Starting phenix.real_space_refine on Mon Aug 25 12:08:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pen_17632/08_2025/8pen_17632.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pen_17632/08_2025/8pen_17632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pen_17632/08_2025/8pen_17632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pen_17632/08_2025/8pen_17632.map" model { file = "/net/cci-nas-00/data/ceres_data/8pen_17632/08_2025/8pen_17632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pen_17632/08_2025/8pen_17632.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.050 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 87 5.49 5 Mg 1 5.21 5 S 111 5.16 5 C 17106 2.51 5 N 4916 2.21 5 O 5511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27734 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "I" Number of atoms: 10423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 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: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 784 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} 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: "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 11683 SG CYS J 70 24.339 70.116 82.825 1.00158.85 S ATOM 11697 SG CYS J 72 23.467 66.390 82.627 1.00157.54 S ATOM 11805 SG CYS J 85 21.833 68.586 85.226 1.00162.84 S ATOM 11829 SG CYS J 88 25.555 67.757 85.507 1.00159.71 S ATOM 17517 SG CYS J 814 57.178 127.202 91.358 1.00127.02 S ATOM 18082 SG CYS J 888 58.687 123.881 90.311 1.00123.55 S ATOM 18133 SG CYS J 895 57.708 126.423 87.633 1.00123.37 S ATOM 18154 SG CYS J 898 60.659 127.089 89.908 1.00122.70 S Time building chain proxies: 6.63, per 1000 atoms: 0.24 Number of scatterers: 27734 At special positions: 0 Unit cell: (139.776, 169.728, 157.248, 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 111 16.00 P 87 15.00 Mg 1 11.99 O 5511 8.00 N 4916 7.00 C 17106 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: 1.91 Conformation dependent library (CDL) restraints added in 856.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " 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 895 " Number of angles added : 12 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6122 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 51 sheets defined 39.0% alpha, 18.5% beta 39 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 71 removed outlier: 3.581A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 99 Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.569A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.676A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.909A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) removed outlier: 3.626A 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: 3.927A 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 removed outlier: 3.758A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 4.032A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 3.972A 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 329 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 389 removed outlier: 3.863A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 410 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.512A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.708A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 488 through 493' Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.800A 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: 4.024A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.582A 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: 3.761A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.863A 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: 3.780A pdb=" N HIS I 628 " --> pdb=" O GLU I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.006A 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 863 removed outlier: 3.588A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.571A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 997 removed outlier: 3.704A pdb=" N ARG I 996 " --> pdb=" O PRO I 993 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.107A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 3.996A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.617A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.523A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 4.098A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE I1164 " --> pdb=" O LEU I1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1160 through 1164' Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.647A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1293 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.751A 