVERT: C 599 VAL cc_start: 0.8178 (t) cc_final: 0.7920 (m) REVERT: C 681 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8264 (mtp) REVERT: C 731 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8394 (ttp80) REVERT: C 739 GLU cc_start: 0.7814 (mp0) cc_final: 0.7392 (mp0) REVERT: C 758 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8036 (ttt-90) REVERT: C 772 MET cc_start: 0.8085 (mmp) cc_final: 0.7045 (mmp) REVERT: C 775 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: C 805 MET cc_start: 0.8842 (ptp) cc_final: 0.8631 (ptm) REVERT: C 899 GLU cc_start: 0.7900 (tp30) cc_final: 0.7390 (tp30) REVERT: C 903 ARG cc_start: 0.8275 (mtp85) cc_final: 0.8048 (mtp85) REVERT: C 1318 MET cc_start: 0.8514 (tpp) cc_final: 0.8263 (tpp) REVERT: D 75 TYR cc_start: 0.8292 (m-10) cc_final: 0.8007 (m-10) REVERT: D 126 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8419 (tt) REVERT: D 134 ASP cc_start: 0.7346 (m-30) cc_final: 0.7085 (m-30) REVERT: D 140 TYR cc_start: 0.8438 (m-10) cc_final: 0.8091 (m-10) REVERT: D 201 MET cc_start: 0.6981 (mmp) cc_final: 0.6625 (mmm) REVERT: D 281 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7756 (mtp-110) REVERT: D 387 THR cc_start: 0.8694 (t) cc_final: 0.8383 (p) REVERT: D 568 LYS cc_start: 0.8392 (ptmt) cc_final: 0.8108 (ptmt) REVERT: D 644 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7759 (mtp) REVERT: D 662 ARG cc_start: 0.7580 (mtm180) cc_final: 0.7174 (mtm-85) REVERT: D 705 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8054 (mp10) REVERT: D 738 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7992 (ptp90) REVERT: D 785 ASP cc_start: 0.7875 (t0) cc_final: 0.7422 (t0) REVERT: D 832 LYS cc_start: 0.8236 (mmpt) cc_final: 0.7882 (mmpt) REVERT: D 892 PHE cc_start: 0.7612 (t80) cc_final: 0.7233 (t80) REVERT: D 905 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8424 (mmt180) REVERT: D 907 HIS cc_start: 0.7478 (p90) cc_final: 0.7251 (p-80) REVERT: D 1187 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: D 1281 TYR cc_start: 0.8644 (t80) cc_final: 0.8324 (t80) REVERT: D 1302 GLU cc_start: 0.7720 (pm20) cc_final: 0.7500 (pm20) REVERT: A 9 LEU cc_start: 0.8350 (mt) cc_final: 0.8093 (mp) REVERT: A 215 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7009 (tm-30) REVERT: A 219 ARG cc_start: 0.8022 (mtp-110) cc_final: 0.7798 (mtp-110) REVERT: B 104 ASN cc_start: 0.8635 (m-40) cc_final: 0.8401 (m-40) REVERT: B 149 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8408 (ttm-80) REVERT: B 216 GLU cc_start: 0.8185 (tp30) cc_final: 0.7757 (tp30) REVERT: B 220 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8046 (mtm-85) REVERT: F 285 MET cc_start: 0.7719 (tpt) cc_final: 0.7484 (tpt) REVERT: F 356 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6254 (tp30) REVERT: F 372 ARG cc_start: 0.7891 (mmp80) cc_final: 0.7366 (mmt180) REVERT: F 385 LYS cc_start: 0.8264 (ttpt) cc_final: 0.8052 (ptmm) REVERT: F 464 MET cc_start: 0.8501 (tpp) cc_final: 0.8226 (tpp) REVERT: F 466 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7999 (mt-10) REVERT: F 485 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7468 (mm-30) REVERT: F 530 PHE cc_start: 0.8706 (m-10) cc_final: 0.8442 (m-80) REVERT: F 532 GLU cc_start: 0.7852 (mp0) cc_final: 0.7587 (mp0) REVERT: K 15 THR cc_start: 0.7293 (OUTLIER) cc_final: 0.7056 (m) REVERT: K 52 GLU cc_start: 0.7311 (pm20) cc_final: 0.6999 (pm20) REVERT: H 90 SER cc_start: 0.6189 (OUTLIER) cc_final: 0.5980 (p) outliers start: 117 outliers final: 78 residues processed: 822 average time/residue: 0.2257 time to fit residues: 283.3805 Evaluate side-chains 865 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 770 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 ASN 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 151 ARG Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 273 HIS 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 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 622 LYS Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 644 LEU 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 915 ASP Chi-restraints excluded: chain C residue 935 THR 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 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 192 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 553 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 656 GLU 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 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 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 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 80 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 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 128 