Starting phenix.real_space_refine on Sat Feb 7 13:09:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdr_51276/02_2026/9gdr_51276.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdr_51276/02_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_51276/02_2026/9gdr_51276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdr_51276/02_2026/9gdr_51276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gdr_51276/02_2026/9gdr_51276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdr_51276/02_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 9.45, per 1000 atoms: 0.29 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: 3.32 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: 4.44 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: 8.57 Time building geometry restraints manager: 4.22 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=" N VAL C 212 " pdb=" CA VAL C 212 " ideal model delta sigma weight residual 1.461 1.488 -0.027 1.19e-02 7.06e+03 5.28e+00 bond pdb=" CB VAL F 395 " pdb=" CG2 VAL F 395 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.60e+00 bond pdb=" N PHE C 385 " pdb=" CA PHE C 385 " ideal model delta sigma weight residual 1.458 1.481 -0.022 1.26e-02 6.30e+03 3.18e+00 bond pdb=" C VAL C 212 " pdb=" N LEU C 213 " ideal model delta sigma weight residual 1.333 1.309 0.025 1.49e-02 4.50e+03 2.70e+00 bond pdb=" C ALA C1043 " pdb=" N PRO C1044 " ideal model delta sigma weight residual 1.331 1.349 -0.018 1.20e-02 6.94e+03 2.24e+00 ... (remaining 33586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 45132 2.14 - 4.28: 704 4.28 - 6.43: 82 6.43 - 8.57: 13 8.57 - 10.71: 6 Bond angle restraints: 45937 Sorted by residual: 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=" C ILE C 176 " pdb=" N ILE C 177 " pdb=" CA ILE C 177 " ideal model delta sigma weight residual 122.85 126.27 -3.42 8.70e-01 1.32e+00 1.54e+01 angle pdb=" N PHE C 385 " pdb=" CA PHE C 385 " pdb=" CB PHE C 385 " ideal model delta sigma weight residual 110.20 115.95 -5.75 1.49e+00 4.50e-01 1.49e+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: 4523 0.063 - 0.125: 675 0.125 - 0.188: 27 0.188 - 0.250: 2 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=" CG LEU G 271 " pdb=" CB LEU G 271 " pdb=" CD1 LEU G 271 " pdb=" CD2 LEU G 271 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+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: 11.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 42.670 Find NCS groups from input model: 0.300 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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= 0.171 Angle : 0.648 10.709 45949 Z= 0.348 Chirality : 0.043 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 covalent geometry : bond 0.00391 (33591) covalent geometry : angle 0.64378 (45937) hydrogen bonds : bond 0.12291 ( 1550) hydrogen bonds : angle 5.68613 ( 4311) metal coordination : bond 0.00917 ( 8) metal coordination : angle 4.63013 ( 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 : 1.186 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: 0.8640 time to fit residues: 748.1002 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 : 1.197 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 D 929 GLN D1217 HIS A 75 GLN F 238 ASN F 472 ASN F 477 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.168308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129416 restraints weight = 73198.211| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.63 r_work: 0.3469 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 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 = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 33599 Z= 0.257 Angle : 0.637 12.196 45949 Z= 0.341 Chirality : 0.045 0.290 5228 Planarity : 0.005 0.052 5510 Dihedral : 18.063 177.480 5730 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.53 % Allowed : 20.77 % Favored : 74.70 % 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: 0.77 (0.13), residues: 3775 helix: 1.19 (0.13), residues: 1603 sheet: 0.76 (0.24), residues: 442 loop : -0.12 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 101 TYR 0.023 0.002 TYR D 631 PHE 0.024 0.002 PHE C 514 TRP 0.018 0.001 TRP K 15 HIS 0.011 0.001 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00599 (33591) covalent geometry : angle 0.63180 (45937) hydrogen bonds : bond 0.05189 ( 1550) hydrogen bonds : angle 4.67674 ( 4311) metal coordination : bond 0.01431 ( 8) metal coordination : angle 5.27836 ( 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 929 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 781 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.7114 (mm) cc_final: 0.6863 (mp) REVERT: H 43 GLN cc_start: 0.7821 (mt0) cc_final: 0.7422 (mt0) REVERT: K 48 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7088 (tptt) REVERT: K 63 ILE cc_start: 0.7866 (tt) cc_final: 0.7622 (pt) REVERT: G 291 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7684 (tt) REVERT: C 44 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7395 (mp0) REVERT: C 187 GLU cc_start: 0.7376 (pt0) cc_final: 0.6850 (pt0) REVERT: C 197 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7040 (mtt90) REVERT: C 622 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8160 (mmmm) REVERT: C 734 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8550 (t) REVERT: C 837 SER cc_start: 0.8902 (p) cc_final: 0.8673 (m) REVERT: C 849 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: C 890 LYS cc_start: 0.8377 (ptmt) cc_final: 0.8041 (ptmm) REVERT: C 899 GLU cc_start: 0.7648 (tt0) cc_final: 0.7133 (tm-30) REVERT: C 914 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7897 (ttpp) REVERT: C 1092 GLN cc_start: 0.8443 (tt0) cc_final: 0.8178 (tt0) REVERT: C 1151 LEU cc_start: 0.8726 (tt) cc_final: 0.8481 (tp) REVERT: C 1159 ASP cc_start: 0.7571 (p0) cc_final: 0.7052 (p0) REVERT: C 1199 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7852 (mp0) REVERT: C 1215 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7829 (mtm180) REVERT: D 148 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7594 (mt-10) REVERT: D 180 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7307 (ttt) REVERT: D 204 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7421 (tm-30) REVERT: D 213 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7588 (mtpp) REVERT: D 219 LYS cc_start: 0.8326 (mtpp) cc_final: 0.8117 (mtmm) REVERT: D 298 MET cc_start: 0.8412 (mmm) cc_final: 0.7473 (mtm) REVERT: D 330 MET cc_start: 0.8504 (mmm) cc_final: 0.8053 (mtm) REVERT: D 388 ARG cc_start: 0.8416 (ptp90) cc_final: 0.8136 (ptp-170) REVERT: D 414 GLU cc_start: 0.7988 (tt0) cc_final: 0.7726 (tt0) REVERT: D 430 HIS cc_start: 0.9004 (OUTLIER) cc_final: 0.8661 (p90) REVERT: D 688 SER cc_start: 0.8136 (m) cc_final: 0.7802 (p) REVERT: D 704 GLU cc_start: 0.7209 (pt0) cc_final: 0.6922 (pt0) REVERT: D 712 GLU cc_start: 0.7405 (mp0) cc_final: 0.7047 (pm20) REVERT: D 738 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8033 (ttm170) REVERT: D 739 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: D 754 ILE cc_start: 0.8722 (mt) cc_final: 0.8503 (mm) REVERT: D 785 ASP cc_start: 0.7694 (t0) cc_final: 0.7390 (t0) REVERT: D 1329 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8273 (mtt-85) REVERT: D 1333 GLU cc_start: 0.7951 (tp30) cc_final: 0.7640 (tp30) REVERT: A 75 GLN cc_start: 0.8389 (tt0) cc_final: 0.8187 (tt0) REVERT: B 149 ARG cc_start: 0.8430 (ttp-170) cc_final: 0.8088 (ttm170) REVERT: F 100 VAL cc_start: 0.6902 (OUTLIER) cc_final: 0.6635 (p) REVERT: F 102 MET cc_start: 0.7489 (mtp) cc_final: 0.7199 (mtp) REVERT: F 386 GLU cc_start: 0.8252 (tp30) cc_final: 0.7886 (tp30) REVERT: F 393 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7888 (ttm170) REVERT: