Starting phenix.real_space_refine on Sat Aug 8 21:03:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pil_17685/08_2026/8pil_17685.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pil_17685/08_2026/8pil_17685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pil_17685/08_2026/8pil_17685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pil_17685/08_2026/8pil_17685.map" model { file = "/net/cci-nas-00/data/ceres_data/8pil_17685/08_2026/8pil_17685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pil_17685/08_2026/8pil_17685.cif" } resolution = 3.2 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= 0.010 sd= 0.053 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 83 5.49 5 Mg 1 5.21 5 S 116 5.16 5 C 18823 2.51 5 N 5389 2.21 5 O 6026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30440 Number of models: 1 Model: "" Number of chains: 11 Chain: "P" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1294 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 150} Chain: "I" Number of atoms: 10604 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1342, 10585 Classifications: {'peptide': 1342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1285} Conformer: "B" Number of residues, atoms: 1342, 10585 Classifications: {'peptide': 1342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1285} bond proxies already assigned to first conformer: 10732 Chain: "J" Number of atoms: 10440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1342, 10440 Classifications: {'peptide': 1342} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1286} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "G" Number of atoms: 1807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Conformer: "B" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} bond proxies already assigned to first conformer: 1812 Chain: "H" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2299 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "A" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 733 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "B" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 740 Classifications: {'DNA': 36} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 35} Chain: "R" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "F" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1605 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "J" 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 12347 SG CYS J 70 37.176 71.372 91.436 1.00116.29 S ATOM 12361 SG CYS J 72 36.058 67.868 90.486 1.00116.32 S ATOM 12469 SG CYS J 85 34.292 69.564 93.247 1.00115.34 S ATOM 12493 SG CYS J 88 37.812 68.495 93.894 1.00112.63 S ATOM 18181 SG CYS J 814 71.028 125.865 100.007 1.00 95.84 S ATOM 18746 SG CYS J 888 73.003 123.151 98.573 1.00 95.46 S ATOM 18797 SG CYS J 895 71.736 126.014 96.256 1.00 89.23 S ATOM 18818 SG CYS J 898 74.623 126.536 98.574 1.00 89.44 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE I 156 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE I 156 " occ=0.50 Time building chain proxies: 9.32, per 1000 atoms: 0.31 Number of scatterers: 30440 At special positions: 0 Unit cell: (153.92, 170.56, 163.904, 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 116 16.00 P 83 15.00 Mg 1 11.99 O 6026 8.00 N 5389 7.00 C 18823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " Number of angles added : 12 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6786 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 52 sheets defined 39.2% alpha, 17.6% beta 32 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 71 Processing helix chain 'P' and resid 89 through 99 removed outlier: 4.111A pdb=" N VAL P 98 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.711A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.632A pdb=" N ASP I 33 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.728A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.837A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 4.090A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS I 295 " --> pdb=" O TYR I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 295' Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.959A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.580A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.556A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.819A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.882A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP I 549 " --> pdb=" O PHE I 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 544 through 549' Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.811A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 624 through 628 removed outlier: 3.702A pdb=" N HIS I 628 " --> pdb=" O GLU I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.117A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 858 through 864 removed outlier: 4.143A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 895 through 902 Processing helix chain 'I' and resid 942 through 982 Processing helix chain 'I' and resid 985 through 991 Processing helix chain 'I' and resid 993 through 1000 Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.158A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.518A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.801A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.700A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.557A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1239 