Starting phenix.real_space_refine on Mon Jul 6 07:20:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdr_51276/07_2026/9gdr_51276.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdr_51276/07_2026/9gdr_51276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gdr_51276/07_2026/9gdr_51276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdr_51276/07_2026/9gdr_51276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gdr_51276/07_2026/9gdr_51276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdr_51276/07_2026/9gdr_51276.map" } resolution = 2.7 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= 0.007 sd= 1.079 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 134 5.49 5 Mg 1 5.21 5 S 123 5.16 5 C 20206 2.51 5 N 5792 2.21 5 O 6539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32797 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 898 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "K" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 909 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 101} Chain: "N" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1399 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain: "T" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1374 Classifications: {'DNA': 67} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 66} Chain breaks: 1 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: "C" Number of atoms: 10421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1328, 10410 Classifications: {'peptide': 1328} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1272} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1328, 10410 Classifications: {'peptide': 1328} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1272} Chain breaks: 2 bond proxies already assigned to first conformer: 10562 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: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1697 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 7, '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: "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 16006 SG CYS D 70 102.513 120.494 116.767 1.00 95.93 S ATOM 16020 SG CYS D 72 100.911 121.697 119.663 1.00 85.66 S ATOM 16128 SG CYS D 85 104.594 121.450 120.014 1.00 96.90 S ATOM 16152 SG CYS D 88 102.607 118.168 119.704 1.00 95.44 S ATOM 21862 SG CYS D 814 131.617 67.992 85.463 1.00 89.80 S ATOM 22422 SG CYS D 888 128.400 69.251 86.821 1.00 82.39 S ATOM 22471 SG CYS D 895 129.570 70.491 83.414 1.00 74.38 S ATOM 22491 SG CYS D 898 128.439 66.932 83.725 1.00 81.79 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG C 97 " occ=0.41 ... (20 atoms not shown) pdb=" NH2BARG C 97 " occ=0.59 Time building chain proxies: 6.59, per 1000 atoms: 0.20 Number of scatterers: 32797 At special positions: 0 Unit cell: (156.434, 222.955, 195.177, 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 123 16.00 P 134 15.00 Mg 1 11.99 O 6539 8.00 N 5792 7.00 C 20206 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: 2.49 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " 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 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " Number of angles added : 12 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7098 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 48 sheets defined 45.9% alpha, 15.7% beta 40 base pairs and 112 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'H' and resid 40 through 53 Processing helix chain 'H' and resid 59 through 68 Processing helix chain 'H' and resid 74 through 89 removed outlier: 4.333A pdb=" N LEU H 78 " --> pdb=" O SER H 74 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU H 89 " --> pdb=" O THR H 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 52 Processing helix chain 'K' and resid 59 through 68 Processing helix chain 'K' and resid 74 through 90 removed outlier: 3.626A pdb=" N LEU K 78 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE K 88 " --> pdb=" O ARG K 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 262 Processing helix chain 'G' and resid 264 through 274 Processing helix chain 'G' and resid 278 through 285 removed outlier: 3.730A pdb=" N ARG G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 292 Processing helix chain 'G' and resid 297 through 311 removed outlier: 3.690A pdb=" N ARG G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.056A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.724A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.097A pdb=" N LEU C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.970A 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 removed outlier: 3.766A pdb=" N VAL C 261 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.709A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.972A 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 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.733A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 410 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.951A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.176A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.685A pdb=" N TYR C 555 " --> pdb=" O VAL C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 3.714A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 614' 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 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 4.135A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 713 removed outlier: 4.183A 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 896 through 906 removed outlier: 4.085A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.864A pdb=" N ILE C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1000 removed outlier: 3.707A pdb=" N GLN C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1038 removed outlier: 3.657A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.561A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (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 1237 through 1242 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 1309 removed outlier: 3.595A pdb=" N THR C1301 " --> pdb=" O VAL C1297 " (cutoff:3.500A) Processing helix chain 'C' and resid 1319 through 1332 removed outlier: 3.601A 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: 3.677A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 122 through 129 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 removed outlier: 3.605A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 207 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 283 removed outlier: 4.023A 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 341 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 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 581 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.543A pdb=" N LEU D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.828A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.619A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.076A pdb=" N THR D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 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: 3.601A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.504A pdb=" N LEU D 838 " --> pdb=" O ALA D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1215 through 1223 Processing helix chain 'D' and resid 1224 through 1243 removed outlier: 3.833A pdb=" N GLN D1243 " --> pdb=" O VAL D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1260 removed outlier: 4.237A 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 1307 through 1314 Processing helix chain 'D' and resid 1317 through 1325 removed outlier: 3.511A pdb=" N ALA D1321 " --> pdb=" O SER D1317 " (cutoff:3.500A) Processing helix chain 'D' and resid 1326 through 1338 Processing helix chain 'D' and resid 1345 through 1352 removed outlier: 3.613A pdb=" N ASN D1349 " --> pdb=" O GLY D1345 " (cutoff:3.500A) 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 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 56 Processing helix chain 'E' and resid 60 through 74 Processing helix chain 'A' and resid 34 through 48 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 213 through 234 removed outlier: 4.163A pdb=" N ALA A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.525A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.592A 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: 3.586A pdb=" N LEU B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 108 removed outlier: 3.539A pdb=" N MET F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 138 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.500A pdb=" N ALA F 155 " --> pdb=" O ASP F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.863A 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 Processing helix chain 'F' and resid 250 through 266 removed outlier: 3.608A pdb=" N SER F 254 " --> pdb=" O SER F 250 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER F 257 " --> pdb=" O ALA F 253 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU F 266 " --> pdb=" O ASP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 300 Processing helix chain 'F' and resid 308 through 318 removed outlier: 4.637A pdb=" N THR F 315 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLY F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 330 removed outlier: 4.007A pdb=" N LEU F 324 " --> pdb=" O ASN F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 360 removed outlier: 3.514A pdb=" N VAL F 338 " --> pdb=" O TYR F 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU F 344 " --> pdb=" O GLU F 340 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET F 354 " --> pdb=" O GLN F 350 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE F 355 " --> pdb=" O LYS F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 400 removed outlier: 5.344A pdb=" N ARG F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 5.157A 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 removed outlier: 3.559A pdb=" N LYS F 426 " --> pdb=" O LYS F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 455 removed outlier: 4.009A pdb=" N TYR F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP F 442 " --> pdb=" O TYR F 438 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA F 455 " --> pdb=" O ILE F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 483 Processing helix chain 'F' and resid 487 through 496 Processing helix chain 'F' and resid 498 through 507 Processing helix chain 'F' and resid 526 through 530 Processing helix chain 'F' and resid 538 through 558 Processing helix chain 'F' and resid 560 through 572 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 591 through 608 removed outlier: 3.656A pdb=" N ILE F 595 " --> pdb=" O THR F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 617 removed outlier: 3.556A pdb=" N SER F 617 " --> pdb=" O GLU F 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 34 through 37 removed outlier: 6.547A pdb=" N VAL H 23 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU H 14 " --> pdb=" O PHE H 10 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN H 111 " --> pdb=" O GLN H 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 97 through 100 Processing sheet with id=AA3, first strand: chain 'K' and resid 34 through 37 removed outlier: 6.482A pdb=" N VAL K 23 " --> pdb=" O ILE K 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 97 through 100 Processing sheet with id=AA5, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.472A pdb=" N LYS C 13 " --> pdb=" O ALA C1182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.015A pdb=" N SER C 66 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU C 126 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AA8, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.325A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 154 through 159 removed outlier: 4.830A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AB2, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.990A pdb=" N ILE C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.867A pdb=" N GLU C 602 " --> pdb=" O ARG C 593 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR C 600 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.508A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.522A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AB9, first strand: chain 'C' and resid 1208 through 1209 removed outlier: 7.423A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR C1225 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.844A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.828A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1243 through 1245 Processing sheet with id=AC5, first strand: chain 'C' and resid 1268 through 1269 Processing sheet with id=AC6, first strand: chain 'C' and resid 1334 through 1339 removed outlier: 3.550A pdb=" N ALA D 19 " --> pdb=" O GLU C1339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.463A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 159 through 160 removed outlier: 6.742A pdb=" N THR D 177 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD1, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD2, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AD3, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AD4, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD5, first strand: chain 'D' and resid 825 through 826 removed outlier: 6.931A pdb=" N HIS D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 848 through 849 Processing sheet with id=AD7, first strand: chain 'D' and resid 991 through 995 Processing sheet with id=AD8, first strand: chain 'D' and resid 1155 through 1156 removed outlier: 6.417A pdb=" N ILE D1155 " --> pdb=" O ILE D1209 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1184 through 1189 Processing sheet with id=AE1, first strand: chain 'D' and resid 1278 through 1280 removed outlier: 4.649A pdb=" N LYS D1262 " --> pdb=" O GLU D1304 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG D1300 " --> pdb=" O THR D1266 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 12 through 20 removed outlier: 6.656A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N HIS A 23 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR A 208 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYS A 25 " --> pdb=" O MET A 206 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N MET A 206 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N THR A 27 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE A 204 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLU A 29 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU A 202 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 116 through 117 removed outlier: 7.292A pdb=" N ALA A 142 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE A 61 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG A 144 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 59 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A 146 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AE5, first strand: chain 'A' and resid 109 through 112 removed outlier: 6.566A pdb=" N GLY A 109 " --> pdb=" O HIS A 133 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N HIS A 133 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 111 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AE7, first strand: chain 'B' and resid 13 through 18 removed outlier: 5.734A pdb=" N HIS B 23 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR B 208 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LYS B 25 " --> pdb=" O MET B 206 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET B 206 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N THR B 27 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE B 204 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLU B 29 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU B 202 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N THR B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL B 193 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.671A pdb=" N THR B 102 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 58 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU B 148 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL B 56 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY B 150 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N CYS B 54 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AF1, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AF2, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AF3, first strand: chain 'F' and resid 164 through 166 removed outlier: 6.651A pdb=" N ARG F 268 " --> pdb=" O SER F 165 " (cutoff:3.500A) 1458 hydrogen bonds defined for protein. 4123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 112 stacking parallelities Total time for adding SS restraints: 9.17 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8961 1.33 - 1.45: 5720 1.45 - 1.57: 18427 1.57 - 1.69: 266 1.69 - 1.81: 217 Bond restraints: 33591 Sorted by residual: bond pdb=" C3' DT T 3 " pdb=" C2' DT T 3 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DA T 33 " pdb=" C2' DA T 33 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DT T 39 " pdb=" C2' DT T 39 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DA T 44 " pdb=" C2' DA T 44 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT N -36 " pdb=" C2' DT N -36 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 ... (remaining 33586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 44980 2.14 - 4.28: 856 4.28 - 6.43: 82 6.43 - 8.57: 13 8.57 - 10.71: 6 Bond angle restraints: 45937 Sorted by residual: angle pdb=" O4' DT N -33 " pdb=" C1' DT N -33 " pdb=" N1 DT N -33 " ideal model delta sigma weight residual 108.00 111.59 -3.59 7.00e-01 2.04e+00 2.63e+01 angle pdb=" N LEU C 213 " pdb=" CA LEU C 213 " pdb=" C LEU C 213 " ideal model delta sigma weight residual 113.18 107.06 6.12 1.21e+00 6.83e-01 2.56e+01 angle pdb=" N ARG C 211 " pdb=" CA ARG C 211 " pdb=" C ARG C 211 " ideal model delta sigma weight residual 111.36 106.30 5.06 1.09e+00 8.42e-01 2.16e+01 angle pdb=" N VAL F 243 " pdb=" CA VAL F 243 " pdb=" C VAL F 243 " ideal model delta sigma weight residual 110.23 114.96 -4.73 1.04e+00 9.25e-01 2.07e+01 angle pdb=" N3 DT N 5 " pdb=" C4 DT N 5 " pdb=" O4 DT N 5 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 ... (remaining 45932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 19120 35.61 - 71.21: 1210 