F 397 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8286 (p) REVERT: F 415 GLU cc_start: 0.7783 (mm-30) cc_final: 0.6943 (tp30) REVERT: F 445 GLN cc_start: 0.8314 (tm-30) cc_final: 0.8102 (tm130) REVERT: F 459 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7614 (ttp80) REVERT: F 489 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7304 (tm-30) REVERT: F 493 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: F 603 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8185 (mp) REVERT: F 616 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.7276 (ttm110) outliers start: 148 outliers final: 53 residues processed: 849 average time/residue: 0.7582 time to fit residues: 749.9662 Evaluate side-chains 799 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 730 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain K residue 48 LYS 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 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 197 ARG 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 471 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 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 1085 MET 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 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 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 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 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 1215 SER Chi-restraints excluded: chain D residue 1329 ARG 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 118 HIS Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 134 SER 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 493 GLU Chi-restraints excluded: chain F residue 535 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 132 optimal weight: 1.9990 chunk 328 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 143 optimal weight: 0.3980 chunk 278 optimal weight: 0.6980 chunk 371 optimal weight: 0.2980 chunk 284 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 299 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN D 80 HIS D 335 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN D1243 GLN F 353 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 = 0.4207 r_free = 0.4207 target = 0.170417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.132486 restraints weight = 71643.551| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.53 r_work: 0.3515 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 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 = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33599 Z= 0.130 Angle : 0.542 10.009 45949 Z= 0.292 Chirality : 0.041 0.209 5228 Planarity : 0.004 0.047 5510 Dihedral : 17.934 175.664 5720 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.12 % Allowed : 22.24 % Favored : 74.64 % 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: 1.08 (0.14), residues: 3775 helix: 1.52 (0.13), residues: 1601 sheet: 0.74 (0.23), residues: 475 loop : 0.02 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 101 TYR 0.017 0.001 TYR D 631 PHE 0.018 0.001 PHE C 906 TRP 0.012 0.001 TRP K 15 HIS 0.005 0.001 HIS D1365 Details of bonding type rmsd covalent geometry : bond 0.00291 (33591) covalent geometry : angle 0.53854 (45937) hydrogen bonds : bond 0.04057 ( 1550) hydrogen bonds : angle 4.35677 ( 4311) metal coordination : bond 0.00631 ( 8) metal coordination : angle 3.63986 ( 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 868 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 766 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.7136 (mm) cc_final: 0.6908 (mp) REVERT: K 48 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7118 (tptt) REVERT: C 44 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7296 (mp0) REVERT: C 84 GLU cc_start: 0.7813 (pm20) cc_final: 0.7508 (pm20) REVERT: C 99 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7944 (mtpp) REVERT: C 175 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7554 (ttm-80) REVERT: C 192 ASP cc_start: 0.7694 (t0) cc_final: 0.7427 (t0) REVERT: C 194 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7797 (pp) REVERT: C 476 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7866 (ttmm) REVERT: C 545 PHE cc_start: 0.7100 (t80) cc_final: 0.6886 (t80) REVERT: C 622 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8183 (mmmm) REVERT: C 734 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8518 (t) REVERT: C 837 SER cc_start: 0.8875 (p) cc_final: 0.8671 (m) REVERT: C 849 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: C 890 LYS cc_start: 0.8324 (ptmt) cc_final: 0.8017 (ptmm) REVERT: C 899 GLU cc_start: 0.7692 (tt0) cc_final: 0.7164 (tm-30) REVERT: C 902 LEU cc_start: 0.8629 (tt) cc_final: 0.8385 (mp) REVERT: C 914 LYS cc_start: 0.8221 (ttpp) cc_final: 0.7933 (ttpp) REVERT: C 1053 TYR cc_start: 0.8608 (m-80) cc_final: 0.8339 (m-80) REVERT: C 1151 LEU cc_start: 0.8710 (tt) cc_final: 0.8475 (tp) REVERT: C 1249 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.7991 (m) REVERT: D 144 TYR cc_start: 0.8203 (m-80) cc_final: 0.7945 (m-80) REVERT: D 148 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7553 (mt-10) REVERT: D 180 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7165 (ttt) REVERT: D 204 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7575 (tm-30) REVERT: D 330 MET cc_start: 0.8473 (mmm) cc_final: 0.8034 (mtm) REVERT: D 414 GLU cc_start: 0.7954 (tt0) cc_final: 0.7653 (tt0) REVERT: D 704 GLU cc_start: 0.7167 (pt0) cc_final: 0.6907 (pt0) REVERT: D 712 GLU cc_start: 0.7435 (mp0) cc_final: 0.7106 (pm20) REVERT: D 739 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: D 754 ILE cc_start: 0.8668 (mt) cc_final: 0.8466 (mm) REVERT: D 1221 ARG cc_start: 0.8475 (ttm170) cc_final: 0.8258 (ttm110) REVERT: D 1333 GLU cc_start: 0.7907 (tp30) cc_final: 0.7615 (tp30) REVERT: D 1360 THR cc_start: 0.8703 (m) cc_final: 0.7290 (t) REVERT: A 86 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8480 (mtmm) REVERT: F 100 VAL cc_start: 0.6990 (OUTLIER) cc_final: 0.6719 (p) REVERT: F 102 MET cc_start: 0.7419 (mtp) cc_final: 0.7112 (mtp) REVERT: F 278 VAL cc_start: 0.8607 (t) cc_final: 0.8261 (m) REVERT: F 386 GLU cc_start: 0.8185 (tp30) cc_final: 0.7846 (tp30) REVERT: F 397 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8239 (p) REVERT: F 415 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6929 (tp30) REVERT: F 422 LYS cc_start: 0.8149 (tttm) cc_final: 0.7941 (tttm) REVERT: F 445 GLN cc_start: 0.8217 (tm-30) cc_final: 0.8008 (tm130) REVERT: F 451 ILE cc_start: 0.8613 (tt) cc_final: 0.8401 (tt) REVERT: F 459 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7671 (ttp80) REVERT: F 462 VAL cc_start: 0.8645 (t) cc_final: 0.8395 (m) REVERT: F 489 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7318 (tm-30) REVERT: F 601 LYS cc_start: 0.8280 (tttt) cc_final: 0.7276 (tttt) outliers start: 102 outliers final: 44 residues processed: 805 average time/residue: 0.8623 time to fit residues: 804.1541 Evaluate side-chains 798 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 742 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain K residue 48 LYS 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 79 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 194 LEU Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 603 VAL 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 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 1249 SER Chi-restraints excluded: chain C residue 1251 SER Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 291 ILE 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 710 GLN Chi-restraints excluded: chain D residue 713 GLN Chi-restraints excluded: chain D residue 739 GLN 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 