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.731A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.701A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.811A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 588 through 592 removed outlier: 4.008A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.598A pdb=" N VAL J 618 " --> pdb=" O LEU J 614 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.217A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.070A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.878A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.356A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.611A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 4.168A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA J1375 " --> pdb=" O ARG J1371 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.597A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.740A pdb=" N GLY G 40 " --> pdb=" O GLY G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.663A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 162 removed outlier: 3.501A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.104A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.528A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 159 Processing helix chain 'H' and resid 161 through 166 removed outlier: 4.076A pdb=" N ASP H 164 " --> pdb=" O SER H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 228 through 233 removed outlier: 4.005A pdb=" N ASP H 233 " --> pdb=" O GLU H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 255 Processing helix chain 'H' and resid 256 through 260 Processing helix chain 'H' and resid 263 through 273 Processing helix chain 'H' and resid 277 through 284 removed outlier: 3.794A pdb=" N LEU H 281 " --> pdb=" O TYR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 311 removed outlier: 3.863A pdb=" N LYS H 304 " --> pdb=" O LEU H 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 19 through 39 Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'F' and resid 103 through 128 Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 34 Processing sheet with id=AA3, first strand: chain 'P' and resid 150 through 154 removed outlier: 8.345A pdb=" N MET P 140 " --> pdb=" O THR P 131 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR P 131 " --> pdb=" O MET P 140 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE P 129 " --> pdb=" O LEU P 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.349A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.864A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA7, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.206A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 154 through 159 removed outlier: 5.351A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB1, first strand: chain 'I' and resid 239 through 240 removed outlier: 3.566A pdb=" N MET I 239 " --> pdb=" O ILE I 285 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE I 285 " --> pdb=" O MET I 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 255 through 257 removed outlier: 3.823A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.614A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.527A pdb=" N LYS I 593 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.539A pdb=" N ASP I 654 " --> pdb=" O ALA I 617 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.629A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.373A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 755 through 758 Processing sheet with id=AB9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.701A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.826A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.859A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL I 887 " --> pdb=" O GLU I 849 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.256A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.744A pdb=" N HIS I1244 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC7, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.605A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.778A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.985A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD2, first strand: chain 'J' and resid 706 through 709 Processing sheet with id=AD3, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD4, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD5, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.144A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 842 through 843 removed outlier: 3.803A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.301A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AD9, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.267A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE2, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.145A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.675A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.628A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 97 through 105 removed outlier: 6.293A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AE7, first strand: chain 'G' and resid 108 through 111 removed outlier: 4.081A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AE9, first strand: chain 'H' and resid 15 through 18 removed outlier: 6.596A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N THR H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL H 192 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 97 through 105 removed outlier: 3.634A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AF3, first strand: chain 'H' and resid 109 through 111 removed outlier: 6.752A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AF5, first strand: chain 'F' and resid 60 through 61 Processing sheet with id=AF6, first strand: chain 'F' and resid 137 through 138 removed outlier: 3.571A pdb=" N SER F 185 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 141 through 144 removed outlier: 6.830A pdb=" N SER F 151 " --> pdb=" O LYS F 143 " (cutoff:3.500A) 1239 hydrogen bonds defined for protein. 