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 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.519A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.781A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 128 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 191 removed outlier: 3.549A 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 483 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.598A 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: 3.925A 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: 4.203A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.047A 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: 4.085A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA J 804 " --> pdb=" O LEU J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 4.023A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 874 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 1146 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.724A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.308A 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: 3.792A 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 removed outlier: 3.607A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 4.350A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 33 removed outlier: 3.638A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 4.186A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 removed outlier: 4.279A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.576A 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: 3.795A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.122A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.582A 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 160 removed outlier: 3.599A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.795A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 233 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 37 removed outlier: 3.821A pdb=" N THR P 44 " --> pdb=" O LYS P 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.501A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 66 through 75 removed outlier: 6.063A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA6, first strand: chain 'I' and resid 148 through 151 Processing sheet with id=AA7, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.853A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AA9, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB1, first strand: chain 'I' and resid 256 through 257 Processing sheet with id=AB2, first strand: chain 'I' and resid 296 through 297 removed outlier: 4.147A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.790A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 529 through 531 Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.573A pdb=" N LYS I 593 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB7, first strand: chain 'I' and resid 716 through 717 removed outlier: 7.043A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 748 through 752 removed outlier: 7.050A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC1, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC2, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.475A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 830 through 841 removed outlier: 6.230A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.736A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC6, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.810A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC8, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AC9, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.747A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.964A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 159 through 160 removed outlier: 7.217A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 253 through 254 removed outlier: 4.155A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD4, first strand: chain 'J' and resid 705 through 709 removed outlier: 3.746A pdb=" N THR J 705 " --> pdb=" O GLN J 716 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD6, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD7, first strand: chain 'J' and resid 825 through 827 removed outlier: 3.657A pdb=" N GLU J 833 " --> pdb=" O VAL J 825 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 842 through 843 removed outlier: 4.075A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.494A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.718A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 957 through 961 Processing sheet with id=AE3, first strand: chain 'J' and resid 1024 through 1029 removed outlier: 6.242A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP J1119 " --> pdb=" O THR J1029 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 4.844A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.552A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.505A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.615A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.007A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.575A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AF2, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.897A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AF4, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.720A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 97 through 105 removed outlier: 8.000A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.579A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) 1118 hydrogen bonds defined for protein. 3170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 7.08 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5794 1.33 - 1.45: 6318 1.45 - 1.57: 15865 1.57 - 1.70: 172 1.70 - 1.82: 192 Bond restraints: 28341 Sorted by residual: bond pdb=" CB ARG H 12 " pdb=" CG ARG H 12 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CB GLN K 70 " pdb=" CG GLN K 70 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" CB GLU J1317 " pdb=" CG GLU J1317 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" CB GLN P 15 " pdb=" CG GLN P 15 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CA MET J1025 " pdb=" CB MET J1025 " ideal model delta sigma weight residual 1.534 1.556 -0.022 1.57e-02 4.06e+03 1.96e+00 ... (remaining 28336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 38508 3.19 - 6.38: 136 6.38 - 9.58: 26 9.58 - 12.77: 4 12.77 - 15.96: 1 Bond angle restraints: 38675 Sorted by residual: angle pdb=" C GLU K 74 " pdb=" N GLN K 75 " pdb=" CA GLN K 75 " ideal model delta sigma weight residual 121.66 112.88 8.78 1.76e+00 3.23e-01 2.49e+01 angle pdb=" CA LEU I 237 " pdb=" CB LEU I 237 " pdb=" CG LEU I 237 " ideal model delta sigma weight residual 116.30 132.26 -15.96 3.50e+00 8.16e-02 2.08e+01 angle pdb=" CA GLN K 70 " pdb=" CB GLN K 70 " pdb=" CG GLN K 70 " ideal model delta sigma weight residual 114.10 122.12 -8.02 2.00e+00 2.50e-01 1.61e+01 angle pdb=" CB MET P 32 " pdb=" CG MET P 32 " pdb=" SD MET P 32 " ideal model delta sigma weight residual 112.70 124.44 -11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CA GLU P 48 " pdb=" CB GLU P 48 " pdb=" CG GLU P 48 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 ... (remaining 38670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 16286 35.75 - 71.50: 904 71.50 - 107.25: 42 107.25 - 142.99: 2 142.99 - 178.74: 2 Dihedral angle restraints: 17236 sinusoidal: 7723 harmonic: 9513 Sorted by residual: dihedral pdb=" C4' DC B 28 " pdb=" C3' DC B 28 " pdb=" O3' DC B 28 " pdb=" P DC B 29 " ideal model delta sinusoidal sigma weight residual 220.00 41.26 178.74 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC A 39 " pdb=" C3' DC A 39 " pdb=" O3' DC A 39 " pdb=" P DC A 40 " ideal model delta sinusoidal sigma weight residual 220.00 71.71 148.29 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" C4' DC A 6 " pdb=" C3' DC A 6 " pdb=" O3' DC A 6 " pdb=" P DC A 7 " ideal model delta sinusoidal sigma weight residual -140.00 -4.73 -135.27 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 17233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4071 0.076 - 0.151: 346 0.151 - 0.227: 1 0.227 - 0.303: 0 0.303 - 0.379: 1 Chirality restraints: 4419 Sorted by residual: chirality pdb=" CB ILE J 500 " pdb=" CA ILE J 500 " pdb=" CG1 ILE J 500 " pdb=" CG2 ILE J 500 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA ILE H 99 " pdb=" N ILE H 99 " pdb=" C ILE H 99 " pdb=" CB ILE H 99 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA GLN K 75 " pdb=" N GLN K 75 " pdb=" C GLN K 75 " pdb=" CB GLN K 75 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 4416 not shown) Planarity restraints: 4753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 67 " -0.155 9.50e-02 1.11e+02 7.02e-02 3.94e+00 pdb=" NE ARG K 67 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG K 67 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG K 67 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG K 67 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 8 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" CG ASP K 8 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP K 8 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP K 8 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 71 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" CD GLU K 71 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU K 71 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU K 