GLU Chi-restraints excluded: chain B residue 134 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 127 ASP Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 478 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 496 GLN Chi-restraints excluded: chain F residue 502 ILE 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 15 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 90 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 365 optimal weight: 2.9990 chunk 318 optimal weight: 0.7980 chunk 205 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 360 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 327 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** 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 H 78 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.147844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121201 restraints weight = 52499.809| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.17 r_work: 0.3396 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1697 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= 0.168 Angle : 0.585 12.715 45679 Z= 0.305 Chirality : 0.042 0.186 5212 Planarity : 0.004 0.065 5466 Dihedral : 17.746 175.031 5693 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.73 % Rotamer: Outliers : 3.23 % Allowed : 18.62 % Favored : 78.15 % 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: 0.96 (0.14), residues: 3744 helix: 1.52 (0.13), residues: 1557 sheet: 0.54 (0.26), residues: 413 loop : -0.05 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1340 TYR 0.030 0.001 TYR D 144 PHE 0.012 0.001 PHE D1301 TRP 0.010 0.001 TRP F 323 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00394 (33397) covalent geometry : angle 0.57921 (45667) hydrogen bonds : bond 0.04098 ( 1500) hydrogen bonds : angle 4.33451 ( 4146) metal coordination : bond 0.00898 ( 8) metal coordination : angle 5.10160 ( 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 885 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 780 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8145 (m) REVERT: C 119 GLU cc_start: 0.7595 (pp20) cc_final: 0.7106 (pp20) REVERT: C 238 MET cc_start: 0.1769 (mmm) cc_final: 0.0492 (mmm) REVERT: C 273 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6679 (m170) REVERT: C 337 PHE cc_start: 0.8254 (t80) cc_final: 0.7985 (t80) REVERT: C 339 ASN cc_start: 0.8343 (m-40) cc_final: 0.7902 (m-40) REVERT: C 354 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.5265 (t0) REVERT: C 461 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7488 (tp30) REVERT: C 565 GLU cc_start: 0.7333 (mp0) cc_final: 0.6979 (mp0) REVERT: C 593 ARG cc_start: 0.8440 (ptp90) cc_final: 0.7948 (ptp90) REVERT: C 599 VAL cc_start: 0.8191 (t) cc_final: 0.7958 (m) REVERT: C 681 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8273 (mtp) REVERT: C 731 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8384 (ttp80) REVERT: C 739 GLU cc_start: 0.7805 (mp0) cc_final: 0.7383 (mp0) REVERT: C 758 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8030 (ttt-90) REVERT: C 772 MET cc_start: 0.8091 (mmp) cc_final: 0.7007 (mmm) REVERT: C 775 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7478 (pm20) REVERT: C 805 MET cc_start: 0.8833 (ptp) cc_final: 0.8617 (ptm) REVERT: C 899 GLU cc_start: 0.7906 (tp30) cc_final: 0.7391 (tp30) REVERT: C 903 ARG cc_start: 0.8273 (mtp85) cc_final: 0.8054 (mtp85) REVERT: C 1318 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8264 (tpp) REVERT: D 75 TYR cc_start: 0.8289 (m-10) cc_final: 0.8002 (m-10) REVERT: D 126 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8430 (tt) REVERT: D 134 ASP cc_start: 0.7350 (m-30) cc_final: 0.7072 (m-30) REVERT: D 140 TYR cc_start: 0.8429 (m-10) cc_final: 0.8075 (m-10) REVERT: D 158 GLN cc_start: 0.7908 (tt0) cc_final: 0.7560 (tm-30) REVERT: D 281 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7745 (mtp-110) REVERT: D 301 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7473 (tp30) REVERT: D 387 THR cc_start: 0.8695 (t) cc_final: 0.8381 (p) REVERT: D 568 LYS cc_start: 0.8389 (ptmt) cc_final: 0.8103 (ptmt) REVERT: D 644 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7823 (mtp) REVERT: D 662 ARG cc_start: 0.7612 (mtm180) cc_final: 0.7207 (mtm-85) REVERT: D 705 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: D 738 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7992 (ptp90) REVERT: D 785 ASP cc_start: 0.7876 (t0) cc_final: 0.7421 (t0) REVERT: D 832 LYS cc_start: 0.8254 (mmpt) cc_final: 0.7896 (mmpt) REVERT: D 892 PHE cc_start: 0.7632 (t80) cc_final: 0.7254 (t80) REVERT: D 905 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8390 (mmt180) REVERT: D 907 HIS cc_start: 