3479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 7.68 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10054 1.34 - 1.46: 4848 1.46 - 1.58: 15809 1.58 - 1.70: 164 1.70 - 1.82: 201 Bond restraints: 31076 Sorted by residual: bond pdb=" C1' DT B 33 " pdb=" N1 DT B 33 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" C3' DA B 10 " pdb=" C2' DA B 10 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.36e+00 bond pdb=" C3' DG B 16 " pdb=" C2' DG B 16 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.39e+00 bond pdb=" C3' DT A 38 " pdb=" C2' DT A 38 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.22e+00 bond pdb=" C3' DA A 34 " pdb=" C2' DA A 34 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.12e+00 ... (remaining 31071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 41895 2.22 - 4.43: 403 4.43 - 6.65: 37 6.65 - 8.86: 13 8.86 - 11.08: 4 Bond angle restraints: 42352 Sorted by residual: angle pdb=" CA ARG I 996 " pdb=" CB ARG I 996 " pdb=" CG ARG I 996 " ideal model delta sigma weight residual 114.10 123.16 -9.06 2.00e+00 2.50e-01 2.05e+01 angle pdb=" N3 DT B 33 " pdb=" C4 DT B 33 " pdb=" O4 DT B 33 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT A 38 " pdb=" C4 DT A 38 " pdb=" O4 DT A 38 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" CA GLU I 908 " pdb=" CB GLU I 908 " pdb=" CG GLU I 908 " ideal model delta sigma weight residual 114.10 122.82 -8.72 2.00e+00 2.50e-01 1.90e+01 angle pdb=" O4' DC B 28 " pdb=" C4' DC B 28 " pdb=" C3' DC B 28 " ideal model delta sigma weight residual 106.00 103.39 2.61 6.00e-01 2.78e+00 1.90e+01 ... (remaining 42347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.59: 17263 27.59 - 55.19: 1485 55.19 - 82.78: 201 82.78 - 110.37: 13 110.37 - 137.96: 2 Dihedral angle restraints: 18964 sinusoidal: 8431 harmonic: 10533 Sorted by residual: dihedral pdb=" CA MET F 125 " pdb=" C MET F 125 " pdb=" N VAL F 126 " pdb=" CA VAL F 126 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ASP I 995 " pdb=" C ASP I 995 " pdb=" N ARG I 996 " pdb=" CA ARG I 996 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASN I 314 " pdb=" C ASN I 314 " pdb=" N MET I 315 " pdb=" CA MET I 315 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 18961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3528 0.038 - 0.076: 874 0.076 - 0.114: 379 0.114 - 0.152: 61 0.152 - 0.191: 4 Chirality restraints: 4846 Sorted by residual: chirality pdb=" CA GLU I 908 " pdb=" N GLU I 908 " pdb=" C GLU I 908 " pdb=" CB GLU I 908 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CB ILE P 38 " pdb=" CA ILE P 38 " pdb=" CG1 ILE P 38 " pdb=" CG2 ILE P 38 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA MET F 125 " pdb=" N MET F 125 " pdb=" C MET F 125 " pdb=" CB MET F 125 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 4843 not shown) Planarity restraints: 5251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP J 460 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" CG ASP J 460 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASP J 460 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP J 460 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 464 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" CG ASP J 464 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP J 464 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP J 464 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG H 166 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO H 167 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO H 167 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 167 " 0.031 5.00e-02 4.00e+02 ... (remaining 5248 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 15 2.28 - 2.93: 12795 2.93 - 3.59: 46076 3.59 - 4.24: 70506 4.24 - 4.90: 117844 Nonbonded interactions: 247236 Sorted by model distance: nonbonded pdb=" CB ASP J 460 " pdb="MG MG J1503 " model vdw 1.621 2.570 nonbonded pdb=" OD2 ASP J 460 " pdb=" OP1 U R 17 " model vdw 2.008 3.040 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.049 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb=" OD2 ASP J 462 " model vdw 2.115 3.040 nonbonded pdb=" CG ASP J 460 " pdb="MG MG J1503 " model vdw 2.130 2.400 ... (remaining 247231 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 5.450 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: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 41.940 Find NCS groups from input model: 0.250 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.003 0.045 31084 Z= 0.186 Angle : 0.530 11.077 42364 Z= 0.333 Chirality : 0.041 0.191 4846 Planarity : 0.003 0.055 5251 Dihedral : 18.896 137.964 12178 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.19 % Allowed : 25.44 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 3641 helix: 2.08 (0.15), residues: 1258 sheet: 0.31 (0.23), residues: 522 loop : -0.08 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG I 996 TYR 0.011 0.001 TYR P 99 PHE 0.013 0.001 PHE J 461 TRP 0.018 0.001 TRP I 183 HIS 0.003 0.000 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.19 (31076) covalent geometry : angle 0.52715 / 0.33 (42352) hydrogen bonds : bond 0.13736 / 9.17 ( 1319) hydrogen bonds : angle 5.30831 / 3.66 ( 3643) metal coordination : bond 0.00396 / 0.19 ( 8) metal coordination : angle 3.47256 / 1.