71 " -0.011 2.00e-02 2.50e+03 ... (remaining 4750 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 316 2.60 - 3.18: 23215 3.18 - 3.75: 45458 3.75 - 4.33: 59329 4.33 - 4.90: 98060 Nonbonded interactions: 226378 Sorted by model distance: nonbonded pdb=" OP1 U R 17 " pdb="MG MG J1503 " model vdw 2.030 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG J1503 " model vdw 2.091 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.099 2.170 nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG J1503 " model vdw 2.104 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.122 2.170 ... (remaining 226373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 4 through 218 or resid 220 through 233)) selection = (chain 'H' and (resid 4 through 218 or resid 220 through 233)) } 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.340 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.002 0.046 28349 Z= 0.110 Angle : 0.559 15.961 38687 Z= 0.290 Chirality : 0.040 0.379 4419 Planarity : 0.004 0.070 4753 Dihedral : 19.244 178.743 11114 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 1.49 % Allowed : 28.76 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: 1.05 (0.15), residues: 3292 helix: 2.05 (0.16), residues: 1170 sheet: 0.38 (0.23), residues: 501 loop : -0.16 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG K 67 TYR 0.028 0.001 TYR H 185 PHE 0.008 0.001 PHE I 405 TRP 0.010 0.001 TRP I 183 HIS 0.002 0.000 HIS J 430 Details of bonding type rmsd covalent geometry : bond 0.00246 (28341) covalent geometry : angle 0.55859 (38675) hydrogen bonds : bond 0.13060 ( 1213) hydrogen bonds : angle 4.97674 ( 3368) metal coordination : bond 0.00264 ( 8) metal coordination : angle 0.96461 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 546 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8965 (mp0) REVERT: J 497 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8439 (mm-30) REVERT: J 513 MET cc_start: 0.8829 (mtp) cc_final: 0.8600 (mtp) REVERT: J 1100 PHE cc_start: 0.8512 (t80) cc_final: 0.7712 (t80) REVERT: J 1193 TRP cc_start: 0.8822 (p90) cc_final: 0.8502 (p90) outliers start: 41 outliers final: 38 residues processed: 247 average time/residue: 0.1831 time to fit residues: 74.2269 Evaluate side-chains 238 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 HIS I 518 ASN I1236 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.070642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.050019 restraints weight = 115670.367| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.59 r_work: 0.2757 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28349 Z= 0.229 Angle : 0.574 13.920 38687 Z= 0.300 Chirality : 0.042 0.326 4419 Planarity : 0.004 0.045 4753 Dihedral : 15.896 175.202 4690 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 3.08 % Allowed : 25.54 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: 1.00 (0.15), residues: 3292 helix: 2.08 (0.16), residues: 1167 sheet: 0.25 (0.23), residues: 505 loop : -0.20 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 67 TYR 0.016 0.001 TYR J 631 PHE 0.013 0.001 PHE G 35 TRP 0.020 0.001 TRP I 183 HIS 0.007 0.001 HIS P 65 Details of bonding type rmsd covalent geometry : bond 0.00521 (28341) covalent geometry : angle 0.57020 (38675) hydrogen bonds : bond 0.04063 ( 1213) hydrogen bonds : angle 4.25577 ( 3368) metal coordination : bond 0.02839 ( 8) metal coordination : angle 3.87310 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 208 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: I 370 MET cc_start: 0.9229 (mmm) cc_final: 0.8984 (tpt) REVERT: I 696 ASP cc_start: 0.8520 (t0) cc_final: 0.8293 (t0) REVERT: I 1107 MET cc_start: 0.8951 (mmm) cc_final: 0.8714 (tpp) REVERT: J 136 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8721 (tp30) REVERT: J 1100 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7751 (t80) REVERT: J 1101 LEU cc_start: 0.8820 (mm) cc_final: 0.8475 (mp) REVERT: K 8 ASP cc_start: 0.8152 (p0) cc_final: 0.7852 (p0) REVERT: K 67 ARG cc_start: 0.8171 (ttm110) cc_final: 0.7942 (ttm110) REVERT: H 205 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8457 (ttm) outliers start: 86 outliers final: 50 residues processed: 272 average time/residue: 0.1650 time to fit residues: 75.1789 Evaluate side-chains 241 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1254 GLU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 75 GLN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 176 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 chunk 335 optimal weight: 4.9990 chunk 128 optimal weight: 0.1980 chunk 161 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.070844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.051143 restraints weight = 92435.046| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.13 r_work: 0.2810 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28349 Z= 0.140 Angle : 0.509 13.697 38687 Z= 0.267 Chirality : 0.040 0.316 4419 Planarity : 0.003 0.041 4753 Dihedral : 15.797 175.710 4658 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Rotamer: Outliers : 3.15 % Allowed : 25.04 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: 1.03 (0.15), residues: 3292 helix: 2.12 (0.15), residues: 1168 sheet: 0.32 (0.23), residues: 511 loop : -0.23 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 67 TYR 0.012 0.001 TYR J 631 PHE 0.011 0.001 PHE I 405 TRP 0.022 0.001 TRP I 183 HIS 0.003 0.001 HIS P 65 Details of bonding type rmsd covalent geometry : bond 0.00315 (28341) covalent geometry : angle 0.50568 (38675) hydrogen bonds : bond 0.03535 ( 1213) hydrogen bonds : angle 4.04729 ( 3368) metal coordination : bond 0.00951 ( 8) metal coordination : angle 3.12830 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 211 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 165 HIS cc_start: 0.8068 (t-90) cc_final: 0.7802 (t70) REVERT: I 370 MET cc_start: 0.9246 (mmm) cc_final: 0.8938 (tpt) REVERT: I 696 ASP cc_start: 0.8504 (t0) cc_final: 0.8268 (t0) REVERT: I 968 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8372 (pp20) REVERT: J 115 TRP cc_start: 0.9378 (m-10) cc_final: 0.9138 (m-10) REVERT: J 136 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8659 (tp30) REVERT: J 1100 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7677 (t80) REVERT: J 1189 MET cc_start: 0.8328 (tpt) cc_final: 0.8076 (tpt) REVERT: K 8 ASP cc_start: 0.8144 (p0) cc_final: 0.7776 (p0) REVERT: K 30 MET cc_start: 0.9161 (mtt) cc_final: 0.8848 (mtt) REVERT: K 67 ARG cc_start: 0.8264 (ttm110) cc_final: 0.8031 (ttm110) REVERT: G 51 MET cc_start: 0.9138 (tpt) cc_final: 0.8729 (tpt) REVERT: G 101 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8951 (p) REVERT: H 205 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8379 (ttm) outliers start: 88 outliers final: 55 residues processed: 283 average time/residue: 0.1786 time to fit residues: 83.0769 Evaluate side-chains 258 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1254 GLU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 205 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 184 optimal weight: 3.9990 chunk 234 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 312 optimal weight: 10.0000 chunk 306 optimal weight: 0.0570 chunk 327 optimal weight: 6.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 921 GLN J1279 GLN K 15 ASN K 75 GLN ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.068206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.047710 restraints weight = 94758.882| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.21 r_work: 0.2704 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 28349 Z= 0.279 Angle : 0.609 12.545 38687 Z= 0.317 Chirality : 0.043 0.330 4419 Planarity : 0.004 0.043 4753 Dihedral : 15.947 172.045 4653 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 4.00 % Allowed : 24.76 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: 0.75 (0.15), residues: 3292 helix: 1.83 (0.15), residues: 1172 sheet: 0.19 (0.23), residues: 512 loop : -0.37 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 69 TYR 0.016 0.001 TYR J 631 PHE 0.015 0.002 PHE I 385 TRP 0.033 0.002 TRP I 183 HIS 0.007 0.001 HIS P 65 Details of bonding type rmsd covalent geometry : bond 0.00633 (28341) covalent geometry : angle 0.60393 (38675) hydrogen bonds : bond 0.04521 ( 1213) hydrogen bonds : angle 4.26548 ( 3368) metal coordination : bond 0.01610 ( 8) metal coordination : angle 4.27591 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 189 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 60 ASP cc_start: 0.8429 (t0) cc_final: 0.8225 (t0) REVERT: I 165 HIS cc_start: 0.8293 (t-90) cc_final: 0.7792 (t-90) REVERT: I 370 MET cc_start: 0.9228 (mmm) cc_final: 0.8848 (tpt) REVERT: I 696 ASP cc_start: 0.8541 (t0) cc_final: 0.8257 (t0) REVERT: I 968 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8420 (pp20) REVERT: J 431 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.8114 (ptm-80) REVERT: J 1100 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7800 (t80) REVERT: J 1101 LEU cc_start: 0.8708 (mm) cc_final: 0.8502 (mm) REVERT: K 8 ASP cc_start: 0.8135 (p0) cc_final: 0.7849 (p0) REVERT: K 30 MET cc_start: 0.9246 (mtt) cc_final: 0.8963 (mtt) REVERT: K 69 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7474 (ttm110) REVERT: G 51 MET cc_start: 0.9177 (tpt) cc_final: 0.8916 (tpt) REVERT: G 101 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.9064 (p) REVERT: H 205 