1238 GLU 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 196 ARG Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 ILE 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 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 608 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 114 optimal weight: 0.0870 chunk 359 optimal weight: 40.0000 chunk 104 optimal weight: 1.9990 chunk 354 optimal weight: 7.9990 chunk 273 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 374 optimal weight: 0.5980 chunk 363 optimal weight: 7.9990 chunk 292 optimal weight: 0.0040 chunk 109 optimal weight: 0.8980 chunk 288 optimal weight: 3.9990 overall best weight: 0.7172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 21 ASN ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 ASN C 450 ASN C1256 GLN D 716 GLN D 805 GLN D 861 ASN B 84 ASN F 454 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.172051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133717 restraints weight = 64036.804| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.55 r_work: 0.3495 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33599 Z= 0.164 Angle : 0.557 14.160 45949 Z= 0.296 Chirality : 0.042 0.186 5228 Planarity : 0.004 0.047 5510 Dihedral : 17.845 175.558 5717 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.36 % Allowed : 22.91 % Favored : 73.72 % 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: 1.56 (0.13), residues: 1601 sheet: 0.75 (0.23), residues: 470 loop : 0.01 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1169 TYR 0.020 0.001 TYR D 631 PHE 0.022 0.001 PHE C 390 TRP 0.010 0.001 TRP K 15 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00378 (33591) covalent geometry : angle 0.55313 (45937) hydrogen bonds : bond 0.04196 ( 1550) hydrogen bonds : angle 4.30759 ( 4311) metal coordination : bond 0.00913 ( 8) metal coordination : angle 3.98791 ( 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: 110 poor density : 764 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.7190 (mm) cc_final: 0.6965 (mp) REVERT: K 48 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7085 (tptt) REVERT: C 44 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7288 (mp0) REVERT: C 84 GLU cc_start: 0.7815 (pm20) cc_final: 0.7488 (pm20) REVERT: C 122 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8142 (p) REVERT: C 175 ARG cc_start: 0.7805 (ttm110) cc_final: 0.7542 (ttm-80) REVERT: C 192 ASP cc_start: 0.7757 (t0) cc_final: 0.7454 (t0) REVERT: C 194 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7760 (pp) REVERT: C 470 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7659 (mtp180) REVERT: C 476 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7789 (ttmm) REVERT: C 618 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7419 (mt0) REVERT: C 622 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8127 (mmmm) REVERT: C 734 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8502 (t) REVERT: C 837 SER cc_start: 0.8882 (p) cc_final: 0.8650 (m) REVERT: C 899 GLU cc_start: 0.7660 (tt0) cc_final: 0.7132 (tm-30) REVERT: C 902 LEU cc_start: 0.8558 (tt) cc_final: 0.8313 (mp) REVERT: C 914 LYS cc_start: 0.8213 (ttpp) cc_final: 0.7929 (ttpp) REVERT: C 1151 LEU cc_start: 0.8698 (tt) cc_final: 0.8454 (tp) REVERT: D 128 MET cc_start: 0.8448 (ptp) cc_final: 0.8244 (ptm) REVERT: D 144 TYR cc_start: 0.8202 (m-80) cc_final: 0.7914 (m-80) REVERT: D 148 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7566 (mt-10) REVERT: D 180 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7168 (ttt) REVERT: D 204 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7548 (tm-30) REVERT: D 704 GLU cc_start: 0.7180 (pt0) cc_final: 0.6899 (pt0) REVERT: D 712 GLU cc_start: 0.7470 (mp0) cc_final: 0.7081 (pm20) REVERT: D 739 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: D 754 ILE cc_start: 0.8668 (mt) cc_final: 0.8440 (mm) REVERT: D 1214 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7047 (mt-10) REVERT: D 1333 GLU cc_start: 0.7935 (tp30) cc_final: 0.7613 (tp30) REVERT: D 1360 THR cc_start: 0.8741 (m) cc_final: 0.7386 (t) REVERT: B 86 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8349 (tttt) REVERT: F 100 VAL cc_start: 0.6989 (OUTLIER) cc_final: 0.6755 (p) REVERT: F 102 MET cc_start: 0.7523 (mtp) cc_final: 0.7222 (mtp) REVERT: F 278 VAL cc_start: 0.8542 (t) cc_final: 0.8205 (m) REVERT: F 386 GLU cc_start: 0.8134 (tp30) cc_final: 0.7846 (tp30) REVERT: F 388 VAL cc_start: 0.8514 (p) cc_final: 0.8312 (m) REVERT: F 415 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6908 (tp30) REVERT: F 422 LYS cc_start: 0.8169 (tttm) cc_final: 0.7958 (tttm) REVERT: F 459 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7936 (ttp80) REVERT: F 462 VAL cc_start: 0.8635 (t) cc_final: 0.8401 (m) REVERT: F 489 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7359 (tm-30) REVERT: F 490 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7598 (pt0) REVERT: F 569 MET cc_start: 0.7495 (ttm) cc_final: 0.7220 (ttm) outliers start: 110 outliers final: 56 residues processed: 804 average time/residue: 0.8510 time to fit residues: 794.1425 Evaluate side-chains 812 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 745 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain K residue 48 LYS 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 C residue 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 122 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 470 ARG Chi-restraints excluded: chain C residue 488 MET 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 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 133 ARG Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 291 ILE 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 567 THR Chi-restraints excluded: chain D residue 569 MET 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 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 A residue 196 ARG Chi-restraints excluded: chain B residue 29 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 187 SER Chi-restraints excluded: chain B residue 198 ASP 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 459 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 590 VAL Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 617 SER 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: 0.0980 chunk 195 optimal weight: 0.3980 chunk 321 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.0770 chunk 173 optimal weight: 0.9990 chunk 379 optimal weight: 0.9980 chunk 371 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 227 optimal weight: 0.6980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1311 ASN D 489 ASN D 805 GLN D 861 ASN D 875 ASN B 84 ASN 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 = 0.4223 r_free = 0.4223 target = 0.173129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.133842 restraints weight = 80492.227| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.88 r_work: 0.3482 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- 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 = 0.42 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33599 Z= 0.121 Angle : 0.531 13.387 45949 Z= 0.283 Chirality : 0.040 0.216 5228 Planarity : 0.004 0.047 5510 Dihedral : 17.762 175.504 5717 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.43 % Allowed : 22.67 % Favored : 73.91 % 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: 1.22 (0.14), residues: 3775 helix: 1.68 (0.13), residues: 1607 sheet: 0.72 (0.23), residues: 480 loop : 0.08 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1148 TYR 0.017 0.001 TYR D 631 PHE 0.025 0.001 PHE C 906 TRP 0.013 0.001 TRP D 172 HIS 0.004 0.000 HIS D1365 Details of bonding type rmsd covalent geometry : bond 