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 221 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 32 MET cc_start: 0.7991 (mmm) cc_final: 0.7762 (mmm) REVERT: I 856 ASN cc_start: 0.7852 (p0) cc_final: 0.7646 (p0) REVERT: J 822 MET cc_start: 0.8460 (tpp) cc_final: 0.8196 (mtp) REVERT: K 69 ARG cc_start: 0.8740 (ttm110) cc_final: 0.8222 (ptp90) REVERT: K 72 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8691 (tm-30) REVERT: F 141 VAL cc_start: 0.0367 (OUTLIER) cc_final: 0.0156 (m) REVERT: F 167 MET cc_start: 0.5697 (mmt) cc_final: 0.4913 (mmp) outliers start: 5 outliers final: 2 residues processed: 225 average time/residue: 0.1971 time to fit residues: 71.6170 Evaluate side-chains 205 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain F residue 141 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0050 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 2 GLN J 435 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.081443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053054 restraints weight = 163483.996| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.43 r_work: 0.2783 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31084 Z= 0.226 Angle : 0.583 7.927 42364 Z= 0.307 Chirality : 0.042 0.231 4846 Planarity : 0.004 0.053 5251 Dihedral : 14.926 140.958 4988 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.14 % Allowed : 24.26 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.14), residues: 3641 helix: 1.94 (0.15), residues: 1306 sheet: 0.17 (0.23), residues: 541 loop : -0.13 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 996 TYR 0.029 0.001 TYR F 92 PHE 0.014 0.001 PHE I 385 TRP 0.021 0.002 TRP F 62 HIS 0.006 0.001 HIS F 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 (31076) covalent geometry : angle 0.57893 / 0.31 (42352) hydrogen bonds : bond 0.04196 / 2.78 ( 1319) hydrogen bonds : angle 4.54749 / 3.11 ( 3643) metal coordination : bond 0.01113 / 0.55 ( 8) metal coordination : angle 4.29991 / 2.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 209 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 165 HIS cc_start: 0.8599 (t-90) cc_final: 0.8386 (t-90) REVERT: I 741 MET cc_start: 0.8779 (mmm) cc_final: 0.8419 (mmm) REVERT: J 172 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6666 (p90) REVERT: J 1239 ASP cc_start: 0.9307 (t0) cc_final: 0.8969 (m-30) REVERT: J 1334 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8012 (mp0) REVERT: K 69 ARG cc_start: 0.9021 (ttm110) cc_final: 0.8217 (ptp90) REVERT: K 72 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8860 (tm-30) REVERT: G 93 GLN cc_start: 0.9106 (tt0) cc_final: 0.8788 (tm-30) REVERT: H 66 HIS cc_start: 0.8502 (m170) cc_final: 0.8217 (m90) REVERT: H 294 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.6981 (t0) REVERT: F 62 TRP cc_start: 0.4295 (m100) cc_final: 0.3832 (m100) outliers start: 66 outliers final: 38 residues processed: 261 average time/residue: 0.1927 time to fit residues: 81.5094 Evaluate side-chains 237 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 294 ASN Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 59 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 296 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.054242 restraints weight = 152859.645| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 4.23 r_work: 0.2782 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31084 Z= 0.132 Angle : 0.506 7.850 42364 Z= 0.271 Chirality : 0.041 0.218 4846 Planarity : 0.003 0.055 5251 Dihedral : 14.911 139.279 4984 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.82 % Allowed : 24.70 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 3641 helix: 2.01 (0.15), residues: 1304 sheet: 0.23 (0.23), residues: 519 loop : -0.13 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 394 TYR 0.011 0.001 TYR J 631 PHE 0.011 0.001 PHE I 405 TRP 0.012 0.001 TRP I 183 HIS 0.003 0.001 HIS H 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (31076) covalent geometry : angle 0.50133 / 0.27 (42352) hydrogen bonds : bond 0.03787 / 2.51 ( 1319) hydrogen bonds : angle 4.34691 / 2.97 ( 3643) metal coordination : bond 0.00710 / 0.35 ( 8) metal coordination : angle 4.25442 / 2.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 215 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 813 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7606 (tm-30) REVERT: J 298 MET cc_start: 0.9397 (mmt) cc_final: 0.9161 (mpp) REVERT: J 458 ASN cc_start: 0.8996 (t0) cc_final: 0.8697 (t0) REVERT: J 1189 MET cc_start: 0.8510 (mmt) cc_final: 0.8308 (mmt) REVERT: J 1239 ASP cc_start: 0.9224 (t0) cc_final: 0.8985 (m-30) REVERT: J 1334 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8063 (mp0) REVERT: K 69 ARG cc_start: 0.9060 (ttm110) cc_final: 0.8269 (ptp90) REVERT: K 72 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8910 (tm-30) REVERT: G 93 GLN cc_start: 0.9097 (tt0) cc_final: 0.8788 (tm-30) REVERT: H 66 HIS cc_start: 0.8515 (m170) cc_final: 0.8222 (m90) REVERT: F 38 LYS cc_start: 0.7974 (tmmt) cc_final: 0.6983 (mttm) REVERT: F 62 TRP cc_start: 0.4320 (m100) cc_final: 0.3953 (m100) outliers start: 56 outliers final: 33 