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8387 (ttm) outliers start: 112 outliers final: 72 residues processed: 284 average time/residue: 0.1855 time to fit residues: 86.2920 Evaluate side-chains 269 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 192 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 704 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1254 GLU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 185 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 273 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 230 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN I 494 ASN J 341 ASN J 477 GLN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.069617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.049724 restraints weight = 96408.827| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.21 r_work: 0.2763 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28349 Z= 0.116 Angle : 0.514 12.984 38687 Z= 0.268 Chirality : 0.040 0.316 4419 Planarity : 0.003 0.039 4753 Dihedral : 15.835 176.086 4653 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % Rotamer: Outliers : 2.76 % Allowed : 25.89 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: 0.95 (0.15), residues: 3292 helix: 2.11 (0.15), residues: 1162 sheet: 0.25 (0.23), residues: 529 loop : -0.31 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 67 TYR 0.020 0.001 TYR I 47 PHE 0.014 0.001 PHE I 405 TRP 0.027 0.001 TRP I 183 HIS 0.003 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00260 (28341) covalent geometry : angle 0.51110 (38675) hydrogen bonds : bond 0.03458 ( 1213) hydrogen bonds : angle 3.99791 ( 3368) metal coordination : bond 0.00699 ( 8) metal coordination : angle 3.23892 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 210 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 42 LYS cc_start: 0.8445 (pptt) cc_final: 0.7850 (pptt) REVERT: P 60 ASP cc_start: 0.8415 (t0) cc_final: 0.8211 (t0) REVERT: I 1 MET cc_start: 0.8064 (tmm) cc_final: 0.7554 (tmm) REVERT: I 37 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8970 (ttpp) REVERT: I 165 HIS cc_start: 0.8202 (t-90) cc_final: 0.7808 (t-90) REVERT: I 370 MET cc_start: 0.9255 (mmm) cc_final: 0.8878 (tpt) REVERT: I 696 ASP cc_start: 0.8566 (t0) cc_final: 0.8265 (t0) REVERT: I 800 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8451 (mtp) REVERT: I 968 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8383 (pp20) REVERT: I 1107 MET cc_start: 0.9151 (tpp) cc_final: 0.8944 (tpp) REVERT: J 503 SER cc_start: 0.8700 (m) cc_final: 0.8437 (t) REVERT: J 833 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8571 (tp30) REVERT: J 1100 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7854 (t80) REVERT: J 1101 LEU cc_start: 0.8705 (mm) cc_final: 0.8500 (mm) REVERT: K 30 MET cc_start: 0.9202 (mtt) cc_final: 0.8933 (mtt) REVERT: K 74 GLU cc_start: 0.9179 (pp20) cc_final: 0.8958 (pp20) REVERT: K 76 GLU cc_start: 0.9060 (pp20) cc_final: 0.8681 (mm-30) REVERT: G 51 MET cc_start: 0.9121 (tpt) cc_final: 0.8865 (tpt) REVERT: G 101 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8953 (p) outliers start: 77 outliers final: 55 residues processed: 273 average time/residue: 0.1872 time to fit residues: 83.5508 Evaluate side-chains 257 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 833 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 211 optimal weight: 0.2980 chunk 105 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 192 optimal weight: 0.0000 chunk 271 optimal weight: 0.9980 chunk 301 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 921 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.071252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.050986 restraints weight = 92879.653| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.20 r_work: 0.2800 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28349 Z= 0.105 Angle : 0.503 13.059 38687 Z= 0.262 Chirality : 0.040 0.347 4419 Planarity : 0.003 0.040 4753 Dihedral : 15.756 176.978 4651 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % Rotamer: Outliers : 2.73 % Allowed : 25.68 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: 1.03 (0.15), residues: 3292 helix: 2.22 (0.15), residues: 1156 sheet: 0.21 (0.23), residues: 506 loop : -0.26 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 67 TYR 0.017 0.001 TYR I 47 PHE 0.014 0.001 PHE I 405 TRP 0.021 0.001 TRP I 183 HIS 0.003 0.000 HIS J 430 Details of bonding type rmsd covalent geometry : bond 0.00234 (28341) covalent geometry : angle 0.50090 (38675) hydrogen bonds : bond 0.03192 ( 1213) hydrogen bonds : angle 3.85805 ( 3368) metal coordination : bond 0.00529 ( 8) metal coordination : angle 2.56710 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 