0.00271 (33591) covalent geometry : angle 0.52856 (45937) hydrogen bonds : bond 0.03726 ( 1550) hydrogen bonds : angle 4.16968 ( 4311) metal coordination : bond 0.00634 ( 8) metal coordination : angle 3.39249 ( 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 879 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 767 time to evaluate : 1.178 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: 0.7217 (mm) cc_final: 0.6969 (mp) REVERT: C 44 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7348 (mp0) REVERT: C 84 GLU cc_start: 0.7852 (pm20) cc_final: 0.7492 (pm20) REVERT: C 99 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8070 (mtpp) REVERT: C 175 ARG cc_start: 0.7829 (ttm110) cc_final: 0.7560 (ttm-80) REVERT: C 194 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7720 (pp) REVERT: C 470 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7711 (mtp180) REVERT: C 545 PHE cc_start: 0.7174 (t80) cc_final: 0.6913 (t80) REVERT: C 563 THR cc_start: 0.8603 (p) cc_final: 0.8376 (t) REVERT: C 583 GLU cc_start: 0.7975 (pt0) cc_final: 0.7769 (pm20) REVERT: C 618 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7184 (mt0) REVERT: C 622 LYS cc_start: 0.8472 (mtmt) cc_final: 0.8145 (mmmm) REVERT: C 734 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8486 (t) REVERT: C 890 LYS cc_start: 0.8322 (ptmt) cc_final: 0.8039 (ptmm) REVERT: C 899 GLU cc_start: 0.7723 (tt0) cc_final: 0.7098 (tm-30) REVERT: C 902 LEU cc_start: 0.8550 (tt) cc_final: 0.8321 (mp) REVERT: C 914 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7965 (ttpp) REVERT: C 1140 LYS cc_start: 0.8361 (mtpp) cc_final: 0.8154 (mtmm) REVERT: C 1151 LEU cc_start: 0.8732 (tt) cc_final: 0.8499 (tp) REVERT: D 144 TYR cc_start: 0.8240 (m-80) cc_final: 0.7920 (m-80) REVERT: D 148 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7577 (mt-10) REVERT: D 180 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7096 (ttt) REVERT: D 204 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7551 (tm-30) REVERT: D 704 GLU cc_start: 0.7310 (pt0) cc_final: 0.6912 (pt0) REVERT: D 712 GLU cc_start: 0.7497 (mp0) cc_final: 0.7132 (pm20) REVERT: D 739 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: D 754 ILE cc_start: 0.8645 (mt) cc_final: 0.8430 (mm) REVERT: D 875 ASN cc_start: 0.6894 (m-40) cc_final: 0.6277 (t0) REVERT: D 1214 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7153 (mm-30) REVERT: D 1333 GLU cc_start: 0.8027 (tp30) cc_final: 0.7698 (tp30) REVERT: D 1360 THR cc_start: 0.8759 (m) cc_final: 0.7364 (t) REVERT: A 86 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8488 (mtmm) REVERT: B 58 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: B 86 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8327 (tttt) REVERT: F 100 VAL cc_start: 0.6998 (OUTLIER) cc_final: 0.6711 (p) REVERT: F 102 MET cc_start: 0.7573 (mtp) cc_final: 0.7323 (mtp) REVERT: F 278 VAL cc_start: 0.8528 (t) cc_final: 0.8216 (m) REVERT: F 386 GLU cc_start: 0.8173 (tp30) cc_final: 0.7844 (tp30) REVERT: F 415 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7054 (tp30) REVERT: F 422 LYS cc_start: 0.8203 (tttm) cc_final: 0.7990 (tttm) REVERT: F 459 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7852 (ttp80) REVERT: F 462 VAL cc_start: 0.8651 (t) cc_final: 0.8409 (m) REVERT: F 489 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7376 (tm-30) REVERT: F 490 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7614 (pt0) REVERT: F 549 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8348 (ttmm) outliers start: 112 outliers final: 54 residues processed: 813 average time/residue: 0.8585 time to fit residues: 810.6054 Evaluate side-chains 805 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 739 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 82 ILE 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 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 79 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 194 LEU 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 589 THR Chi-restraints excluded: chain C residue 618 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 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 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 291 ILE Chi-restraints excluded: chain D residue 394 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 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 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 1188 MET 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 196 ARG Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 65 LEU 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 212 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 459 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 590 VAL Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 617 SER 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: 2.9990 chunk 238 optimal weight: 0.9990 chunk 341 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 chunk 310 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 373 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 357 optimal weight: 9.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN D 335 GLN D 805 GLN D 861 ASN D1243 GLN A 75 GLN B 84 ASN F 454 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.170810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.132335 restraints weight = 60059.025| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.26 r_work: 0.3489 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 33599 Z= 0.202 Angle : 0.579 13.702 45949 Z= 0.306 Chirality : 0.043 0.191 5228 Planarity : 0.004 0.052 5510 Dihedral : 17.722 176.112 5715 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.40 % Allowed : 23.00 % Favored : 73.60 % 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: 1.07 (0.14), residues: 3775 helix: 1.53 (0.13), residues: 1620 sheet: 0.69 (0.24), residues: 457 loop : -0.00 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1169 TYR 0.024 0.001 TYR C 123 PHE 0.015 0.001 PHE C 186 TRP 0.009 0.001 TRP D 580 HIS 0.004 0.001 HIS D1365 Details of bonding type rmsd covalent geometry : bond 0.00470 (33591) covalent geometry : angle 0.57397 (45937) hydrogen bonds : bond 0.04487 ( 1550) hydrogen bonds : angle 4.28380 ( 4311) metal coordination : bond 0.01147 ( 8) metal coordination : angle 4.52860 ( 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 866 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 755 time to evaluate : 1.151 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 82 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7597 (mp) REVERT: C 44 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7469 (mp0) REVERT: C 84 GLU cc_start: 0.8036 (pm20) cc_final: 0.7594 (pm20) REVERT: C 99 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8200 (mtpp) REVERT: C 122 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8314 (p) REVERT: C 175 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7879 (ttm-80) REVERT: C 182 SER cc_start: 0.8619 (m) cc_final: 0.8290 (p) REVERT: C 194 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7821 (pp) REVERT: C 470 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7883 (mtp180) REVERT: C 476 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8147 (ttpp) REVERT: C 503 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8590 (mtpt) REVERT: C 515 MET cc_start: 0.8095 (ttt) cc_final: 0.7827 (ttt) REVERT: C 545 PHE cc_start: 0.7481 (t80) cc_final: 0.7157 (t80) REVERT: C 622 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8235 (mmmm) REVERT: C 734 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8627 (t) REVERT: C 890 LYS cc_start: 0.8406 (ptmt) cc_final: 0.8134 (ptmm) REVERT: C 899 GLU cc_start: 0.7947 (tt0) cc_final: 