residues processed: 261 average time/residue: 0.1846 time to fit residues: 78.8069 Evaluate side-chains 235 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 71 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 346 optimal weight: 20.0000 chunk 311 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.081236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053867 restraints weight = 122877.490| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.79 r_work: 0.2788 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31084 Z= 0.167 Angle : 0.518 8.123 42364 Z= 0.275 Chirality : 0.041 0.208 4846 Planarity : 0.004 0.055 5251 Dihedral : 14.927 139.691 4984 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.56 % Allowed : 23.91 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 0.95 (0.14), residues: 3641 helix: 2.01 (0.15), residues: 1295 sheet: 0.13 (0.23), residues: 531 loop : -0.18 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 191 TYR 0.019 0.001 TYR P 99 PHE 0.011 0.001 PHE I 385 TRP 0.009 0.001 TRP I 183 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (31076) covalent geometry : angle 0.51271 / 0.27 (42352) hydrogen bonds : bond 0.03734 / 2.47 ( 1319) hydrogen bonds : angle 4.30315 / 2.95 ( 3643) metal coordination : bond 0.00904 / 0.45 ( 8) metal coordination : angle 4.44114 / 2.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 204 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1 MET cc_start: 0.8013 (pmm) cc_final: 0.7806 (pmm) REVERT: I 165 HIS cc_start: 0.8564 (t-90) cc_final: 0.8341 (t-90) REVERT: I 813 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7499 (tm-30) REVERT: I 1340 GLU cc_start: 0.8688 (tp30) cc_final: 0.8425 (tp30) REVERT: J 172 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.6633 (p90) REVERT: J 298 MET cc_start: 0.9365 (mmt) cc_final: 0.9083 (mpp) REVERT: J 1189 MET cc_start: 0.8513 (mmt) cc_final: 0.8313 (mmt) REVERT: J 1239 ASP cc_start: 0.9219 (t0) cc_final: 0.8979 (m-30) REVERT: J 1334 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8015 (mp0) REVERT: K 69 ARG cc_start: 0.9054 (ttm110) cc_final: 0.8287 (ptp90) REVERT: K 72 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8915 (tm-30) REVERT: G 93 GLN cc_start: 0.9096 (tt0) cc_final: 0.8765 (tm-30) REVERT: H 66 HIS cc_start: 0.8528 (m170) cc_final: 0.8240 (m90) REVERT: F 62 TRP cc_start: 0.4524 (m100) cc_final: 0.4249 (m100) outliers start: 79 outliers final: 55 residues processed: 272 average time/residue: 0.1894 time to fit residues: 84.1050 Evaluate side-chains 260 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 110 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 245 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 300 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 798 GLN J 164 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.080626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053475 restraints weight = 110623.082| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.53 r_work: 0.2785 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31084 Z= 0.178 Angle : 0.530 8.816 42364 Z= 0.281 Chirality : 0.041 0.202 4846 Planarity : 0.004 0.055 5251 Dihedral : 14.949 139.777 4984 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.84 % Allowed : 23.43 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3641 helix: 1.96 (0.15), residues: 1290 sheet: 0.16 (0.23), residues: 517 loop : -0.21 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 191 TYR 0.030 0.001 TYR F 39 PHE 0.012 0.001 PHE I 385 TRP 0.010 0.001 TRP I 183 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (31076) covalent geometry : angle 0.52396 / 0.28 (42352) hydrogen bonds : bond 0.03789 / 2.50 ( 1319) hydrogen bonds : angle 4.28648 / 2.94 ( 3643) metal coordination : bond 0.00953 / 0.47 ( 8) metal coordination : angle 4.63364 / 2.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 208 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 165 HIS cc_start: 0.8615 (t-90) cc_final: 0.8345 (t-90) REVERT: I 541 GLU cc_start: 0.9204 (pm20) cc_final: 0.8994 (pm20) REVERT: I 813 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7482 (tm-30) REVERT: I 1340 GLU cc_start: 0.8707 (tp30) cc_final: 0.8454 (tp30) REVERT: J 172 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6574 (p90) REVERT: J 298 MET cc_start: 0.9371 (mmt) cc_final: 0.9082 (mpp) REVERT: J 1189 MET cc_start: 0.8506 (mmt) cc_final: 0.8303 (mmt) REVERT: J 1239 ASP cc_start: 0.9208 (t0) cc_final: 0.8973 (m-30) REVERT: J 1334 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8011 (mp0) REVERT: K 56 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: K 69 ARG cc_start: 0.9042 (ttm110) cc_final: 0.8321 (ptp90) REVERT: K 72 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8808 (tm-30) REVERT: G 93 GLN cc_start: 0.9095 (tt0) cc_final: 0.8773 (tm-30) REVERT: G 194 GLN cc_start: 0.8990 (mp10) cc_final: 0.8761 (pm20) REVERT: H 66 HIS cc_start: 0.8507 (m170) cc_final: 0.8219 (m90) REVERT: F 62 TRP cc_start: 0.4440 (m100) cc_final: 0.4169 (m100) outliers start: 88 outliers final: 63 residues processed: 282 average time/residue: 0.1937 time to fit residues: 89.0805 Evaluate side-chains 265 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 200 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 114 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 358 optimal weight: 20.0000 chunk 360 optimal weight: 10.0000 chunk 36 optimal weight: 0.0050 chunk 43 optimal weight: 3.9990 chunk 289 