203 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 60 ASP cc_start: 0.8416 (t0) cc_final: 0.8192 (t0) REVERT: I 1 MET cc_start: 0.8014 (tmm) cc_final: 0.7488 (tmm) REVERT: I 37 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8966 (ttpp) REVERT: I 165 HIS cc_start: 0.8241 (t-90) cc_final: 0.7789 (t70) REVERT: I 370 MET cc_start: 0.9273 (mmm) cc_final: 0.8909 (tpt) REVERT: I 696 ASP cc_start: 0.8562 (t0) cc_final: 0.8257 (t0) REVERT: I 800 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8362 (mtp) REVERT: J 400 MET cc_start: 0.8932 (mtp) cc_final: 0.8729 (mtm) REVERT: J 1100 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7725 (t80) REVERT: J 1189 MET cc_start: 0.8343 (tpt) cc_final: 0.8140 (tpt) REVERT: K 8 ASP cc_start: 0.8137 (p0) cc_final: 0.7859 (p0) REVERT: K 30 MET cc_start: 0.9169 (mtt) cc_final: 0.8925 (mtt) REVERT: K 69 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7398 (ttm110) REVERT: G 101 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8931 (p) outliers start: 76 outliers final: 56 residues processed: 264 average time/residue: 0.1862 time to fit residues: 80.4585 Evaluate side-chains 259 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 275 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** 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 = 0.3448 r_free = 0.3448 target = 0.070766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.050074 restraints weight = 114452.972| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.56 r_work: 0.2763 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28349 Z= 0.127 Angle : 0.516 13.177 38687 Z= 0.268 Chirality : 0.040 0.376 4419 Planarity : 0.003 0.038 4753 Dihedral : 15.749 176.736 4650 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.60 % Rotamer: Outliers : 2.73 % Allowed : 25.68 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: 1.03 (0.15), residues: 3292 helix: 2.22 (0.15), residues: 1163 sheet: 0.22 (0.23), residues: 517 loop : -0.27 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 67 TYR 0.015 0.001 TYR I 47 PHE 0.012 0.001 PHE I 405 TRP 0.022 0.001 TRP J1193 HIS 0.003 0.001 HIS P 65 Details of bonding type rmsd covalent geometry : bond 0.00291 (28341) covalent geometry : angle 0.51441 (38675) hydrogen bonds : bond 0.03287 ( 1213) hydrogen bonds : angle 3.84779 ( 3368) metal coordination : bond 0.00698 ( 8) metal coordination : angle 2.65637 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 201 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 42 LYS cc_start: 0.8491 (pptt) cc_final: 0.7941 (pptt) REVERT: P 60 ASP cc_start: 0.8455 (t0) cc_final: 0.8228 (t0) REVERT: I 1 MET cc_start: 0.8062 (tmm) cc_final: 0.7578 (tmm) REVERT: I 37 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8976 (ttpp) REVERT: I 370 MET cc_start: 0.9290 (mmm) cc_final: 0.8920 (tpt) REVERT: I 696 ASP cc_start: 0.8622 (t0) cc_final: 0.8320 (t0) REVERT: I 825 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8538 (mm-30) REVERT: I 968 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8381 (pp20) REVERT: I 1107 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8732 (mpp) REVERT: J 1100 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7716 (t80) REVERT: K 30 MET cc_start: 0.9207 (mtt) cc_final: 0.8973 (mtt) REVERT: K 55 GLU cc_start: 0.8341 (tp30) cc_final: 0.8054 (tt0) REVERT: K 69 ARG cc_start: 0.7743 (ttp80) cc_final: 0.7451 (ttm110) REVERT: K 76 GLU cc_start: 0.9004 (pp20) cc_final: 0.8701 (mm-30) REVERT: G 101 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8972 (p) REVERT: H 186 ASN cc_start: 0.8686 (m110) cc_final: 0.8480 (m-40) REVERT: H 205 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8415 (ttm) outliers start: 76 outliers final: 65 residues processed: 262 average time/residue: 0.1691 time to fit residues: 72.3126 Evaluate side-chains 264 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 193 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 704 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 127 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 196 optimal weight: 0.0470 chunk 215 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 279 optimal weight: 0.2980 chunk 67 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN I 387 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.070123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.050333 restraints weight = 92994.971| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.13 r_work: 0.2777 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28349 Z= 0.142 Angle : 0.528 13.348 38687 Z= 0.274 Chirality : 0.041 0.379 4419 Planarity : 0.003 0.039 4753 Dihedral : 15.765 176.874 4650 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 