0.7274 (tm-30) REVERT: C 902 LEU cc_start: 0.8692 (tt) cc_final: 0.8474 (mp) REVERT: C 914 LYS cc_start: 0.8316 (ttpp) cc_final: 0.8048 (ttpp) REVERT: C 1140 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8343 (mtmm) REVERT: C 1151 LEU cc_start: 0.8819 (tt) cc_final: 0.8579 (tp) REVERT: D 144 TYR cc_start: 0.8412 (m-80) cc_final: 0.8137 (m-80) REVERT: D 148 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7783 (mt-10) REVERT: D 180 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7483 (ttt) REVERT: D 204 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7487 (tm-30) REVERT: D 213 LYS cc_start: 0.8069 (mtpp) cc_final: 0.7668 (mtpp) REVERT: D 298 MET cc_start: 0.8494 (mtp) cc_final: 0.8223 (mtp) REVERT: D 430 HIS cc_start: 0.9065 (OUTLIER) cc_final: 0.8771 (p90) REVERT: D 566 GLU cc_start: 0.7933 (pp20) cc_final: 0.7688 (pp20) REVERT: D 704 GLU cc_start: 0.7578 (pt0) cc_final: 0.7282 (pt0) REVERT: D 712 GLU cc_start: 0.7606 (mp0) cc_final: 0.7188 (pm20) REVERT: D 739 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: D 754 ILE cc_start: 0.8769 (mt) cc_final: 0.8551 (mm) REVERT: D 875 ASN cc_start: 0.7155 (m-40) cc_final: 0.6497 (t0) REVERT: D 1214 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7316 (mm-30) REVERT: D 1333 GLU cc_start: 0.8239 (tp30) cc_final: 0.7918 (tp30) REVERT: D 1360 THR cc_start: 0.8853 (m) cc_final: 0.8409 (p) REVERT: B 58 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: B 86 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8437 (tttt) REVERT: F 102 MET cc_start: 0.7707 (mtp) cc_final: 0.7488 (mtp) REVERT: F 278 VAL cc_start: 0.8536 (t) cc_final: 0.8219 (m) REVERT: F 385 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8335 (tttp) REVERT: F 386 GLU cc_start: 0.8339 (tp30) cc_final: 0.7994 (tp30) REVERT: F 388 VAL cc_start: 0.8664 (m) cc_final: 0.8448 (p) REVERT: F 415 GLU cc_start: 0.8062 (mm-30) cc_final: 0.6980 (tp30) REVERT: F 459 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7941 (ttp80) REVERT: F 489 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7533 (tm-30) REVERT: F 490 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7677 (pt0) REVERT: F 589 ASP cc_start: 0.5836 (p0) cc_final: 0.5633 (p0) REVERT: F 593 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6651 (mm-30) REVERT: F 604 ARG cc_start: 0.8268 (mtm-85) cc_final: 0.8024 (mtm-85) outliers start: 111 outliers final: 61 residues processed: 799 average time/residue: 0.8484 time to fit residues: 789.1266 Evaluate side-chains 812 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 739 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 82 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 282 LEU 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 122 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 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 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 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 1254 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 67 ASP 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 240 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 468 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 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 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1156 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 117 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 65 LEU 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 385 LYS Chi-restraints excluded: chain F residue 396 ILE 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 590 VAL Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 608 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 299 optimal weight: 0.5980 chunk 345 optimal weight: 0.9980 chunk 137 optimal weight: 30.0000 chunk 190 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 254 optimal weight: 0.3980 chunk 374 optimal weight: 0.7980 chunk 140 optimal weight: 30.0000 chunk 263 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN G 269 ASN C 618 GLN D 504 GLN D 805 GLN D 861 ASN D 961 HIS D1243 GLN A 75 GLN B 84 ASN ** 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 = 0.4204 r_free = 0.4204 target = 0.171425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133410 restraints weight = 64315.720| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.51 r_work: 0.3493 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2192 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= 0.159 Angle : 0.552 14.054 45949 Z= 0.293 Chirality : 0.042 0.192 5228 Planarity : 0.004 0.055 5510 Dihedral : 17.696 176.402 5715 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.18 % Allowed : 23.52 % Favored : 73.29 % 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: 1.11 (0.14), residues: 3775 helix: 1.55 (0.13), residues: 1623 sheet: 0.70 (0.24), residues: 457 loop : 0.03 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C1169 TYR 0.022 0.001 TYR C 123 PHE 0.023 0.001 PHE C 906 TRP 0.008 0.001 TRP K 15 HIS 0.005 0.001 HIS D1365 Details of bonding type rmsd covalent geometry : bond 0.00366 (33591) covalent geometry : angle 0.54867 (45937) hydrogen bonds : bond 0.04055 ( 1550) hydrogen bonds : angle 4.19794 ( 4311) metal coordination : bond 0.00902 ( 8) metal coordination : angle 3.93213 ( 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 864 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 760 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ILE cc_start: 0.7745 (mp) cc_final: 0.7541 (mm) REVERT: C 84 GLU cc_start: 0.7810 (pm20) cc_final: 0.7364 (pm20) REVERT: C 99 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8077 (mtpp) REVERT: C 175 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7544 (ttm-80) REVERT: C 182 SER cc_start: 0.8589 (m) cc_final: 0.8233 (p) REVERT: C 187 GLU cc_start: 0.7418 (pt0) cc_final: 0.7132 (pt0) REVERT: C 194 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7779 (pp) REVERT: C 197 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7227 (mtt180) REVERT: C 470 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7716 (mtp180) REVERT: C 476 LYS cc_start: 0.8310 (ttmm) cc_final: 0.8052 (ttpp) REVERT: C 503 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8458 (mtpt) REVERT: C 515 MET cc_start: 0.7789 (ttt) cc_final: 0.7520 (ttt) REVERT: C 545 PHE cc_start: 0.7163 (t80) cc_final: 0.6902 (t80) REVERT: C 622 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8126 (mmmm) REVERT: C 734 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8543 (t) REVERT: C 865 LEU cc_start: 0.8563 (mp) cc_final: 0.8361 (mt) REVERT: C 890 LYS cc_start: 0.8307 (ptmt) cc_final: 0.8039 (ptmm) REVERT: C 899 GLU cc_start: 0.7700 (tt0) cc_final: 0.7072 (tm-30) REVERT: C 902 LEU cc_start: 0.8543 (tt) cc_final: 0.8336 (mp) REVERT: C 914 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7963 (ttpp) REVERT: C 1140 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8145 (mtmm) REVERT: C 1151 LEU cc_start: 0.8688 (tt) cc_final: 0.8451 (tp) REVERT: C 1199 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: D 144 TYR cc_start: 0.8233 (m-80) cc_final: 0.7882 (m-80) REVERT: D 148 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7661 (mt-10) REVERT: D 180 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7077 (ttt) REVERT: D 204 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7377 (tm-30) REVERT: D 213 LYS cc_start: 0.7897 (mtpp) cc_final: 0.7611 (mtpp) REVERT: D 298 MET cc_start: 0.8317 (mtp) cc_final: 0.8039 (mtp) REVERT: D 430 HIS cc_start: 0.9012 (OUTLIER) cc_final: 0.8654 (p90) REVERT: D 566 GLU cc_start: 0.7676 (pp20) cc_final: 0.7471 (pp20) REVERT: D 704 GLU cc_start: 0.7261 (pt0) cc_final: 0.6901 (pt0) REVERT: D 712 GLU cc_start: 0.7476 (mp0) cc_final: 0.7107 (pm20) REVERT: D 739 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: D 747 MET cc_start: 0.8012 (mmm) cc_final: 0.7618 (mtm) REVERT: D 754 ILE cc_start: 0.8634 (mt) cc_final: 0.8418 (mm) REVERT: D 875 ASN cc_start: 0.7054 (m-40) cc_final: 0.6473 (t0) REVERT: D 1214 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7140 (mm-30) REVERT: D 1329 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8269 (mtt-85) REVERT: D 1333 GLU cc_start: 0.7918 (tp30) cc_final: 0.7577 (tp30) REVERT: D 1360 THR cc_start: 0.8721 (m) cc_final: 0.8295 (p) REVERT: B 58 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: B 86 LYS cc_start: 0.8611 (ttmm) cc_final: 0.8338 (tttt) REVERT: F 278 VAL cc_start: 0.8506 (t) cc_final: 0.8179 (m) REVERT: F 386 GLU cc_start: 0.8092 (tp30) cc_final: 0.7744 (tp30) REVERT: F 397 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8339 (p) REVERT: F 415 GLU cc_start: 0.7835 (mm-30) cc_final: 0.6927 (tp30) REVERT: F 459 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7810 (ttp80) REVERT: F 462 VAL cc_start: 0.8647 (t) cc_final: 0.8391 (m) REVERT: F 489 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7391 (tm-30) REVERT: F 490 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7581 (pt0) REVERT: F 604 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7833 (mtm-85) outliers start: 104 outliers final: 57 residues processed: 802 average time/residue: 0.7762 time to fit residues: 721.0927 Evaluate side-chains 818 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 748 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 47 LEU 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 C residue 6 THR 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 176 ILE 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 416 GLU Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 488 MET 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 839 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1199 GLU Chi-restraints excluded: chain C residue 1249 SER Chi-restraints excluded: chain C residue 1254 THR 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 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 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 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 1156 LEU Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1329 ARG 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 169 ILE 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 487 LEU Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 608 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 321 optimal weight: 0.9990 chunk 123 optimal weight: 0.0170 chunk 293 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 199 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN G 269 ASN C 193 ASN D 335 GLN D 504 GLN D 805 GLN D 861 ASN A 75 GLN B 84 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.171811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133201 restraints weight = 65814.170| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.53 r_work: 0.3492 rms_B_bonded: 3.09 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 = 0.38 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33599 Z= 0.141 Angle : 0.548 14.289 45949 Z= 0.291 Chirality : 0.041 0.201 5228 Planarity : 0.004 0.052 5510 Dihedral : 17.646 176.117 5715 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.75 % Allowed : 24.38 % Favored : 72.87 % 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: 1.17 (0.14), residues: 3775 helix: 1.63 (0.13), residues: 1619 sheet: 0.69 (0.23), residues: 482 loop : 0.05 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1169 TYR 0.025 0.001 TYR C 123 PHE 0.013 0.001 PHE C 385 TRP 0.009 0.001 TRP H 68 HIS 0.005 0.001 HIS D1365 Details of bonding type rmsd covalent geometry : bond 0.00323 (33591) covalent geometry : angle 0.54498 (45937) hydrogen bonds : bond 0.03868 ( 1550) hydrogen bonds : angle 4.16037 ( 4311) metal coordination : bond 0.00825 ( 8) metal coordination : angle 3.80590 ( 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 845 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 755 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLN cc_start: 0.7390 (pm20) cc_final: 0.7107 (pm20) REVERT: C 84 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: C 99 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8042 (mtpp) REVERT: C 175 ARG cc_start: 0.7803 (ttm110) cc_final: 0.7597 (ttm-80) REVERT: C 182 SER cc_start: 0.8596 (m) cc_final: 0.8245 (p) REVERT: C 187 GLU cc_start: 0.7430 (pt0) cc_final: 0.7146 (pt0) REVERT: C 197 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7199 (mtt180) REVERT: C 390 PHE cc_start: 0.8185 (m-80) cc_final: 0.7941 (m-80) REVERT: C 470 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7720 (mtp180) REVERT: C 476 LYS cc_start: 0.8297 (ttmm) cc_final: 0.8041 (ttpp) REVERT: C 503 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8445 (mtpt) REVERT: C 515 MET cc_start: 0.7760 (ttt) cc_final: 0.7476 (ttt) REVERT: C 545 PHE cc_start: 0.7147 (t80) cc_final: 0.6929 (t80) REVERT: C 622 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8130 (mmmm) REVERT: C 734 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8534 (t) REVERT: C 865 LEU cc_start: 0.8567 (mp) cc_final: 0.8342 (mt) REVERT: C 890 LYS cc_start: 0.8291 (ptmt) cc_final: 0.8016 (ptmm) REVERT: C 899 GLU cc_start: 0.7725 (tt0) cc_final: 0.7081 (tm-30) REVERT: C 914 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7952 (ttpp) REVERT: C 1140 LYS cc_start: 0.8341 (mtpp) cc_final: 0.8130 (mtmm) REVERT: C 1151 LEU cc_start: 0.8685 (tt) cc_final: 0.8448 (tp) REVERT: D 144 TYR cc_start: 0.8251 (m-80) cc_final: 0.7912 (m-80) REVERT: D 148 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7631 (mt-10) REVERT: D 167 ASP cc_start: 0.7913 (m-30) cc_final: 0.7571 (p0) REVERT: D 180 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7025 (ttt) REVERT: D 204 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7493 (tm-30) REVERT: D 298 MET cc_start: 0.8309 (mtp) cc_final: 0.8060 (mtp) REVERT: D 340 GLN cc_start: 0.8288 (tp40) cc_final: 0.7914 (tp40) REVERT: D 430 HIS cc_start: 0.9011 (OUTLIER) cc_final: 0.8637 (p90) REVERT: D 704 GLU cc_start: 0.7278 (pt0) cc_final: 0.6908 (pt0) REVERT: D 712 GLU cc_start: 0.7483 (mp0) cc_final: 0.7114 (pm20) REVERT: D 739 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: D 747 MET cc_start: 0.8009 (mmm) cc_final: 0.7601 (mtm) REVERT: D 754 ILE cc_start: 0.8627 (mt) cc_final: 0.8412 (mm) REVERT: D 861 ASN cc_start: 0.8193 (m-40) cc_final: 0.7895 (m110) REVERT: D 875 ASN cc_start: 0.7085 (m-40) cc_final: 0.6539 (t0) REVERT: D 1214 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7187 (mm-30) REVERT: D 1333 GLU cc_start: 0.7931 (tp30) cc_final: 0.7591 (tp30) REVERT: D 1360 THR cc_start: 0.8720 (m) cc_final: 0.7191 (t) REVERT: A 86 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8484 (mtmm) REVERT: B 58 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: B 86 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8335 (tttt) REVERT: B 99 VAL cc_start: 0.8161 (m) cc_final: 0.7955 (p) REVERT: B 102 THR cc_start: 0.8472 (m) cc_final: 0.8003 (p) REVERT: B 149 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.7954 (ttt180) REVERT: F 386 GLU cc_start: 0.8067 (tp30) cc_final: 0.7688 (tp30) REVERT: F 397 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8348 (p) REVERT: F 415 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7006 (tp30) REVERT: F 445 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8196 (tm130) REVERT: F 459 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7798 (ttp80) REVERT: F 462 VAL cc_start: 0.8635 (t) cc_final: 0.8378 (m) REVERT: F 484 