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 308 optimal weight: 0.8980 chunk 336 optimal weight: 0.7980 chunk 271 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.081886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.054119 restraints weight = 153782.967| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 4.26 r_work: 0.2790 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31084 Z= 0.105 Angle : 0.495 8.262 42364 Z= 0.263 Chirality : 0.041 0.196 4846 Planarity : 0.003 0.056 5251 Dihedral : 14.908 140.218 4984 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.24 % Allowed : 24.16 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 3641 helix: 1.99 (0.15), residues: 1302 sheet: 0.24 (0.23), residues: 513 loop : -0.19 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 67 TYR 0.015 0.001 TYR F 39 PHE 0.011 0.001 PHE I 405 TRP 0.012 0.001 TRP I 183 HIS 0.003 0.000 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (31076) covalent geometry : angle 0.48949 / 0.26 (42352) hydrogen bonds : bond 0.03421 / 2.27 ( 1319) hydrogen bonds : angle 4.16381 / 2.85 ( 3643) metal coordination : bond 0.00485 / 0.25 ( 8) metal coordination : angle 4.26491 / 2.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1 MET cc_start: 0.8138 (pmm) cc_final: 0.7913 (pmm) REVERT: I 165 HIS cc_start: 0.8594 (t-90) cc_final: 0.8324 (t-90) REVERT: I 541 GLU cc_start: 0.9261 (pm20) cc_final: 0.9057 (pm20) REVERT: I 813 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7470 (tm-30) REVERT: I 1340 GLU cc_start: 0.8766 (tp30) cc_final: 0.8511 (tp30) REVERT: J 172 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6618 (p90) REVERT: J 298 MET cc_start: 0.9396 (mmt) cc_final: 0.9114 (mpp) REVERT: J 822 MET cc_start: 0.8971 (tpp) cc_final: 0.8761 (mtp) REVERT: J 1134 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6843 (mp) REVERT: J 1189 MET cc_start: 0.8531 (mmt) cc_final: 0.8329 (mmt) REVERT: J 1239 ASP cc_start: 0.9178 (t0) cc_final: 0.8973 (m-30) REVERT: J 1334 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8052 (mp0) REVERT: K 56 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: K 69 ARG cc_start: 0.9020 (ttm110) cc_final: 0.8300 (ptp90) REVERT: K 72 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8914 (tm-30) REVERT: G 93 GLN cc_start: 0.9123 (tt0) cc_final: 0.8781 (tm-30) REVERT: G 194 GLN cc_start: 0.9003 (mp10) cc_final: 0.8787 (pm20) REVERT: H 66 HIS cc_start: 0.8474 (m170) cc_final: 0.8200 (m90) REVERT: F 38 LYS cc_start: 0.8002 (pptt) cc_final: 0.6900 (mttp) REVERT: F 62 TRP cc_start: 0.4591 (m100) cc_final: 0.4207 (m100) outliers start: 69 outliers final: 51 residues processed: 268 average time/residue: 0.1943 time to fit residues: 84.8557 Evaluate side-chains 258 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 328 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 136 optimal weight: 0.0670 chunk 43 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 197 optimal weight: 0.2980 chunk 336 optimal weight: 0.9980 overall best weight: 1.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 24 GLN I 856 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN F 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.081241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.053130 restraints weight = 180970.952| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.61 r_work: 0.2751 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31084 Z= 0.140 Angle : 0.506 8.244 42364 Z= 0.268 Chirality : 0.041 0.195 4846 Planarity : 0.004 0.108 5251 Dihedral : 14.906 140.284 4984 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.46 % Allowed : 24.19 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 0.94 (0.14), residues: 3641 helix: 1.99 (0.15), residues: 1303 sheet: 0.15 (0.23), residues: 521 loop : -0.19 (0.15), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 33 TYR 0.012 0.001 TYR J 631 PHE 0.010 0.001 PHE I 405 TRP 0.016 0.001 TRP I 183 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (31076) covalent geometry : angle 0.50042 / 0.27 (42352) hydrogen bonds : bond 0.03499 / 2.33 ( 1319) hydrogen bonds : angle 4.16455 / 2.85 ( 3643) metal coordination : bond 0.00732 / 0.36 ( 8) metal coordination : angle 4.32402 / 2.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 203 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1 MET cc_start: 0.8158 (pmm) cc_final: 0.7915 (pmm) REVERT: I 165 HIS cc_start: 0.8677 (t-90) cc_final: 0.8367 (t-90) REVERT: I 541 GLU cc_start: 0.9266 (pm20) cc_final: 0.9046 (pm20) REVERT: I 813 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7500 (tm-30) REVERT: I 1340 GLU cc_start: 0.8789 (tp30) cc_final: 0.8489 (tp30) REVERT: J 172 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6560 (p90) REVERT: J 298 MET cc_start: 0.9408 (mmt) cc_final: 0.9125 (mpp) REVERT: J 1134 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6889 (mp) REVERT: J 1189 MET cc_start: 0.8523 (mmt) cc_final: 0.8297 (mmt) REVERT: J 1239 ASP cc_start: 0.9199 (t0) cc_final: 0.8980 (m-30) REVERT: J 1334 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8103 (mp0) REVERT: K 56 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: K 69 ARG cc_start: 0.9054 (ttm110) cc_final: 0.8424 (ptp90) REVERT: K 72 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8873 (tm-30) REVERT: G 93 GLN cc_start: 0.9138 (tt0) cc_final: 0.8798 (tm-30) REVERT: G 125 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8723 (ttpp) REVERT: G 194 GLN cc_start: 0.9037 (mp10) cc_final: 0.8827 (pm20) REVERT: H 66 HIS