71.21 - 106.82: 39 106.82 - 142.42: 0 142.42 - 178.03: 3 Dihedral angle restraints: 20372 sinusoidal: 9387 harmonic: 10985 Sorted by residual: dihedral pdb=" CA ARG D 388 " pdb=" C ARG D 388 " pdb=" N GLY D 389 " pdb=" CA GLY D 389 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" C4' DT N -9 " pdb=" C3' DT N -9 " pdb=" O3' DT N -9 " pdb=" P DA N -8 " ideal model delta sinusoidal sigma weight residual -140.00 38.03 -178.03 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT T -8 " pdb=" C3' DT T -8 " pdb=" O3' DT T -8 " pdb=" P DA T -7 " ideal model delta sinusoidal sigma weight residual -140.00 35.47 -175.47 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 20369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4423 0.063 - 0.125: 770 0.125 - 0.188: 31 0.188 - 0.250: 3 0.250 - 0.313: 1 Chirality restraints: 5228 Sorted by residual: chirality pdb=" CB ILE F 508 " pdb=" CA ILE F 508 " pdb=" CG1 ILE F 508 " pdb=" CG2 ILE F 508 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB ILE D 685 " pdb=" CA ILE D 685 " pdb=" CG1 ILE D 685 " pdb=" CG2 ILE D 685 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C3' DT N -9 " pdb=" C4' DT N -9 " pdb=" O3' DT N -9 " pdb=" C2' DT N -9 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 5225 not shown) Planarity restraints: 5510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 211 " 0.336 9.50e-02 1.11e+02 1.51e-01 1.40e+01 pdb=" NE ARG C 211 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 211 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 211 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 211 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 21 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C ASN H 21 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN H 21 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN H 22 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 963 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C GLU C 963 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU C 963 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE C 964 " -0.014 2.00e-02 2.50e+03 ... (remaining 5507 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 210 2.56 - 3.14: 24902 3.14 - 3.73: 51725 3.73 - 4.31: 71994 4.31 - 4.90: 118168 Nonbonded interactions: 266999 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 1.975 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.093 2.170 nonbonded pdb=" OG1 THR D1264 " pdb=" OE2 GLU D1304 " model vdw 2.173 3.040 nonbonded pdb=" OH TYR H 105 " pdb=" OP2 DA T 36 " model vdw 2.180 3.040 nonbonded pdb=" N GLU C 244 " pdb=" OE1 GLU C 244 " model vdw 2.192 3.120 ... (remaining 266994 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 169 through 233)) selection = chain 'B' } ncs_group { reference = chain 'H' selection = (chain 'K' and resid 6 through 114) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 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: 10.430 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: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 37.120 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 0.063 33599 Z= 0.278 Angle : 0.679 10.709 45949 Z= 0.432 Chirality : 0.045 0.313 5228 Planarity : 0.005 0.151 5510 Dihedral : 19.558 178.028 13274 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.70 % Allowed : 26.52 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.70 (0.13), residues: 3775 helix: 1.10 (0.13), residues: 1582 sheet: 0.74 (0.23), residues: 460 loop : -0.11 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG F 476 TYR 0.022 0.002 TYR D 144 PHE 0.018 0.001 PHE C 514 TRP 0.017 0.001 TRP K 15 HIS 0.012 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.28 (33591) covalent geometry : angle 0.67469 / 0.43 (45937) hydrogen bonds : bond 0.12291 / 8.00 ( 1550) hydrogen bonds : angle 5.68613 / 5.67 ( 4311) metal coordination : bond 0.00917 / 0.50 ( 8) metal coordination : angle 4.63013 / 2.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 737 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.6970 (mm) cc_final: 0.6648 (mp) REVERT: H 40 SER cc_start: 0.6420 (p) cc_final: 0.6173 (p) REVERT: C 67 GLU cc_start: 0.6990 (pt0) cc_final: 0.6755 (pt0) REVERT: C 204 LEU cc_start: 0.7595 (mp) cc_final: 0.7278 (mp) REVERT: C 515 MET cc_start: 0.7856 (ttt) cc_final: 0.7363 (ttt) REVERT: C 545 PHE cc_start: 0.7548 (t80) cc_final: 0.7032 (t80) REVERT: C 642 SER cc_start: 0.8635 (p) cc_final: 0.8383 (m) REVERT: C 890 LYS cc_start: 0.8405 (ptmt) cc_final: 0.8079 (ptmm) REVERT: C 899 GLU cc_start: 0.7758 (tt0) cc_final: 0.7293 (tm-30) REVERT: C 1151 LEU cc_start: 0.8764 (tt) cc_final: 0.8503 (tp) REVERT: C 1159 ASP cc_start: 0.7707 (p0) cc_final: 0.7426 (p0) REVERT: C 1199 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7616 (mp0) REVERT: D 128 MET cc_start: 0.8512 (ptp) cc_final: 0.8303 (ptm) REVERT: D 298 MET cc_start: 0.8316 (mmm) cc_final: 0.8070 (mmm) REVERT: D 330 MET cc_start: 0.8601 (mmm) cc_final: 0.8155 (mmm) REVERT: D 388 ARG cc_start: 0.8454 (ptp90) cc_final: 0.8025 (ptp-170) REVERT: D 414 GLU cc_start: 0.8091 (tt0) cc_final: 0.7722 (tt0) REVERT: D 712 GLU cc_start: 0.7364 (mp0) cc_final: 0.6953 (pm20) REVERT: D 725 MET cc_start: 0.8650 (mtt) cc_final: 0.8364 (mtt) REVERT: D 754 ILE cc_start: 0.8561 (mt) cc_final: 0.8327 (mm) REVERT: B 80 GLU cc_start: 0.7990 (tt0) cc_final: 0.7778 (tt0) REVERT: F 102 MET cc_start: 0.7132 (mtp) cc_final: 0.6918 (mtp) REVERT: F 386 GLU cc_start: 0.8376 (tp30) cc_final: 0.8077 (tp30) REVERT: F 459 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7808 (mtp180) REVERT: F 476 ARG cc_start: 0.7326 (tpt170) cc_final: 0.7077 (ttp80) REVERT: F 601 LYS cc_start: 0.8104 (tttt) cc_final: 0.7651 (tttt) outliers start: 23 outliers final: 9 residues processed: 746 average time/residue: 0.7255 time to fit residues: 633.4205 Evaluate side-chains 717 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 707 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 608 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 GLN K 43 GLN G 269 ASN C 339 ASN C 447 HIS C 450 ASN C 707 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D 873 ASN D 910 ASN D1217 HIS A 75 GLN F 238 ASN F 472 ASN F 477 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.169009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130117 restraints weight = 73414.456| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.52 r_work: 0.3483 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 33599 Z= 0.244 Angle : 0.657 11.302 45949 Z= 0.353 Chirality : 0.047 0.372 5228 Planarity : 0.005 0.054 5510 Dihedral : 18.226 174.191 5730 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.31 % Allowed : 21.14 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.73 (0.13), residues: 3775 helix: 1.17 (0.13), residues: 1596 sheet: 0.75 (0.23), residues: 456 loop : -0.16 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 604 TYR 0.023 0.002 TYR D 631 PHE 0.024 0.002 PHE C 514 TRP 0.016 0.002 TRP K 15 HIS 0.013 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 (33591) covalent geometry : angle 0.65177 / 0.35 (45937) hydrogen bonds : bond 0.05198 / 3.43 ( 1550) hydrogen bonds : angle 4.73773 / 4.72 ( 4311) metal coordination : bond 0.01470 / 0.85 ( 8) metal coordination : angle 4.94275 / 2.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 755 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.7070 (mm) cc_final: 0.6831 (mp) REVERT: H 43 GLN cc_start: 0.7746 (mt0) cc_final: 0.7384 (mt0) REVERT: K 63 ILE cc_start: 0.7898 (tt) cc_final: 0.7667 (pt) REVERT: G 291 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7575 (tt) REVERT: C 98 VAL cc_start: 0.8399 (p) cc_final: 0.8148 (t) REVERT: C 158 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.7037 (m-30) REVERT: C 545 PHE cc_start: 0.7178 (t80) cc_final: 0.6887 (t80) REVERT: C 549 ASP cc_start: 0.7821 (m-30) cc_final: 0.7578 (m-30) REVERT: C 734 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8567 (t) REVERT: C 735 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8295 (tttm) REVERT: C 890 LYS cc_start: 0.8402 (ptmt) cc_final: 0.8087 (ptmm) REVERT: C 899 GLU cc_start: 0.7661 (tt0) cc_final: 0.7214 (tm-30) REVERT: C 914 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7899 (ttpp) REVERT: C 1151 LEU cc_start: 0.8733 (tt) cc_final: 0.8505 (tp) REVERT: C 1159 ASP cc_start: 0.7668 (p0) cc_final: 0.7244 (p0) REVERT: D 74 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8057 (ttpt) REVERT: D 148 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7532 (mt-10) REVERT: D 180 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7341 (ttt) REVERT: D 204 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7499 (tm-30) REVERT: D 298 MET cc_start: 0.8355 (mmm) cc_final: 0.7443 (mtm) REVERT: D 330 MET cc_start: 0.8497 (mmm) cc_final: 0.8037 (mtm) REVERT: D 388 ARG cc_start: 0.8388 (ptp90) cc_final: 0.8043 (ptp-170) REVERT: D 430 HIS cc_start: 0.8978 (OUTLIER) cc_final: 0.8642 (p90) REVERT: D 704 GLU cc_start: 0.7178 (pt0) cc_final: 0.6923 (pt0) REVERT: D 712 GLU cc_start: 0.7393 (mp0) cc_final: 0.7002 (pm20) REVERT: D 739 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: D 754 ILE cc_start: 0.8740 (mt) cc_final: 0.8528 (mm) REVERT: D 930 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7711 (mt) REVERT: D 1214 GLU cc_start: 0.7253 (mt-10) cc_final: 0.7001 (tt0) REVERT: D 1333 GLU cc_start: 0.7929 (tp30) cc_final: 0.7639 (tp30) REVERT: D 1360 THR cc_start: 0.8802 (m) cc_final: 0.8071 (p) REVERT: A 17 GLU cc_start: 0.7719 (tt0) cc_final: 0.7494 (tt0) REVERT: A 33 ARG cc_start: 0.7871 (mtp180) cc_final: 0.7670 (mtp180) REVERT: F 100 VAL cc_start: 0.6830 (OUTLIER) cc_final: 0.6620 (p) REVERT: F 102 MET cc_start: 0.7314 (mtp) cc_final: 0.7046 (mtp) REVERT: F 285 MET cc_start: 0.7529 (tmm) cc_final: 0.7186 (tmm) REVERT: F 386 GLU cc_start: 0.8308 (tp30) cc_final: 0.7939 (tp30) REVERT: F 387 MET cc_start: 0.8332 (tpt) cc_final: 0.8111 (tpp) REVERT: F 393 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7962 (ttm170) REVERT: F 415 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6928 (tp30) REVERT: F 445 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7965 (tm130) REVERT: F 459 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7526 (ttp80) REVERT: F 601 LYS cc_start: 0.8343 (tttt) cc_final: 0.7632 (tttt) outliers start: 141 outliers final: 59 residues processed: 822 average time/residue: 0.7131 time to fit residues: 685.8102 Evaluate side-chains 780 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 710 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain C residue 1251 SER Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1369 GLN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 371 HIS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 511 GLU Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 537 GLU Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 617 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 132 optimal weight: 1.9990 chunk 328 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 278 optimal weight: 0.5980 chunk 371 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 299 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 GLN D 504 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D 911 GLN D1243 GLN A 75 GLN B 84 ASN F 353 GLN F 454 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.168807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129735 restraints weight = 71329.954| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.60 r_work: 0.3478 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 33599 Z= 0.211 Angle : 0.608 12.150 45949 Z= 0.328 Chirality : 0.045 0.334 5228 Planarity : 0.005 0.057 5510 Dihedral : 18.193 173.507 5722 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.88 % Allowed : 21.20 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.13), residues: 3775 helix: 1.24 (0.13), residues: 1611 sheet: 0.69 (0.23), residues: 463 loop : -0.10 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG K 34 TYR 0.065 0.002 TYR K 25 PHE 0.017 0.002 PHE C 514 TRP 0.016 0.001 TRP K 15 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (33591) covalent geometry : angle 0.60351 / 0.33 (45937) hydrogen bonds : bond 0.04960 / 3.26 ( 1550) hydrogen bonds : angle 4.59945 / 4.58 ( 4311) metal coordination : bond 0.01162 / 0.66 ( 8) metal coordination : angle 4.38534 / 2.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 742 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.7104 (mm) cc_final: 0.6867 (mp) REVERT: G 291 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7580 (tt) REVERT: C 84 GLU cc_start: 0.7815 (pm20) cc_final: 0.7555 (pm20) REVERT: C 158 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.7070 (m-30) REVERT: C 187 GLU cc_start: 0.7289 (pt0) cc_final: 0.7063 (pt0) REVERT: C 194 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7723 (pp) REVERT: C 197 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7215 (mtt180) REVERT: C 470 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7632 (mtp180) REVERT: C 476 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7803 (ttmm) REVERT: C 734 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8520 (t) REVERT: C 837 SER cc_start: 0.8899 (p) cc_final: 0.8666 (m) REVERT: C 890 LYS cc_start: 0.8403 (ptmt) cc_final: 0.8056 (ptmm) REVERT: C 899 GLU cc_start: 0.7662 (tt0) cc_final: 0.7144 (tm-30) REVERT: C 914 LYS cc_start: 0.8138 (ttpp) cc_final: 0.7852 (ttpp) REVERT: C 1140 LYS cc_start: 0.8358 (mtpp) cc_final: 0.8143 (mtpt) REVERT: C 1151 LEU cc_start: 0.8726 (tt) cc_final: 0.8476 (tp) REVERT: C 1159 ASP cc_start: 0.7639 (p0) cc_final: 0.7268 (p0) REVERT: D 148 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7565 (mt-10) REVERT: D 180 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7291 (ttt) REVERT: D 204 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7499 (tm-30) REVERT: D 330 MET cc_start: 0.8541 (mmm) cc_final: 0.8015 (mtm) REVERT: D 388 ARG cc_start: 0.8419 (ptp90) cc_final: 0.8182 (ptp-170) REVERT: D 430 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.8643 (p90) REVERT: D 704 GLU cc_start: 0.7176 (pt0) cc_final: 0.6886 (pt0) REVERT: D 712 GLU cc_start: 0.7443 (mp0) cc_final: 0.6948 (pm20) REVERT: D 739 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: D 754 ILE cc_start: 0.8704 (mt) cc_final: 0.8472 (mm) REVERT: D 785 ASP cc_start: 0.7667 (t0) cc_final: 0.7367 (t0) REVERT: D 1333 GLU cc_start: 0.7946 (tp30) cc_final: 0.7598 (tp30) REVERT: D 1360 THR cc_start: 0.8789 (m) cc_final: 0.7527 (t) REVERT: A 33 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7586 (mtp180) REVERT: F 100 VAL cc_start: 0.6877 (OUTLIER) cc_final: 0.6567 (p) REVERT: F 102 MET cc_start: 0.7425 (mtp) cc_final: 0.7133 (mtp) REVERT: F 386 GLU cc_start: 0.8230 (tp30) cc_final: 0.7870 (tp30) REVERT: F 393 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7879 (ttm170) REVERT: F 397 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8258 (p) REVERT: F 415 GLU cc_start: 0.7737 (mm-30) cc_final: 0.6993 (tp30) REVERT: F 459 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7832 (ttp80) REVERT: F 489 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7252 (tm-30) REVERT: F 601 LYS cc_start: 0.8396 (tttt) cc_final: 0.8062 (tttt) outliers start: 127 outliers final: 57 residues processed: 796 average time/residue: 0.7038 time to fit residues: 658.3049 Evaluate side-chains 794 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 724 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1369 GLN Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 371 HIS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 617 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 114 optimal weight: 0.7980 chunk 359 optimal weight: 40.0000 chunk 104 optimal weight: 0.5980 chunk 354 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 374 optimal weight: 0.9980 chunk 363 optimal weight: 3.9990 chunk 292 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 288 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN D 504 GLN D 716 GLN D 805 GLN B 84 ASN F 445 GLN F 454 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.169235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130526 restraints weight = 63461.573| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.50 r_work: 0.3490 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33599 Z= 0.161 Angle : 0.565 13.472 45949 Z= 0.306 Chirality : 0.043 0.322 5228 Planarity : 0.005 0.050 5510 Dihedral : 18.169 173.216 5720 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.79 % Allowed : 21.81 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.93 (0.14), residues: 3775 helix: 1.39 (0.13), residues: 1618 sheet: 0.66 (0.23), residues: 463 loop : -0.05 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 101 TYR 0.039 0.001 TYR K 25 PHE 0.015 0.001 PHE C 906 TRP 0.014 0.001 TRP K 15 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (33591) covalent geometry : angle 0.56162 / 0.31 (45937) hydrogen bonds : bond 0.04434 / 2.93 ( 1550) hydrogen bonds : angle 4.42867 / 4.42 ( 4311) metal coordination : bond 0.01482 / 0.82 ( 8) metal coordination : angle 3.77522 / 2.