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7615 (pmt170) REVERT: F 489 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7343 (tm-30) REVERT: F 490 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7556 (pt0) outliers start: 90 outliers final: 52 residues processed: 790 average time/residue: 0.8651 time to fit residues: 791.3299 Evaluate side-chains 810 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 744 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain G residue 258 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 79 VAL Chi-restraints excluded: chain C residue 84 GLU 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 176 ILE 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 416 GLU Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 VAL 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 1254 THR Chi-restraints excluded: chain D residue 67 ASP 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 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 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 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1156 LEU 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 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 169 ILE 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 590 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 274 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 305 optimal weight: 1.9990 chunk 262 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 326 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 ASN D 504 GLN D 805 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN F 131 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.169807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.132157 restraints weight = 72189.969| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.31 r_work: 0.3467 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 33599 Z= 0.238 Angle : 0.615 14.430 45949 Z= 0.324 Chirality : 0.044 0.219 5228 Planarity : 0.005 0.060 5510 Dihedral : 17.638 176.188 5713 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.03 % Allowed : 23.98 % Favored : 72.99 % 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: 0.97 (0.14), residues: 3775 helix: 1.41 (0.13), residues: 1625 sheet: 0.66 (0.24), residues: 461 loop : -0.02 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 604 TYR 0.026 0.002 TYR D 631 PHE 0.017 0.002 PHE C 186 TRP 0.016 0.001 TRP H 16 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00553 (33591) covalent geometry : angle 0.60974 (45937) hydrogen bonds : bond 0.04728 ( 1550) hydrogen bonds : angle 4.33744 ( 4311) metal coordination : bond 0.01403 ( 8) metal coordination : angle 5.01122 ( 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 859 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 760 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: C 99 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8089 (mtpp) REVERT: C 175 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7565 (ttm-80) REVERT: C 182 SER cc_start: 0.8604 (m) cc_final: 0.8267 (p) REVERT: C 187 GLU cc_start: 0.7540 (pt0) cc_final: 0.7180 (pt0) REVERT: C 197 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7178 (mtt180) REVERT: C 470 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7768 (mtp180) REVERT: C 476 LYS cc_start: 0.8301 (ttmm) cc_final: 0.8066 (ttpp) REVERT: C 503 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8409 (mtpt) REVERT: C 515 MET cc_start: 0.7869 (ttt) cc_final: 0.7601 (ttt) REVERT: C 545 PHE cc_start: 0.7170 (t80) cc_final: 0.6942 (t80) REVERT: C 549 ASP cc_start: 0.7944 (t0) cc_final: 0.7671 (m-30) REVERT: C 622 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8178 (mmmm) REVERT: C 734 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8611 (t) REVERT: C 890 LYS cc_start: 0.8315 (ptmt) cc_final: 0.8052 (ptmm) REVERT: C 899 GLU cc_start: 0.7704 (tt0) cc_final: 0.7073 (tm-30) REVERT: C 914 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7932 (ttpp) REVERT: C 1092 GLN cc_start: 0.8393 (tt0) cc_final: 0.8130 (tt0) REVERT: C 1140 LYS cc_start: 0.8403 (mtpp) cc_final: 0.8176 (mtmm) REVERT: C 1151 LEU cc_start: 0.8688 (tt) cc_final: 0.8448 (tp) REVERT: D 144 TYR cc_start: 0.8266 (m-80) cc_final: 0.7945 (m-80) REVERT: D 148 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7733 (mt-10) REVERT: D 180 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7169 (ttt) REVERT: D 204 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7512 (tm-30) REVERT: D 298 MET cc_start: 0.8381 (mtp) cc_final: 0.8154 (mtp) REVERT: D 430 HIS cc_start: 0.9014 (OUTLIER) cc_final: 0.8716 (p90) REVERT: D 566 GLU cc_start: 0.7655 (pp20) cc_final: 0.7431 (pp20) REVERT: D 704 GLU cc_start: 0.7264 (pt0) cc_final: 0.7011 (pt0) REVERT: D 712 GLU cc_start: 0.7460 (mp0) cc_final: 0.7086 (pm20) REVERT: D 739 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: D 754 ILE cc_start: 0.8695 (mt) cc_final: 0.8464 (mm) REVERT: D 875 ASN cc_start: 0.7273 (m-40) cc_final: 0.6727 (t0) REVERT: D 1214 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7234 (mm-30) REVERT: D 1333 GLU cc_start: 0.7888 (tp30) cc_final: 0.7539 (tp30) REVERT: D 1360 THR cc_start: 0.8754 (m) cc_final: 0.8341 (p) REVERT: B 58 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: B 86 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8323 (tttt) REVERT: B 99 VAL cc_start: 0.8167 (m) cc_final: 0.7959 (p) REVERT: B 102 THR cc_start: 0.8575 (m) cc_final: 0.8109 (p) REVERT: B 144 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7670 (ttt-90) REVERT: B 149 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.7996 (ttt180) REVERT: F 386 GLU cc_start: 0.8064 (tp30) cc_final: 0.7646 (tp30) REVERT: F 397 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8417 (p) REVERT: F 415 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7045 (tp30) REVERT: F 424 VAL cc_start: 0.8452 (t) cc_final: 0.7883 (m) REVERT: F 459 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7800 (ttp80) REVERT: F 489 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7323 (tm-30) REVERT: F 490 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7685 (mt-10) REVERT: F 593 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6424 (mm-30) outliers start: 99 outliers final: 58 residues processed: 801 average time/residue: 0.8220 time to fit residues: 765.6273 Evaluate side-chains 816 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 746 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 47 LEU 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 C residue 6 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 GLU 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 197 ARG 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 423 VAL Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 726 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 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 1254 THR 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 240 THR Chi-restraints excluded: chain D residue 390 LEU 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 553 THR Chi-restraints excluded: chain D residue 565 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 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1156 LEU 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 86 LYS Chi-restraints excluded: chain B residue 97 ASP 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 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 590 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 362 optimal weight: 10.0000 chunk 179 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 374 optimal weight: 0.7980 chunk 246 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 216 