0.7491 (p90) cc_final: 0.7281 (p-80) REVERT: D 1187 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6740 (pm20) REVERT: D 1281 TYR cc_start: 0.8669 (t80) cc_final: 0.8342 (t80) REVERT: A 215 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7060 (tm-30) REVERT: B 67 GLU cc_start: 0.8189 (pm20) cc_final: 0.7902 (pm20) REVERT: B 104 ASN cc_start: 0.8629 (m-40) cc_final: 0.8397 (m-40) REVERT: B 216 GLU cc_start: 0.8178 (tp30) cc_final: 0.7716 (tp30) REVERT: B 220 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8064 (mtm-85) REVERT: F 261 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7100 (mt) REVERT: F 285 MET cc_start: 0.7672 (tpt) cc_final: 0.7423 (tpt) REVERT: F 356 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6315 (tp30) REVERT: F 372 ARG cc_start: 0.7913 (mmp80) cc_final: 0.7399 (mmt180) REVERT: F 385 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8038 (ptmm) REVERT: F 426 LYS cc_start: 0.8372 (ptpp) cc_final: 0.8048 (mtmm) REVERT: F 464 MET cc_start: 0.8517 (tpp) cc_final: 0.8246 (tpp) REVERT: F 466 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8003 (mt-10) REVERT: F 485 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7478 (mm-30) REVERT: F 530 PHE cc_start: 0.8738 (m-10) cc_final: 0.8471 (m-80) REVERT: F 532 GLU cc_start: 0.7864 (mp0) cc_final: 0.7587 (mp0) REVERT: F 563 GLU cc_start: 0.6818 (tt0) cc_final: 0.5797 (tt0) REVERT: G 271 LEU cc_start: 0.9041 (mt) cc_final: 0.8819 (mm) REVERT: K 15 THR cc_start: 0.7291 (OUTLIER) cc_final: 0.7053 (m) REVERT: K 52 GLU cc_start: 0.7263 (pm20) cc_final: 0.6947 (pm20) outliers start: 105 outliers final: 78 residues processed: 819 average time/residue: 0.2350 time to fit residues: 293.7782 Evaluate side-chains 872 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 775 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 ASN 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 261 VAL Chi-restraints excluded: chain C residue 273 HIS 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 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 622 LYS Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET 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 915 ASP Chi-restraints excluded: chain C residue 935 THR 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 C residue 1318 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 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 283 LEU 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 553 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 656 GLU 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 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 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 1350 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 80 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 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 128 GLU Chi-restraints excluded: chain B residue 134 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 127 ASP Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 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 437 THR Chi-restraints excluded: chain F residue 471 LEU 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 560 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 21 optimal weight: 1.9990 chunk 318 optimal weight: 0.8980 chunk 353 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 377 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 307 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 H 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.146845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120239 restraints weight = 52248.155| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.17 r_work: 0.3382 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33405 Z= 0.211 Angle : 0.614 14.019 45679 Z= 0.319 Chirality : 0.043 0.220 5212 Planarity : 0.004 0.052 5466 Dihedral : 17.756 174.042 5693 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.76 % Rotamer: Outliers : 3.32 % Allowed : 19.24 % Favored : 77.44 % 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: 0.86 (0.14), residues: 3744 helix: 1.44 (0.13), residues: 1558 sheet: 0.37 (0.25), residues: 429 loop : -0.08 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1340 TYR 0.030 0.002 TYR D 144 PHE 0.012 0.001 PHE C 284 TRP 0.008 0.001 TRP F 323 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00498 (33397) covalent geometry : angle 0.60733 (45667) hydrogen bonds : bond 0.04425 ( 1500) hydrogen bonds : angle 4.39992 ( 4146) metal coordination : bond 0.01072 ( 8) metal coordination : angle 5.52913 ( 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 887 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 