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 750 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.7187 (mm) cc_final: 0.6960 (mp) REVERT: C 84 GLU cc_start: 0.7804 (pm20) cc_final: 0.7488 (pm20) REVERT: C 194 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7737 (pp) REVERT: C 197 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7456 (mtt180) REVERT: C 470 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7656 (mtp180) REVERT: C 476 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7757 (ttmm) REVERT: C 583 GLU cc_start: 0.8009 (pt0) cc_final: 0.7788 (pm20) REVERT: C 734 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8519 (t) REVERT: C 837 SER cc_start: 0.8890 (p) cc_final: 0.8657 (m) REVERT: C 849 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: C 865 LEU cc_start: 0.8567 (mp) cc_final: 0.8349 (mt) REVERT: C 890 LYS cc_start: 0.8357 (ptmt) cc_final: 0.8018 (ptmm) REVERT: C 899 GLU cc_start: 0.7648 (tt0) cc_final: 0.7083 (tm-30) REVERT: C 914 LYS cc_start: 0.8138 (ttpp) cc_final: 0.7845 (ttpp) REVERT: C 1151 LEU cc_start: 0.8721 (tt) cc_final: 0.8471 (tp) REVERT: C 1249 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.8049 (m) REVERT: D 148 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7569 (mt-10) REVERT: D 180 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7228 (ttt) REVERT: D 204 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7472 (tm-30) REVERT: D 388 ARG cc_start: 0.8428 (ptp90) cc_final: 0.8226 (ptp-170) REVERT: D 414 GLU cc_start: 0.7999 (tt0) cc_final: 0.7731 (tt0) REVERT: D 704 GLU cc_start: 0.7148 (pt0) cc_final: 0.6866 (pt0) REVERT: D 712 GLU cc_start: 0.7469 (mp0) cc_final: 0.7232 (mp0) REVERT: D 739 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: D 754 ILE cc_start: 0.8686 (mt) cc_final: 0.8469 (mm) REVERT: D 861 ASN cc_start: 0.8181 (m-40) cc_final: 0.7884 (m-40) REVERT: D 1333 GLU cc_start: 0.7932 (tp30) cc_final: 0.7607 (tp30) REVERT: D 1360 THR cc_start: 0.8740 (m) cc_final: 0.7411 (t) REVERT: F 102 MET cc_start: 0.7481 (mtp) cc_final: 0.7165 (mtp) REVERT: F 278 VAL cc_start: 0.8603 (t) cc_final: 0.8274 (m) REVERT: F 386 GLU cc_start: 0.8197 (tp30) cc_final: 0.7842 (tp30) REVERT: F 397 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8263 (p) REVERT: F 415 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7035 (tp30) REVERT: F 422 LYS cc_start: 0.8162 (tttm) cc_final: 0.7953 (tttm) REVERT: F 459 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7999 (ttp80) REVERT: F 462 VAL cc_start: 0.8649 (t) cc_final: 0.8399 (m) REVERT: F 480 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7963 (mm-40) REVERT: F 484 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7585 (pmt170) REVERT: F 489 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7263 (tm-30) REVERT: F 601 LYS cc_start: 0.8372 (tttt) cc_final: 0.8143 (tttt) outliers start: 124 outliers final: 63 residues processed: 802 average time/residue: 0.7086 time to fit residues: 665.0378 Evaluate side-chains 808 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 734 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1249 SER Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1369 GLN Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 484 ARG Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 130 optimal weight: 0.5980 chunk 183 optimal weight: 0.5980 chunk 195 optimal weight: 0.0170 chunk 321 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 173 optimal weight: 0.8980 chunk 379 optimal weight: 0.7980 chunk 371 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN D 335 GLN D 805 GLN B 84 ASN F 445 GLN F 454 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.172610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133053 restraints weight = 80296.365| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.82 r_work: 0.3479 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33599 Z= 0.125 Angle : 0.545 13.582 45949 Z= 0.294 Chirality : 0.041 0.302 5228 Planarity : 0.004 0.077 5510 Dihedral : 18.132 173.762 5720 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.21 % Allowed : 22.85 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.10 (0.14), residues: 3775 helix: 1.59 (0.13), residues: 1605 sheet: 0.68 (0.23), residues: 484 loop : -0.01 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 101 TYR 0.026 0.001 TYR K 25 PHE 0.025 0.001 PHE C 390 TRP 0.010 0.001 TRP K 15 HIS 0.005 0.001 HIS D1365 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (33591) covalent geometry : angle 0.54241 / 0.29 (45937) hydrogen bonds : bond 0.04042 / 2.67 ( 1550) hydrogen bonds : angle 4.31351 / 4.30 ( 4311) metal coordination : bond 0.00858 / 0.50 ( 8) metal coordination : angle 3.36831 / 1.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 761 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.7190 (mm) cc_final: 0.6955 (mp) REVERT: K 63 ILE cc_start: 0.7874 (tt) cc_final: 0.7659 (pt) REVERT: C 84 GLU cc_start: 0.7873 (pm20) cc_final: 0.7552 (pm20) REVERT: C 175 ARG cc_start: 0.7843 (ttm110) cc_final: 0.7596 (ttm-80) REVERT: C 194 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7745 (pp) REVERT: C 197 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7135 (mtt90) REVERT: C 476 LYS cc_start: 0.8057 (mtmt) cc_final: 0.7838 (ttmm) REVERT: C 583 GLU cc_start: 0.8030 (pt0) cc_final: 0.7756 (pm20) REVERT: C 734 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8480 (t) REVERT: C 837 SER cc_start: 0.8900 (p) cc_final: 0.8668 (m) REVERT: C 849 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: C 865 LEU cc_start: 0.8589 (mp) cc_final: 0.8371 (mt) REVERT: C 899 GLU cc_start: 0.7711 (tt0) cc_final: 0.7128 (tm-30) REVERT: C 902 LEU cc_start: 0.8602 (tt) cc_final: 0.8347 (mp) REVERT: C 914 LYS cc_start: 0.8181 (ttpp) cc_final: 0.7879 (ttpp) REVERT: C 1140 LYS cc_start: 0.8323 (mtpp) cc_final: 0.8101 (mtpt) REVERT: C 1151 LEU cc_start: 0.8731 (tt) cc_final: 0.8490 (tp) REVERT: D 21 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8107 (tttm) REVERT: D 144 TYR cc_start: 0.8275 (m-80) cc_final: 0.7998 (m-10) REVERT: D 148 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7576 (mt-10) REVERT: D 180 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7257 (ttt) REVERT: D 204 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 414 GLU cc_start: 0.8033 (tt0) cc_final: 0.7739 (tt0) REVERT: D 704 GLU cc_start: 0.7290 (pt0) cc_final: 0.6996 (pt0) REVERT: D 712 GLU cc_start: 0.7509 (mp0) cc_final: 0.7249 (mp0) REVERT: D 739 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8138 (mt0) REVERT: D 754 ILE cc_start: 0.8670 (mt) cc_final: 0.8443 (mm) REVERT: D 1333 GLU cc_start: 0.8010 (tp30) cc_final: 0.7690 (tp30) REVERT: D 1360 THR cc_start: 0.8746 (m) cc_final: 0.7375 (t) REVERT: B 86 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8252 (tttt) REVERT: F 100 VAL cc_start: 0.6956 (OUTLIER) cc_final: 0.6673 (p) REVERT: F 102 MET cc_start: 0.7505 (mtp) cc_final: 0.7192 (mtp) REVERT: F 278 VAL cc_start: 0.8576 (t) cc_final: 0.8262 (m) REVERT: F 386 GLU cc_start: 0.8194 (tp30) cc_final: 0.7898 (tp30) REVERT: F 388 VAL cc_start: 0.8532 (p) cc_final: 0.8323 (m) REVERT: F 397 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8244 (p) REVERT: F 415 GLU cc_start: 0.7792 (mm-30) cc_final: 0.6917 (tp30) REVERT: F 422 LYS cc_start: 0.8210 (tttm) cc_final: 0.7994 (tttm) REVERT: F 459 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7894 (ttp80) REVERT: F 462 VAL cc_start: 0.8635 (t) cc_final: 0.8397 (m) REVERT: F 480 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7936 (mm-40) REVERT: F 484 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7730 (ppt170) REVERT: F 489 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7292 (tm-30) REVERT: F 490 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7634 (pt0) REVERT: F 601 LYS cc_start: 0.8373 (tttt) cc_final: 0.8135 (tttt) outliers start: 105 outliers final: 57 residues processed: 804 average time/residue: 0.7302 time to fit residues: 685.8630 Evaluate side-chains 804 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 735 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1369 GLN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 484 ARG Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 1 optimal weight: 2.9990 chunk 346 optimal weight: 8.9990 chunk 155 optimal weight: 0.3980 chunk 238 optimal weight: 0.6980 chunk 341 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 310 optimal weight: 0.1980 chunk 242 optimal weight: 1.9990 chunk 373 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 357 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN G 269 ASN C 339 ASN C 450 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D 861 ASN D1243 GLN B 84 ASN F 454 GLN F 480 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.171797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133390 restraints weight = 66124.918| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.51 r_work: 0.3492 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33599 Z= 0.166 Angle : 0.567 14.034 45949 Z= 0.303 Chirality : 0.042 0.304 5228 Planarity : 0.005 0.075 5510 Dihedral : 18.096 175.913 5720 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.58 % Allowed : 22.55 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.09 (0.14), residues: 3775 helix: 1.58 (0.13), residues: 1608 sheet: 0.67 (0.23), residues: 484 loop : -0.01 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 101 TYR 0.027 0.001 TYR K 25 PHE 0.024 0.001 PHE C 906 TRP 0.010 0.001 TRP K 15 HIS 0.005 0.001 HIS D1365 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (33591) covalent geometry : angle 0.56355 / 0.30 (45937) hydrogen bonds : bond 0.04297 / 2.84 ( 1550) hydrogen bonds : angle 4.30272 / 4.29 ( 4311) metal coordination : bond 0.00994 / 0.57 ( 8) metal coordination : angle 3.99764 / 2.