cc_start: 0.8540 (m170) cc_final: 0.8251 (m90) REVERT: F 38 LYS cc_start: 0.8041 (pptt) cc_final: 0.7042 (mttp) REVERT: F 62 TRP cc_start: 0.4482 (m100) cc_final: 0.4130 (m100) outliers start: 76 outliers final: 62 residues processed: 269 average time/residue: 0.1785 time to fit residues: 78.4164 Evaluate side-chains 265 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 200 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 30 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 238 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 chunk 326 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 317 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 301 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.079879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052152 restraints weight = 147181.216| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 4.14 r_work: 0.2739 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31084 Z= 0.230 Angle : 0.563 11.293 42364 Z= 0.294 Chirality : 0.042 0.221 4846 Planarity : 0.004 0.076 5251 Dihedral : 14.960 140.029 4984 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 2.52 % Allowed : 24.16 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3641 helix: 1.91 (0.15), residues: 1295 sheet: 0.02 (0.22), residues: 531 loop : -0.23 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 33 TYR 0.014 0.001 TYR J 631 PHE 0.015 0.001 PHE I 385 TRP 0.015 0.001 TRP I 183 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (31076) covalent geometry : angle 0.55745 / 0.29 (42352) hydrogen bonds : bond 0.03830 / 2.55 ( 1319) hydrogen bonds : angle 4.28911 / 2.94 ( 3643) metal coordination : bond 0.01214 / 0.58 ( 8) metal coordination : angle 4.92248 / 2.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 196 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1 MET cc_start: 0.8245 (pmm) cc_final: 0.7998 (pmm) REVERT: I 165 HIS cc_start: 0.8695 (t-90) cc_final: 0.8357 (t-90) REVERT: I 515 MET cc_start: 0.8932 (ttp) cc_final: 0.8727 (ttp) REVERT: I 541 GLU cc_start: 0.9266 (pm20) cc_final: 0.9041 (pm20) REVERT: I 813 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7461 (tm-30) REVERT: I 1340 GLU cc_start: 0.8785 (tp30) cc_final: 0.8482 (tp30) REVERT: J 172 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.6647 (p90) REVERT: J 298 MET cc_start: 0.9404 (mmt) cc_final: 0.9103 (mpp) REVERT: J 458 ASN cc_start: 0.9047 (t0) cc_final: 0.8764 (t0) REVERT: J 857 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7851 (mt) REVERT: J 1134 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6974 (mp) REVERT: J 1189 MET cc_start: 0.8522 (mmt) cc_final: 0.8304 (mmt) REVERT: J 1334 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8063 (mp0) REVERT: K 56 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: K 69 ARG cc_start: 0.9118 (ttm110) cc_final: 0.8696 (ptp90) REVERT: K 72 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8856 (tm-30) REVERT: G 93 GLN cc_start: 0.9131 (tt0) cc_final: 0.8792 (tm-30) REVERT: H 66 HIS cc_start: 0.8483 (m170) cc_final: 0.8202 (m90) REVERT: F 62 TRP cc_start: 0.4570 (m100) cc_final: 0.4244 (m100) outliers start: 78 outliers final: 67 residues processed: 263 average time/residue: 0.1813 time to fit residues: 78.7370 Evaluate side-chains 263 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 192 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 306 optimal weight: 1.9990 chunk 239 optimal weight: 0.0870 chunk 334 optimal weight: 6.9990 chunk 238 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 265 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 138 optimal weight: 0.0370 chunk 295 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 808 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.081670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.054193 restraints weight = 130977.629| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.91 r_work: 0.2796 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31084 Z= 0.105 Angle : 0.513 10.642 42364 Z= 0.270 Chirality : 0.041 0.188 4846 Planarity : 0.004 0.057 5251 Dihedral : 14.915 140.326 4984 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.27 % Allowed : 24.42 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3641 helix: 1.98 (0.15), residues: 1301 sheet: 0.10 (0.23), residues: 524 loop : -0.22 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 33 TYR 0.015 0.001 TYR F 39 PHE 0.010 0.001 PHE I 405 TRP 0.016 0.001 TRP I 183 HIS 0.003 0.000 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (31076) covalent geometry : angle 0.50766 / 0.27 (42352) hydrogen bonds : bond 0.03418 / 2.28 ( 1319) hydrogen bonds : angle 4.13886 / 2.83 ( 3643) metal coordination : bond 0.00436 / 0.24 ( 8) metal coordination : angle 4.38818 / 2.