779 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8190 (m) REVERT: C 119 GLU cc_start: 0.7595 (pp20) cc_final: 0.7091 (pp20) REVERT: C 238 MET cc_start: 0.1826 (mmm) cc_final: 0.0542 (mmm) REVERT: C 273 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.6679 (m90) REVERT: C 337 PHE cc_start: 0.8291 (t80) cc_final: 0.7952 (t80) REVERT: C 339 ASN cc_start: 0.8370 (m-40) cc_final: 0.7908 (m-40) REVERT: C 354 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.5254 (t0) REVERT: C 461 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7496 (tp30) REVERT: C 565 GLU cc_start: 0.7371 (mp0) cc_final: 0.7111 (mp0) REVERT: C 599 VAL cc_start: 0.8265 (t) cc_final: 0.8050 (m) REVERT: C 681 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8282 (mtp) REVERT: C 731 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8388 (ttp80) REVERT: C 739 GLU cc_start: 0.7830 (mp0) cc_final: 0.7399 (mp0) REVERT: C 758 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8018 (ttt-90) REVERT: C 772 MET cc_start: 0.8103 (mmp) cc_final: 0.7072 (mmp) REVERT: C 775 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: C 805 MET cc_start: 0.8842 (ptp) cc_final: 0.8615 (ptm) REVERT: C 899 GLU cc_start: 0.7921 (tp30) cc_final: 0.7263 (tm-30) REVERT: C 1318 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8248 (tpp) REVERT: D 75 TYR cc_start: 0.8294 (m-10) cc_final: 0.8007 (m-10) REVERT: D 126 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8446 (tt) REVERT: D 134 ASP cc_start: 0.7355 (m-30) cc_final: 0.7074 (m-30) REVERT: D 140 TYR cc_start: 0.8471 (m-10) cc_final: 0.8087 (m-10) REVERT: D 158 GLN cc_start: 0.7873 (tt0) cc_final: 0.7535 (tm-30) REVERT: D 281 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7795 (mtp-110) REVERT: D 568 LYS cc_start: 0.8397 (ptmt) cc_final: 0.8122 (ptmt) REVERT: D 662 ARG cc_start: 0.7611 (mtm180) cc_final: 0.7183 (mtm-85) REVERT: D 705 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: D 738 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7970 (ptp90) REVERT: D 785 ASP cc_start: 0.7895 (t0) cc_final: 0.7444 (t0) REVERT: D 832 LYS cc_start: 0.8245 (mmpt) cc_final: 0.7872 (mmpt) REVERT: D 892 PHE cc_start: 0.7625 (t80) cc_final: 0.7248 (t80) REVERT: D 905 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8396 (mmt180) REVERT: D 907 HIS cc_start: 0.7504 (p90) cc_final: 0.7303 (p-80) REVERT: D 1187 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: D 1281 TYR cc_start: 0.8712 (t80) cc_final: 0.8388 (t80) REVERT: A 32 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7770 (mm-30) REVERT: A 215 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7073 (tm-30) REVERT: B 58 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7998 (mt-10) REVERT: B 67 GLU cc_start: 0.8188 (pm20) cc_final: 0.7898 (pm20) REVERT: B 104 ASN cc_start: 0.8649 (m-40) cc_final: 0.8417 (m-40) REVERT: B 216 GLU cc_start: 0.8191 (tp30) cc_final: 0.7755 (tp30) REVERT: B 220 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8065 (mtm-85) REVERT: F 261 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7112 (mt) REVERT: F 356 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6314 (tp30) REVERT: F 372 ARG cc_start: 0.7945 (mmp80) cc_final: 0.7543 (mmt180) REVERT: F 373 MET cc_start: 0.7542 (mmm) cc_final: 0.7194 (mmm) REVERT: F 385 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8087 (ptmm) REVERT: F 426 LYS cc_start: 0.8363 (ptpp) cc_final: 0.8028 (mtmm) REVERT: F 464 MET cc_start: 0.8537 (tpp) cc_final: 0.8254 (tpp) REVERT: F 466 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8010 (mt-10) REVERT: F 530 PHE cc_start: 0.8751 (m-10) cc_final: 0.8508 (m-80) REVERT: F 532 GLU cc_start: 0.7931 (mp0) cc_final: 0.7652 (mp0) REVERT: F 563 GLU cc_start: 0.6796 (tt0) cc_final: 0.6289 (tt0) REVERT: K 15 THR cc_start: 0.7292 (OUTLIER) cc_final: 0.7052 (m) REVERT: H 60 HIS cc_start: 0.7324 (t-90) cc_final: 0.7087 (t-90) REVERT: H 90 SER cc_start: 0.6461 (OUTLIER) cc_final: 0.6255 (p) outliers start: 108 outliers final: 83 residues processed: 818 average time/residue: 0.2312 time to fit residues: 288.4730 Evaluate side-chains 879 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 777 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 ASN 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 228 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 273 HIS 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 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 622 LYS Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET 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 968 GLU 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 C residue 1221 GLU Chi-restraints excluded: chain C residue 1318 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 192 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 283 LEU 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 553 THR Chi-restraints excluded: chain D residue 656 GLU 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 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 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 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 80 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 128 GLU 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 127 ASP Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 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 437 THR Chi-restraints excluded: chain F residue 471 LEU 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 560 THR 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 90 SER 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: 2.9990 chunk 371 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 321 optimal weight: 0.2980 chunk 256 optimal weight: 0.0000 chunk 68 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 311 optimal weight: 5.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN D1234 ASN A 104 ASN F 579 HIS ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS H 78 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121404 restraints weight = 52437.868| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.18 r_work: 0.3400 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33405 Z= 0.149 Angle : 0.595 12.448 45679 Z= 0.310 Chirality : 0.041 0.217 5212 Planarity : 0.004 0.052 5466 Dihedral : 17.696 175.159 5693 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.19 % Favored : 97.78 % Rotamer: Outliers : 3.23 % Allowed : 19.76 % Favored : 77.01 % 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: 1.01 (0.14), residues: 3744 helix: 1.58 (0.13), residues: 1557 sheet: 0.48 (0.25), residues: 428 loop : -0.03 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1340 TYR 0.031 0.001 TYR D 144 PHE 0.012 0.001 PHE C1029 TRP 0.009 0.001 TRP F 323 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00345 (33397) covalent geometry : angle 0.58974 (45667) hydrogen bonds : bond 0.04009 ( 1500) hydrogen bonds : angle 4.33676 ( 4146) metal coordination : bond 0.00800 ( 8) metal coordination : angle 4.95499 ( 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 874 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 769 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8134 (m) REVERT: C 119 GLU cc_start: 0.7590 (pp20) cc_final: 0.7087 (pp20) REVERT: C 238 MET cc_start: 0.1786 (mmm) cc_final: 0.0553 (mmm) REVERT: C 273 HIS cc_start: 0.6991 (OUTLIER) cc_final: 0.6683 (m90) REVERT: C 337 PHE cc_start: 0.8279 (t80) cc_final: 0.7937 (t80) REVERT: C 339 ASN cc_start: 0.8312 (m-40) cc_final: 0.7820 (m-40) REVERT: C 354 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.5173 (t0) REVERT: C 461 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7488 (tp30) REVERT: C 565 GLU cc_start: 0.7358 (mp0) cc_final: 0.7096 (mp0) REVERT: C 599 VAL cc_start: 0.8222 (t) cc_final: 0.8008 (m) REVERT: C 681 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8265 (mtp) REVERT: C 731 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8398 (ttp80) REVERT: C 739 GLU cc_start: 0.7843 (mp0) cc_final: 0.7423 (mp0) REVERT: C 758 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8029 (ttt-90) REVERT: C 772 MET cc_start: 0.8103 (mmp) cc_final: 0.7084 (mmp) REVERT: C 775 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: C 805 MET cc_start: 0.8827 (ptp) cc_final: 0.8622 (ptm) REVERT: C 899 GLU cc_start: 0.7897 (tp30) cc_final: 0.7263 (tm-30) REVERT: C 1318 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8251 (tpp) REVERT: D 75 TYR cc_start: 0.8278 (m-10) cc_final: 0.8013 (m-10) REVERT: D 126 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8438 (tt) REVERT: D 134 ASP cc_start: 0.7327 (m-30) cc_final: 0.7051 (m-30) REVERT: D 140 TYR cc_start: 0.8449 (m-10) cc_final: 0.8092 (m-10) REVERT: D 158 GLN cc_start: 0.7852 (tt0) cc_final: 0.7498 (tm-30) REVERT: D 228 VAL cc_start: 0.8440 (t) cc_final: 0.8222 (m) REVERT: D 281 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7747 (mtp-110) REVERT: D 568 LYS cc_start: 0.8394 (ptmt) cc_final: 0.8120 (ptmt) REVERT: D 662 ARG cc_start: 0.7613 (mtm180) cc_final: 0.7208 (mtm-85) REVERT: D 705 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: D 738 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7992 (ptp90) REVERT: D 785 ASP cc_start: 0.7869 (t0) cc_final: 0.7416 (t0) REVERT: D 832 LYS cc_start: 0.8248 (mmpt) cc_final: 0.7876 (mmpt) REVERT: D 892 PHE cc_start: 0.7628 (t80) cc_final: 0.7248 (t80) REVERT: D 905 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8378 (mmt180) REVERT: D 907 HIS cc_start: 0.7501 (p90) cc_final: 0.7286 (p-80) REVERT: D 1187 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6832 (pm20) REVERT: D 1281 TYR cc_start: 0.8671 (t80) cc_final: 0.8378 (t80) REVERT: A 32 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7783 (mm-30) REVERT: A 215 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7023 (tm-30) REVERT: B 58 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8147 (mt-10) REVERT: B 67 GLU cc_start: 0.8201 (pm20) cc_final: 0.7909 (pm20) REVERT: B 104 ASN cc_start: 0.8645 (m-40) cc_final: 0.8418 (m-40) REVERT: B 216 GLU cc_start: 0.8163 (tp30) cc_final: 0.7728 (tp30) REVERT: B 220 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8055 (mtm-85) REVERT: F 356 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6291 (tp30) REVERT: F 372 ARG cc_start: 0.7894 (mmp80) cc_final: 0.7516 (mmt180) REVERT: F 373 MET cc_start: 0.7512 (mmm) cc_final: 0.7184 (mmm) REVERT: F 385 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7988 (ptmm) REVERT: F 426 LYS cc_start: 0.8378 (ptpp) cc_final: 0.8061 (mtmm) REVERT: F 464 MET cc_start: 0.8511 (tpp) cc_final: 0.8248 (tpp) REVERT: F 466 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7992 (mt-10) REVERT: F 485 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7477 (mm-30) REVERT: F 530 PHE cc_start: 0.8743 (m-10) cc_final: 0.8495 (m-80) REVERT: F 532 GLU cc_start: 0.7906 (mp0) cc_final: 0.7603 (mp0) REVERT: F 563 GLU cc_start: 0.6806 (tt0) cc_final: 0.6297 (tt0) REVERT: K 15 THR cc_start: 0.7294 (OUTLIER) cc_final: 0.7051 (m) REVERT: K 52 GLU cc_start: 0.7201 (pm20) cc_final: 0.6952 (pm20) REVERT: H 60 HIS cc_start: 0.7319 (t-90) cc_final: 0.7083 (t-90) outliers start: 105 outliers final: 76 residues processed: 808 average time/residue: 0.2278 time to fit residues: 281.6752 Evaluate side-chains 862 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 769 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 261 VAL Chi-restraints excluded: chain C residue 273 HIS 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 622 LYS 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 723 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 775 GLU 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 968 GLU Chi-restraints excluded: chain C residue 1038 GLN 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 C residue 1221 GLU Chi-restraints excluded: chain C residue 1318 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 192 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 283 LEU 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 541 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 699 GLU 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 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 1187 GLU 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 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 80 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 128 GLU 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 127 ASP 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 437 THR Chi-restraints excluded: chain F residue 471 LEU 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 560 THR 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 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 91 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 341 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS A 104 ASN F 579 HIS ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117863 restraints weight = 52348.687| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.14 r_work: 0.3348 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 33405 Z= 0.345 Angle : 0.719 17.501 45679 Z= 0.372 Chirality : 0.049 0.311 5212 Planarity : 0.005 0.062 5466 Dihedral : 17.818 171.251 5693 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 3.23 % Allowed : 19.79 % Favored : 76.98 % 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: 0.58 (0.14), residues: 3744 helix: 1.10 (0.13), residues: 1569 sheet: 0.36 (0.25), residues: 442 loop : -0.18 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 151 TYR 0.039 0.002 TYR D 144 PHE 0.017 0.002 PHE C 284 TRP 0.012 0.002 TRP K 64 HIS 0.009 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00821 (33397) covalent geometry : angle 0.71000 (45667) hydrogen bonds : bond 0.05450 ( 1500) hydrogen bonds : angle 4.67568 ( 4146) metal coordination : bond 0.01512 ( 8) metal coordination : angle 6.87540 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11166.25 seconds wall clock time: 190 minutes 34.62 seconds (11434.62 seconds total)