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 759 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.7232 (mm) cc_final: 0.7007 (mp) REVERT: C 84 GLU cc_start: 0.7818 (pm20) cc_final: 0.7487 (pm20) REVERT: C 175 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7555 (ttm-80) REVERT: C 187 GLU cc_start: 0.7416 (pt0) cc_final: 0.7094 (pt0) REVERT: C 192 ASP cc_start: 0.7735 (t0) cc_final: 0.7401 (t0) REVERT: C 194 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7748 (pp) REVERT: C 197 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7131 (mtt180) REVERT: C 470 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7662 (mtp180) REVERT: C 476 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7832 (ttmm) REVERT: C 503 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8394 (mtpt) REVERT: C 515 MET cc_start: 0.7865 (ttt) cc_final: 0.7598 (ttt) REVERT: C 734 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8482 (t) REVERT: C 837 SER cc_start: 0.8879 (p) cc_final: 0.8652 (m) REVERT: C 890 LYS cc_start: 0.8348 (ptmt) cc_final: 0.8037 (ptmm) REVERT: C 899 GLU cc_start: 0.7673 (tt0) cc_final: 0.7092 (tm-30) REVERT: C 902 LEU cc_start: 0.8579 (tt) cc_final: 0.8351 (mp) REVERT: C 914 LYS cc_start: 0.8152 (ttpp) cc_final: 0.7854 (ttpp) REVERT: C 1092 GLN cc_start: 0.8437 (tt0) cc_final: 0.8177 (tt0) REVERT: C 1140 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8102 (mtpt) REVERT: C 1151 LEU cc_start: 0.8711 (tt) cc_final: 0.8468 (tp) REVERT: D 21 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8093 (tttm) REVERT: D 144 TYR cc_start: 0.8239 (m-80) cc_final: 0.7941 (m-80) REVERT: D 148 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7589 (mt-10) REVERT: D 180 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7193 (ttt) REVERT: D 204 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7465 (tm-30) REVERT: D 430 HIS cc_start: 0.8996 (OUTLIER) cc_final: 0.8650 (p90) REVERT: D 534 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7503 (tp30) REVERT: D 704 GLU cc_start: 0.7259 (pt0) cc_final: 0.6976 (pt0) REVERT: D 712 GLU cc_start: 0.7495 (mp0) cc_final: 0.7213 (mp0) REVERT: D 739 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: D 754 ILE cc_start: 0.8672 (mt) cc_final: 0.8449 (mm) REVERT: D 1214 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7153 (mm-30) REVERT: D 1329 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8277 (mtm-85) REVERT: D 1333 GLU cc_start: 0.7937 (tp30) cc_final: 0.7604 (tp30) REVERT: D 1360 THR cc_start: 0.8742 (m) cc_final: 0.7383 (t) REVERT: A 86 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8493 (mtmm) REVERT: F 100 VAL cc_start: 0.6997 (OUTLIER) cc_final: 0.6784 (p) REVERT: F 102 MET cc_start: 0.7581 (mtp) cc_final: 0.7316 (mtp) REVERT: F 115 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6492 (mtm180) REVERT: F 278 VAL cc_start: 0.8575 (t) cc_final: 0.8267 (m) REVERT: F 382 ARG cc_start: 0.7796 (ttp80) cc_final: 0.7207 (ttp80) REVERT: F 386 GLU cc_start: 0.8217 (tp30) cc_final: 0.7762 (tp30) REVERT: F 388 VAL cc_start: 0.8546 (p) cc_final: 0.8345 (m) REVERT: F 397 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8286 (p) REVERT: F 415 GLU cc_start: 0.7813 (mm-30) cc_final: 0.6998 (tp30) REVERT: F 422 LYS cc_start: 0.8215 (tttm) cc_final: 0.8008 (tttm) REVERT: F 459 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7905 (ttp80) REVERT: F 462 VAL cc_start: 0.8625 (t) cc_final: 0.8395 (m) REVERT: F 480 GLN cc_start: 0.8216 (tp40) cc_final: 0.7997 (mm-40) REVERT: F 489 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7326 (tm-30) REVERT: F 490 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7652 (pt0) REVERT: F 601 LYS cc_start: 0.8353 (tttt) cc_final: 0.7945 (tttt) outliers start: 117 outliers final: 64 residues processed: 806 average time/residue: 0.7237 time to fit residues: 682.5099 Evaluate side-chains 829 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 750 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain K residue 54 HIS Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1251 SER Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1329 ARG Chi-restraints excluded: chain D residue 1369 GLN Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 516 GLU Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 575 MET Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 299 optimal weight: 0.1980 chunk 345 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 94 optimal weight: 0.0030 chunk 254 optimal weight: 2.9990 chunk 374 optimal weight: 0.9990 chunk 140 optimal weight: 30.0000 chunk 263 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN C 339 ASN D 805 GLN D 861 ASN D1234 ASN D1243 GLN B 84 ASN F 445 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.172141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134122 restraints weight = 64472.712| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.43 r_work: 0.3503 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33599 Z= 0.136 Angle : 0.552 14.082 45949 Z= 0.295 Chirality : 0.042 0.293 5228 Planarity : 0.004 0.084 5510 Dihedral : 18.066 176.618 5717 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.27 % Allowed : 22.91 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.15 (0.14), residues: 3775 helix: 1.60 (0.13), residues: 1614 sheet: 0.65 (0.23), residues: 499 loop : 0.05 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 101 TYR 0.020 0.001 TYR K 25 PHE 0.013 0.001 PHE C 385 TRP 0.008 0.001 TRP K 15 HIS 0.005 0.001 HIS D1365 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (33591) covalent geometry : angle 0.54928 / 0.29 (45937) hydrogen bonds : bond 0.04034 / 2.67 ( 1550) hydrogen bonds : angle 4.25892 / 4.25 ( 4311) metal coordination : bond 0.00750 / 0.45 ( 8) metal coordination : angle 3.58114 / 1.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 753 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.7238 (mm) cc_final: 0.6998 (mp) REVERT: H 107 ILE cc_start: 0.5750 (OUTLIER) cc_final: 0.5539 (pt) REVERT: C 84 GLU cc_start: 0.7812 (pm20) cc_final: 0.7453 (pm20) REVERT: C 175 ARG cc_start: 0.7782 (ttm110) cc_final: 0.7510 (ttm-80) REVERT: C 192 ASP cc_start: 0.7737 (t0) cc_final: 0.7409 (t0) REVERT: C 194 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7750 (pp) REVERT: C 197 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7209 (mtt90) REVERT: C 470 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7644 (mtp180) REVERT: C 476 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7833 (ttmm) REVERT: C 503 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8389 (mtpt) REVERT: C 515 MET cc_start: 0.7770 (ttt) cc_final: 0.7510 (ttt) REVERT: C 734 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8481 (t) REVERT: C 837 SER cc_start: 0.8867 (p) cc_final: 0.8640 (m) REVERT: C 865 LEU cc_start: 0.8564 (mp) cc_final: 0.8346 (mt) REVERT: C 890 LYS cc_start: 0.8346 (ptmt) cc_final: 0.8012 (ptmm) REVERT: C 899 GLU cc_start: 0.7659 (tt0) cc_final: 0.7076 (tm-30) REVERT: C 902 LEU cc_start: 0.8579 (tt) cc_final: 0.8349 (mp) REVERT: C 914 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7861 (ttpp) REVERT: C 1092 GLN cc_start: 0.8439 (tt0) cc_final: 0.8179 (tt0) REVERT: C 1140 LYS cc_start: 0.8330 (mtpp) cc_final: 0.8083 (mtpt) REVERT: C 1151 LEU cc_start: 0.8704 (tt) cc_final: 0.8465 (tp) REVERT: D 21 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8078 (tttm) REVERT: D 144 TYR cc_start: 0.8237 (m-80) cc_final: 0.7875 (m-10) REVERT: D 148 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7561 (mt-10) REVERT: D 180 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7112 (ttt) REVERT: D 204 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7510 (tm-30) REVERT: D 534 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: D 704 GLU cc_start: 0.7260 (pt0) cc_final: 0.6882 (pt0) REVERT: D 712 GLU cc_start: 0.7486 (mp0) cc_final: 0.7197 (mp0) REVERT: D 739 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: D 754 ILE cc_start: 0.8628 (mt) cc_final: 0.8413 (mm) REVERT: D 875 ASN cc_start: 0.6918 (m-40) cc_final: 0.6216 (t0) REVERT: D 1214 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7122 (mm-30) REVERT: D 1329 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8254 (mtm-85) REVERT: D 1333 GLU cc_start: 0.7909 (tp30) cc_final: 0.7575 (tp30) REVERT: D 1360 THR cc_start: 0.8734 (m) cc_final: 0.7347 (t) REVERT: A 86 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8472 (mtmm) REVERT: B 86 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8218 (tttt) REVERT: B 220 ARG cc_start: 0.8185 (mpt-90) cc_final: 0.7975 (mpt-90) REVERT: F 100 VAL cc_start: 0.7025 (OUTLIER) cc_final: 0.6810 (p) REVERT: F 102 MET cc_start: 0.7597 (mtp) cc_final: 0.7340 (mtp) REVERT: F 278 VAL cc_start: 0.8573 (t) cc_final: 0.8258 (m) REVERT: F 382 ARG cc_start: 0.7796 (ttp80) cc_final: 0.7247 (ttp80) REVERT: F 386 GLU cc_start: 0.8183 (tp30) cc_final: 0.7722 (tp30) REVERT: F 397 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8246 (p) REVERT: F 415 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7056 (tp30) REVERT: F 422 LYS cc_start: 0.8257 (tttm) cc_final: 0.8050 (tttm) REVERT: F 459 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7823 (ttp80) REVERT: F 462 VAL cc_start: 0.8601 (t) cc_final: 0.8381 (m) REVERT: F 484 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7551 (pmt170) REVERT: F 489 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7309 (tm-30) REVERT: F 490 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7581 (pt0) REVERT: F 601 LYS cc_start: 0.8338 (tttt) cc_final: 0.8083 (tttt) outliers start: 107 outliers final: 68 residues processed: 796 average time/residue: 0.7025 time to fit residues: 655.2985 Evaluate side-chains 825 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 742 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1249 SER Chi-restraints