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 209 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1 MET cc_start: 0.8187 (pmm) cc_final: 0.7932 (pmm) REVERT: I 165 HIS cc_start: 0.8650 (t-90) cc_final: 0.8317 (t-90) REVERT: I 487 LEU cc_start: 0.8925 (mt) cc_final: 0.8618 (mt) REVERT: I 515 MET cc_start: 0.8847 (ttp) cc_final: 0.8599 (ttp) REVERT: I 530 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9212 (pt) REVERT: I 541 GLU cc_start: 0.9241 (pm20) cc_final: 0.9029 (pm20) REVERT: I 813 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7495 (tm-30) REVERT: I 1340 GLU cc_start: 0.8756 (tp30) cc_final: 0.8450 (tp30) REVERT: J 172 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6549 (p90) REVERT: J 298 MET cc_start: 0.9383 (mmt) cc_final: 0.9097 (mpp) REVERT: J 414 GLU cc_start: 0.9325 (tm-30) cc_final: 0.8866 (tm-30) REVERT: J 458 ASN cc_start: 0.8987 (t0) cc_final: 0.8739 (t0) REVERT: J 1134 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6917 (mp) REVERT: J 1189 MET cc_start: 0.8548 (mmt) cc_final: 0.8322 (mmt) REVERT: J 1334 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8031 (mp0) REVERT: K 56 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: K 69 ARG cc_start: 0.9075 (ttm110) cc_final: 0.8333 (ptp90) REVERT: G 93 GLN cc_start: 0.9111 (tt0) cc_final: 0.8774 (tm-30) REVERT: G 125 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8703 (ttpp) REVERT: H 66 HIS cc_start: 0.8452 (m170) cc_final: 0.8163 (m90) REVERT: F 38 LYS cc_start: 0.7719 (pptt) cc_final: 0.7182 (mtmm) REVERT: F 62 TRP cc_start: 0.4564 (m100) cc_final: 0.4247 (m100) outliers start: 70 outliers final: 57 residues processed: 269 average time/residue: 0.1874 time to fit residues: 82.8014 Evaluate side-chains 267 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 206 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 130 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 28 optimal weight: 0.7980 chunk 320 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 346 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.080388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.052885 restraints weight = 144300.102| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.08 r_work: 0.2734 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31084 Z= 0.183 Angle : 0.552 10.642 42364 Z= 0.288 Chirality : 0.041 0.182 4846 Planarity : 0.004 0.054 5251 Dihedral : 14.949 140.295 4984 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.08 % Allowed : 24.90 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3641 helix: 1.92 (0.15), residues: 1296 sheet: 0.02 (0.23), residues: 531 loop : -0.21 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 33 TYR 0.013 0.001 TYR I 62 PHE 0.013 0.001 PHE I 385 TRP 0.017 0.001 TRP I 183 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (31076) covalent geometry : angle 0.54610 / 0.29 (42352) hydrogen bonds : bond 0.03694 / 2.45 ( 1319) hydrogen bonds : angle 4.23107 / 2.90 ( 3643) metal coordination : bond 0.00999 / 0.48 ( 8) metal coordination : angle 4.78678 / 2.39 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 541 GLU cc_start: 0.9283 (pm20) cc_final: 0.9062 (pm20) REVERT: I 813 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7530 (tm-30) REVERT: I 1340 GLU cc_start: 0.8796 (tp30) cc_final: 0.8468 (tp30) REVERT: J 172 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.6568 (p90) REVERT: J 298 MET cc_start: 0.9403 (mmt) cc_final: 0.9093 (mpp) REVERT: J 458 ASN cc_start: 0.9017 (t0) cc_final: 0.8741 (t0) REVERT: J 762 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7759 (m-40) REVERT: J 822 MET cc_start: 0.9039 (tpp) cc_final: 0.8815 (mtp) REVERT: J 857 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7820 (mt) REVERT: J 1134 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6864 (mp) REVERT: J 1189 MET cc_start: 0.8518 (mmt) cc_final: 0.8297 (mmt) REVERT: J 1334 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8062 (mp0) REVERT: K 56 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: K 72 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8717 (tm-30) REVERT: G 93 GLN cc_start: 0.9162 (tt0) cc_final: 0.8800 (tm-30) REVERT: H 66 HIS cc_start: 0.8537 (m170) cc_final: 0.8254 (m90) REVERT: F 38 LYS cc_start: 0.7649 (pptt) cc_final: 0.7143 (mtmm) REVERT: F 62 TRP cc_start: 0.4557 (m100) cc_final: 0.4217 (m100) outliers start: 64 outliers final: 57 residues processed: 256 average time/residue: 0.1852 time to fit residues: 77.9264 Evaluate side-chains 262 residues out of total 3123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 130 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 310 optimal weight: 2.9990 chunk 358 optimal weight: 1.9990 chunk 246 optimal weight: 8.9990 chunk 64 optimal weight: 0.0020 chunk 251 optimal weight: 0.9990 chunk 305 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 72 optimal weight: 0.1980 chunk 75 optimal weight: 0.0470 chunk 50 optimal weight: 0.8980 overall best weight: 0.4288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 760 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.081839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.054263 restraints weight = 142437.428| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.07 r_work: 0.2797 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31084 Z= 0.103 Angle : 0.521 10.881 42364 Z= 0.274 Chirality : 0.041 0.203 4846 Planarity : 0.003 0.056 5251 Dihedral : 14.914 140.589 4984 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.76 % Allowed : 25.06 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3641 helix: 1.98 (0.15), residues: 1302 sheet: 0.08 (0.23), residues: 519 loop : -0.20 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 33 TYR 0.013 0.001 TYR I 62 PHE 0.010 0.001 PHE I 405 TRP 0.017 0.001 TRP I 183 HIS 0.003 0.000 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (31076) covalent geometry : angle 0.51580 / 0.27 (42352) hydrogen bonds : bond 0.03367 / 2.24 ( 1319) hydrogen bonds : angle 4.12897 / 2.82 ( 3643) metal coordination : bond 0.00355 / 0.19 ( 8) metal coordination : angle 4.34647 / 2.07 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9285.70 seconds wall clock time: 159 minutes 20.84 seconds (9560.84 seconds total)