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN G 269 ASN C 339 ASN C 618 GLN D 335 GLN D 504 GLN D 805 GLN D 861 ASN A 75 GLN B 84 ASN ** 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 = 0.4190 r_free = 0.4190 target = 0.170299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132508 restraints weight = 70312.665| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.63 r_work: 0.3477 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33599 Z= 0.171 Angle : 0.582 14.746 45949 Z= 0.307 Chirality : 0.042 0.212 5228 Planarity : 0.004 0.060 5510 Dihedral : 17.627 175.772 5713 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.20 % Allowed : 25.11 % Favored : 72.68 % 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: 1.00 (0.14), residues: 3775 helix: 1.45 (0.13), residues: 1625 sheet: 0.65 (0.24), residues: 453 loop : -0.02 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 604 TYR 0.025 0.001 TYR C 123 PHE 0.028 0.001 PHE C 186 TRP 0.012 0.001 TRP G 322 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00396 (33591) covalent geometry : angle 0.57824 (45937) hydrogen bonds : bond 0.04180 ( 1550) hydrogen bonds : angle 4.26118 ( 4311) metal coordination : bond 0.00973 ( 8) metal coordination : angle 4.25286 ( 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: 72 poor density : 760 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 GLN cc_start: 0.6876 (mm-40) cc_final: 0.6662 (mm110) REVERT: C 44 GLU cc_start: 0.7547 (tp30) cc_final: 0.7135 (tp30) REVERT: C 84 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: C 99 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8062 (mtpp) REVERT: C 175 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7543 (ttm-80) REVERT: C 182 SER cc_start: 0.8608 (m) cc_final: 0.8260 (p) REVERT: C 187 GLU cc_start: 0.7515 (pt0) cc_final: 0.7139 (pt0) REVERT: C 197 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7128 (mtt180) REVERT: C 470 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7730 (mtp180) REVERT: C 476 LYS cc_start: 0.8314 (ttmm) cc_final: 0.8073 (ttpp) REVERT: C 503 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8432 (mtpt) REVERT: C 515 MET cc_start: 0.7793 (ttt) cc_final: 0.7524 (ttt) REVERT: C 545 PHE cc_start: 0.7161 (t80) cc_final: 0.6939 (t80) REVERT: C 549 ASP cc_start: 0.7953 (t0) cc_final: 0.7662 (m-30) REVERT: C 622 LYS cc_start: 0.8475 (mtmt) cc_final: 0.8189 (mmmm) REVERT: C 734 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8591 (t) REVERT: C 865 LEU cc_start: 0.8597 (mp) cc_final: 0.8349 (mt) REVERT: C 890 LYS cc_start: 0.8304 (ptmt) cc_final: 0.8039 (ptmm) REVERT: C 899 GLU cc_start: 0.7750 (tt0) cc_final: 0.7086 (tm-30) REVERT: C 914 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7928 (ttpp) REVERT: C 1092 GLN cc_start: 0.8384 (tt0) cc_final: 0.8115 (tt0) REVERT: C 1140 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8168 (mtmm) REVERT: C 1151 LEU cc_start: 0.8702 (tt) cc_final: 0.8472 (tp) REVERT: C 1199 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7756 (mp0) REVERT: D 144 TYR cc_start: 0.8286 (m-80) cc_final: 0.7929 (m-80) REVERT: D 148 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7693 (mt-10) REVERT: D 167 ASP cc_start: 0.7916 (m-30) cc_final: 0.7626 (p0) REVERT: D 180 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7157 (ttt) REVERT: D 204 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7504 (tm-30) REVERT: D 298 MET cc_start: 0.8390 (mtp) cc_final: 0.8163 (mtp) REVERT: D 430 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.8715 (p90) REVERT: D 566 GLU cc_start: 0.7618 (pp20) cc_final: 0.7401 (pp20) REVERT: D 704 GLU cc_start: 0.7343 (pt0) cc_final: 0.7081 (pt0) REVERT: D 712 GLU cc_start: 0.7492 (mp0) cc_final: 0.7288 (mp0) REVERT: D 739 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: D 754 ILE cc_start: 0.8692 (mt) cc_final: 0.8461 (mm) REVERT: D 861 ASN cc_start: 0.8200 (m-40) cc_final: 0.7920 (m110) REVERT: D 875 ASN cc_start: 0.7267 (m-40) cc_final: 0.6777 (t0) REVERT: D 1214 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7265 (mm-30) REVERT: D 1333 GLU cc_start: 0.7944 (tp30) cc_final: 0.7601 (tp30) REVERT: D 1360 THR cc_start: 0.8730 (m) cc_final: 0.8310 (p) REVERT: A 7 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7148 (mt-10) REVERT: B 86 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8347 (tttt) REVERT: B 102 THR cc_start: 0.8579 (m) cc_final: 0.8121 (p) REVERT: B 144 ARG cc_start: 0.7874 (ttt-90) cc_final: 0.7669 (ttt-90) REVERT: B 149 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.7995 (ttt180) REVERT: F 386 GLU cc_start: 0.8033 (tp30) cc_final: 0.7618 (tp30) REVERT: F 397 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8364 (p) REVERT: F 415 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7041 (tp30) REVERT: F 459 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7903 (ttp80) REVERT: F 484 ARG cc_start: 0.8063 (pmt170) cc_final: 0.7787 (pmt170) REVERT: F 489 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7267 (tm-30) REVERT: F 490 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7608 (mt-10) REVERT: F 495 MET cc_start: 0.8031 (mtm) cc_final: 0.7787 (ttp) outliers start: 72 outliers final: 48 residues processed: 790 average time/residue: 0.8478 time to fit residues: 776.6700 Evaluate side-chains 811 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 752 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 47 LEU 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 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 GLU 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 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 589 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 901 LEU 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 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 240 THR 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 553 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 739 GLN Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1369 GLN Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 97 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 56 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 317 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 67 optimal weight: 0.0060 chunk 111 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 chunk 387 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN G 269 ASN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN D 805 GLN B 84 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.170758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.132828 restraints weight = 59805.006| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.36 r_work: 0.3503 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 33599 Z= 0.191 Angle : 0.697 59.200 45949 Z= 0.386 Chirality : 0.043 0.703 5228 Planarity : 0.004 0.059 5510 Dihedral : 17.626 175.752 5713 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.29 % Allowed : 24.99 % Favored : 72.71 % Cbeta Deviations : 0.03 % 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: 1.01 (0.14), residues: 3775 helix: 1.46 (0.13), residues: 1625 sheet: 0.65 (0.24), residues: 453 loop : -0.01 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 604 TYR 0.025 0.001 TYR G 278 PHE 0.027 0.001 PHE C 186 TRP 0.012 0.001 TRP G 322 HIS 0.005 0.001 HIS D1365 Details of bonding type rmsd covalent geometry : bond 0.00402 (33591) covalent geometry : angle 0.69321 (45937) hydrogen bonds : bond 0.04151 ( 1550) hydrogen bonds : angle 4.26485 ( 4311) metal coordination : bond 0.01057 ( 8) metal coordination : angle 4.34594 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20509.74 seconds wall clock time: 347 minutes 40.20 seconds (20860.20 seconds total)