excluded: chain C residue 1251 SER Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1329 ARG Chi-restraints excluded: chain D residue 1369 GLN Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 484 ARG Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 516 GLU Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 575 MET Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 321 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 317 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 42 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN C 339 ASN C 450 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D 861 ASN D1234 ASN D1243 GLN B 84 ASN F 445 GLN F 480 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.171718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133573 restraints weight = 65879.310| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.59 r_work: 0.3485 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33599 Z= 0.154 Angle : 0.567 14.314 45949 Z= 0.302 Chirality : 0.042 0.287 5228 Planarity : 0.004 0.052 5510 Dihedral : 18.014 177.710 5715 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.27 % Allowed : 23.28 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.12 (0.14), residues: 3775 helix: 1.59 (0.13), residues: 1613 sheet: 0.64 (0.23), residues: 500 loop : 0.03 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 101 TYR 0.019 0.001 TYR D 631 PHE 0.024 0.001 PHE C 906 TRP 0.011 0.001 TRP H 68 HIS 0.005 0.001 HIS D1365 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (33591) covalent geometry : angle 0.56369 / 0.30 (45937) hydrogen bonds : bond 0.04169 / 2.76 ( 1550) hydrogen bonds : angle 4.25594 / 4.25 ( 4311) metal coordination : bond 0.00973 / 0.56 ( 8) metal coordination : angle 4.02029 / 2.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 754 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.7262 (mm) cc_final: 0.7047 (mp) REVERT: C 84 GLU cc_start: 0.7823 (pm20) cc_final: 0.7416 (pm20) REVERT: C 99 LYS cc_start: 0.8317 (mtmt) cc_final: 0.8087 (mtpp) REVERT: C 175 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7562 (ttm-80) REVERT: C 182 SER cc_start: 0.8571 (m) cc_final: 0.8196 (p) REVERT: C 192 ASP cc_start: 0.7754 (t0) cc_final: 0.7445 (t0) REVERT: C 194 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7762 (pp) REVERT: C 197 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7171 (mtt180) REVERT: C 470 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7667 (mtp180) REVERT: C 476 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7851 (ttmm) REVERT: C 503 LYS cc_start: 0.8669 (mtmt) cc_final: 0.8399 (mtpt) REVERT: C 515 MET cc_start: 0.7824 (ttt) cc_final: 0.7577 (ttt) REVERT: C 542 ARG cc_start: 0.7596 (mtp180) cc_final: 0.7186 (mtp180) REVERT: C 734 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8493 (t) REVERT: C 865 LEU cc_start: 0.8565 (mp) cc_final: 0.8344 (mt) REVERT: C 890 LYS cc_start: 0.8350 (ptmt) cc_final: 0.8015 (ptmm) REVERT: C 899 GLU cc_start: 0.7694 (tt0) cc_final: 0.7072 (tm-30) REVERT: C 902 LEU cc_start: 0.8558 (tt) cc_final: 0.8347 (mp) REVERT: C 914 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7911 (ttpp) REVERT: C 1092 GLN cc_start: 0.8440 (tt0) cc_final: 0.8185 (tt0) REVERT: C 1140 LYS cc_start: 0.8353 (mtpp) cc_final: 0.8128 (mtmm) REVERT: C 1151 LEU cc_start: 0.8713 (tt) cc_final: 0.8478 (tp) REVERT: D 144 TYR cc_start: 0.8253 (m-80) cc_final: 0.7925 (m-80) REVERT: D 148 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7627 (mt-10) REVERT: D 180 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7157 (ttt) REVERT: D 204 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7478 (tm-30) REVERT: D 430 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8655 (p90) REVERT: D 534 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7528 (tp30) REVERT: D 566 GLU cc_start: 0.7660 (pp20) cc_final: 0.7397 (pp20) REVERT: D 704 GLU cc_start: 0.7266 (pt0) cc_final: 0.6984 (pt0) REVERT: D 712 GLU cc_start: 0.7496 (mp0) cc_final: 0.7195 (mp0) REVERT: D 739 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: D 754 ILE cc_start: 0.8629 (mt) cc_final: 0.8402 (mm) REVERT: D 875 ASN cc_start: 0.6942 (m-40) cc_final: 0.6286 (t0) REVERT: D 1214 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7132 (mm-30) REVERT: D 1329 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8292 (mtt-85) REVERT: D 1333 GLU cc_start: 0.7969 (tp30) cc_final: 0.7634 (tp30) REVERT: D 1360 THR cc_start: 0.8732 (m) cc_final: 0.7349 (t) REVERT: A 86 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8500 (mtmm) REVERT: B 220 ARG cc_start: 0.8187 (mpt-90) cc_final: 0.7968 (mpt-90) REVERT: F 102 MET cc_start: 0.7637 (mtp) cc_final: 0.7392 (mtp) REVERT: F 278 VAL cc_start: 0.8521 (t) cc_final: 0.8216 (m) REVERT: F 386 GLU cc_start: 0.8198 (tp30) cc_final: 0.7865 (tp30) REVERT: F 388 VAL cc_start: 0.8558 (m) cc_final: 0.8342 (p) REVERT: F 397 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8270 (p) REVERT: F 398 ILE cc_start: 0.8619 (tt) cc_final: 0.8344 (tp) REVERT: F 415 GLU cc_start: 0.7825 (mm-30) cc_final: 0.6968 (tp30) REVERT: F 422 LYS cc_start: 0.8241 (tttm) cc_final: 0.8023 (tttm) REVERT: F 459 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7860 (ttp80) REVERT: F 462 VAL cc_start: 0.8623 (t) cc_final: 0.8400 (m) REVERT: F 489 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7313 (tm-30) REVERT: F 490 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7614 (pt0) REVERT: F 601 LYS cc_start: 0.8357 (tttt) cc_final: 0.8102 (tttt) outliers start: 107 outliers final: 65 residues processed: 797 average time/residue: 0.7164 time to fit residues: 668.1672 Evaluate side-chains 818 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 741 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain K residue 54 HIS Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1249 SER Chi-restraints excluded: chain C residue 1251 SER Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1329 ARG Chi-restraints excluded: chain D residue 1369 GLN Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 516 GLU Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 575 MET Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 274 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 72 optimal weight: 0.0970 chunk 305 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 326 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN D 805 GLN D 861 ASN D1234 ASN B 84 ASN F 445 GLN F 480 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.169360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132260 restraints weight = 72302.716| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.42 r_work: 0.3452 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 33599 Z= 0.286 Angle : 0.652 15.035 45949 Z= 0.343 Chirality : 0.047 0.301 5228 Planarity : 0.005 0.056 5510 Dihedral : 18.043 178.782 5715 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.30 % Allowed : 23.34 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 3775 helix: 1.30 (0.13), residues: 1624 sheet: 0.63 (0.23), residues: 476 loop : -0.12 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1169 TYR 0.024 0.002 TYR D 631 PHE 0.020 0.002 PHE C 186 TRP 0.020 0.002 TRP G 322 HIS 0.006 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.29 (33591) covalent geometry : angle 0.64539 / 0.34 (45937) hydrogen bonds : bond 0.05265 / 3.49 ( 1550) hydrogen bonds : angle 4.46665 / 4.42 ( 4311) metal coordination : bond 0.01639 / 0.91 ( 8) metal coordination : angle 5.91405 / 3.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 758 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 GLU cc_start: 0.7841 (pm20) cc_final: 0.7386 (pm20) REVERT: C 99 LYS cc_start: 0.8359 (mtmt) cc_final: 0.8122 (mtpp) REVERT: C 175 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7612 (ttm-80) REVERT: C 182 SER cc_start: 0.8615 (m) cc_final: 0.8257 (p) REVERT: C 192 ASP cc_start: 0.7761 (t0) cc_final: 0.7465 (t0) REVERT: C 194 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7765 (pp) REVERT: C 197 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7320 (mtt180) REVERT: C 470 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7725 (mtp180) REVERT: C 503 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8412 (mtpt) REVERT: C 515 MET cc_start: 0.7980 (ttt) cc_final: 0.7729 (ttt) REVERT: C 542 ARG cc_start: 0.7598 (mtp180) cc_final: 0.7198 (mtp180) REVERT: C 731 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8099 (mtm-85) REVERT: C 734 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8586 (t) REVERT: C 890 LYS cc_start: 0.8367 (ptmt) cc_final: 0.8041 (ptmm) REVERT: C 899 GLU cc_start: 0.7714 (tt0) cc_final: 0.7107 (tm-30) REVERT: C 902 LEU cc_start: 0.8606 (tt) cc_final: 0.8364 (mp) REVERT: C 914 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7895 (ttpp) REVERT: C 1092 GLN cc_start: 0.8413 (tt0) cc_final: 0.8171 (tt0) REVERT: C 1151 LEU cc_start: 0.8708 (tt) cc_final: 0.8466 (tp) REVERT: C 1199 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7703 (mp0) REVERT: D 144 TYR cc_start: 0.8301 (m-80) cc_final: 0.8023 (m-80) REVERT: D 180 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7253 (ttt) REVERT: D 201 MET cc_start: 0.8072 (mtm) cc_final: 0.7839 (mtm) REVERT: D 204 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7380 (tm-30) REVERT: D 298 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8121 (mtp) REVERT: D 430 HIS cc_start: 0.9011 (OUTLIER) cc_final: 0.8724 (p90) REVERT: D 566 GLU cc_start: 0.7705 (pp20) cc_final: 0.7477 (pp20) REVERT: D 704 GLU cc_start: 0.7305 (pt0) cc_final: 0.7032 (pt0) REVERT: D 712 GLU cc_start: 0.7485 (mp0) cc_final: 0.7192 (mp0) REVERT: D 739 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: D 747 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8136 (mmm) REVERT: D 754 ILE cc_start: 0.8676 (mt) cc_final: 0.8441 (mm) REVERT: D 861 ASN cc_start: 0.8197 (m-40) cc_final: 0.7929 (m110) REVERT: D 875 ASN cc_start: 0.7092 (m-40) cc_final: 0.6430 (t0) REVERT: D 1214 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7154 (mm-30) REVERT: D 1333 GLU cc_start: 0.7938 (tp30) cc_final: 0.7598 (tp30) REVERT: D 1360 THR cc_start: 0.8789 (m) cc_final: 0.8412 (p) REVERT: B 220 ARG cc_start: 0.8197 (mpt-90) cc_final: 0.7979 (mpt-90) REVERT: F 278 VAL cc_start: 0.8552 (t) cc_final: 0.8249 (m) REVERT: F 386 GLU cc_start: 0.8179 (tp30) cc_final: 0.7809 (tp30) REVERT: F 397 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8394 (p) REVERT: F 398 ILE cc_start: 0.8723 (tt) cc_final: 0.8443 (tp) REVERT: F 415 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7103 (tp30) REVERT: F 422 LYS cc_start: 0.8290 (tttm) cc_final: 0.8085 (tttm) REVERT: F 459 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7838 (ttp80) REVERT: F 489 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7347 (tm-30) REVERT: F 490 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7660 (pt0) REVERT: F 601 LYS cc_start: 0.8351 (tttt) cc_final: 0.8107 (tttt) outliers start: 108 outliers final: 67 residues processed: 800 average time/residue: 0.7217 time to fit residues: 675.6607 Evaluate side-chains 825 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 746 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain K residue 54 HIS Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 270 CYS Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1085 MET Chi-restraints excluded: chain C residue 1249 SER Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1369 GLN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 575 MET Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 362 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 374 optimal weight: 1.9990 chunk 246 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 216 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D1234 ASN D1243 GLN B 84 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.169959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131188 restraints weight = 69181.768| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.59 r_work: 0.3468 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 33599 Z= 0.257 Angle : 0.749 59.182 45949 Z= 0.413 Chirality : 0.046 0.825 5228 Planarity : 0.005 0.056 5510 Dihedral : 18.051 178.659 5715 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.69 % Allowed : 24.56 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.85 (0.14), residues: 3775 helix: 1.33 (0.13), residues: 1618 sheet: 0.62 (0.23), residues: 476 loop : -0.13 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1148 TYR 0.023 0.002 TYR D 631 PHE 0.019 0.002 PHE C 186 TRP 0.072 0.003 TRP G 322 HIS 0.006 0.001 HIS D1365 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.26 (33591) covalent geometry : angle 0.74314 / 0.41 (45937) hydrogen bonds : bond 0.05143 / 3.40 ( 1550) hydrogen bonds : angle 4.46826 / 4.42 ( 4311) metal coordination : bond 0.01596 / 0.90 ( 8) metal coordination : angle 5.98790 / 3.07 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 744 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 GLU cc_start: 0.7828 (pm20) cc_final: 0.7370 (pm20) REVERT: C 99 LYS cc_start: 0.8354 (mtmt) cc_final: 0.8132 (mtpp) REVERT: C 175 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7656 (ttm-80) REVERT: C 182 SER cc_start: 0.8598 (m) cc_final: 0.8240 (p) REVERT: C 192 ASP cc_start: 0.7752 (t0) cc_final: 0.7461 (t0) REVERT: C 194 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7772 (pp) REVERT: C 197 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7329 (mtt180) REVERT: C 470 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7698 (mtp180) REVERT: C 503 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8397 (mtpt) REVERT: C 515 MET cc_start: 0.7976 (ttt) cc_final: 0.7726 (ttt) REVERT: C 542 ARG cc_start: 0.7670 (mtp180) cc_final: 0.7258 (mtp180) REVERT: C 618 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: C 731 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8098 (mtm-85) REVERT: C 734 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8585 (t) REVERT: C 890 LYS cc_start: 0.8358 (ptmt) cc_final: 0.8032 (ptmm) REVERT: C 899 GLU cc_start: 0.7721 (tt0) cc_final: 0.7097 (tm-30) REVERT: C 902 LEU cc_start: 0.8589 (tt) cc_final: 0.8362 (mp) REVERT: C 914 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7898 (ttpp) REVERT: C 1092 GLN cc_start: 0.8416 (tt0) cc_final: 0.8174 (tt0) REVERT: C 1151 LEU cc_start: 0.8710 (tt) cc_final: 0.8473 (tp) REVERT: C 1199 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7718 (mp0) REVERT: D 144 TYR cc_start: 0.8282 (m-80) cc_final: 0.8001 (m-80) REVERT: D 180 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7295 (ttt) REVERT: D 204 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7477 (tm-30) REVERT: D 298 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8115 (mtp) REVERT: D 430 HIS cc_start: 0.9014 (OUTLIER) cc_final: 0.8727 (p90) REVERT: D 566 GLU cc_start: 0.7741 (pp20) cc_final: 0.7520 (pp20) REVERT: D 704 GLU cc_start: 0.7303 (pt0) cc_final: 0.7029 (pt0) REVERT: D 712 GLU cc_start: 0.7494 (mp0) cc_final: 0.7091 (pm20) REVERT: D 739 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: D 747 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8148 (mmm) REVERT: D 754 ILE cc_start: 0.8680 (mt) cc_final: 0.8450 (mm) REVERT: D 875 ASN cc_start: 0.7099 (m-40) cc_final: 0.6438 (t0) REVERT: D 1214 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7150 (mm-30) REVERT: D 1333 GLU cc_start: 0.7910 (tp30) cc_final: 0.7581 (tp30) REVERT: D 1360 THR cc_start: 0.8783 (m) cc_final: 0.8410 (p) REVERT: B 220 ARG cc_start: 0.8247 (mpt-90) cc_final: 0.8028 (mpt-90) REVERT: F 278 VAL cc_start: 0.8569 (t) cc_final: 0.8257 (m) REVERT: F 386 GLU cc_start: 0.8161 (tp30) cc_final: 0.7788 (tp30) REVERT: F 397 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8387 (p) REVERT: F 398 ILE cc_start: 0.8712 (tt) cc_final: 0.8429 (tp) REVERT: F 415 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7105 (tp30) REVERT: F 422 LYS cc_start: 0.8285 (tttm) cc_final: 0.8077 (tttm) REVERT: F 459 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8053 (ttp80) REVERT: F 489 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7386 (tm-30) REVERT: F 490 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7609 (pt0) REVERT: F 601 LYS cc_start: 0.8320 (tttt) cc_final: 0.7942 (tttt) outliers start: 88 outliers final: 69 residues processed: 779 average time/residue: 0.7568 time to fit residues: 689.4576 Evaluate side-chains 824 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 742 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain K residue 54 HIS Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1085 MET Chi-restraints excluded: chain C residue 1249 SER Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1369 GLN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 575 MET Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 56 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 317 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 111 optimal weight: 0.5980 chunk 226 optimal weight: 1.9990 chunk 357 optimal weight: 5.9990 chunk 387 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1234 ASN B 84 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.169690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131243 restraints weight = 60107.368| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.27 r_work: 0.3494 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 33599 Z= 0.258 Angle : 0.749 59.182 45949 Z= 0.413 Chirality : 0.046 0.825 5228 Planarity : 0.005 0.056 5510 Dihedral : 18.051 178.659 5715 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.54 % Allowed : 24.63 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.85 (0.14), residues: 3775 helix: 1.33 (0.13), residues: 1618 sheet: 0.62 (0.23), residues: 476 loop : -0.13 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1148 TYR 0.023 0.002 TYR D 631 PHE 0.019 0.002 PHE C 186 TRP 0.072 0.003 TRP G 322 HIS 0.006 0.001 HIS D1365 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.26 (33591) covalent geometry : angle 0.74314 / 0.41 (45937) hydrogen bonds : bond 0.05143 / 3.40 ( 1550) hydrogen bonds : angle 4.46826 / 4.42 ( 4311) metal coordination : bond 0.02061 / 1.13 ( 8) metal coordination : angle 6.07066 / 3.11 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17785.47 seconds wall clock time: 301 minutes 16.30 seconds (18076.30 seconds total)