2.94 % Allowed : 25.61 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: 1.01 (0.15), residues: 3292 helix: 2.20 (0.15), residues: 1164 sheet: 0.26 (0.23), residues: 527 loop : -0.31 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 312 TYR 0.015 0.001 TYR I 47 PHE 0.011 0.001 PHE I 405 TRP 0.023 0.001 TRP I 183 HIS 0.003 0.001 HIS P 65 Details of bonding type rmsd covalent geometry : bond 0.00326 (28341) covalent geometry : angle 0.52545 (38675) hydrogen bonds : bond 0.03391 ( 1213) hydrogen bonds : angle 3.86786 ( 3368) metal coordination : bond 0.00803 ( 8) metal coordination : angle 2.77295 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 198 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 42 LYS cc_start: 0.8474 (pptt) cc_final: 0.7904 (pptt) REVERT: P 60 ASP cc_start: 0.8462 (t0) cc_final: 0.8234 (t0) REVERT: I 1 MET cc_start: 0.7969 (tmm) cc_final: 0.7482 (tmm) REVERT: I 37 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8983 (ttpp) REVERT: I 258 ASN cc_start: 0.8663 (m110) cc_final: 0.8461 (t0) REVERT: I 370 MET cc_start: 0.9280 (mmm) cc_final: 0.8978 (tpt) REVERT: I 374 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8590 (mp0) REVERT: I 465 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8104 (ttt-90) REVERT: I 696 ASP cc_start: 0.8581 (t0) cc_final: 0.8294 (t0) REVERT: I 825 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8526 (mm-30) REVERT: I 968 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8377 (pp20) REVERT: I 1107 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8734 (mpp) REVERT: J 1100 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7734 (t80) REVERT: J 1189 MET cc_start: 0.8569 (tpt) cc_final: 0.8283 (tpp) REVERT: K 8 ASP cc_start: 0.8203 (p0) cc_final: 0.7811 (p0) REVERT: K 30 MET cc_start: 0.9167 (mtt) cc_final: 0.8944 (mtt) REVERT: K 71 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8522 (pt0) REVERT: K 75 GLN cc_start: 0.9282 (tp-100) cc_final: 0.8829 (mp10) REVERT: G 101 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8989 (p) REVERT: H 186 ASN cc_start: 0.8686 (m110) cc_final: 0.8481 (m-40) outliers start: 82 outliers final: 68 residues processed: 266 average time/residue: 0.1740 time to fit residues: 75.8400 Evaluate side-chains 266 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 191 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 374 GLU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 704 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 97 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 121 optimal weight: 0.0010 chunk 264 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 192 optimal weight: 0.0470 chunk 6 optimal weight: 0.6980 chunk 102 optimal weight: 0.1980 overall best weight: 0.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN I 387 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.071936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.051695 restraints weight = 99099.992| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.31 r_work: 0.2814 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28349 Z= 0.101 Angle : 0.521 13.785 38687 Z= 0.270 Chirality : 0.040 0.374 4419 Planarity : 0.003 0.037 4753 Dihedral : 15.704 177.683 4650 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 2.52 % Allowed : 26.07 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: 1.06 (0.15), residues: 3292 helix: 2.21 (0.15), residues: 1171 sheet: 0.27 (0.24), residues: 488 loop : -0.25 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 312 TYR 0.015 0.001 TYR I 47 PHE 0.014 0.001 PHE I 405 TRP 0.018 0.001 TRP I 183 HIS 0.003 0.000 HIS P 77 Details of bonding type rmsd covalent geometry : bond 0.00228 (28341) covalent geometry : angle 0.51928 (38675) hydrogen bonds : bond 0.03035 ( 1213) hydrogen bonds : angle 3.77941 ( 3368) metal coordination : bond 0.00370 ( 8) metal coordination : angle 2.18998 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 203 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 42 LYS cc_start: 0.8494 (pptt) cc_final: 0.7929 (pptt) REVERT: P 60 ASP cc_start: 0.8458 (t0) cc_final: 0.8231 (t0) REVERT: I 1 MET cc_start: 0.8042 (tmm) cc_final: 0.7492 (tmm) REVERT: I 37 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.9017 (ttpp) REVERT: I 370 MET cc_start: 0.9307 (mmm) cc_final: 0.8943 (tpt) REVERT: I 403 MET cc_start: 0.9302 (tmt) cc_final: 0.9053 (tmm) REVERT: I 465 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8089 (ttt-90) REVERT: I 696 ASP cc_start: 0.8601 (t0) cc_final: 0.8297 (t0) REVERT: I 825 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8372 (mm-30) REVERT: I 1107 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8795 (mpp) REVERT: J 115 TRP cc_start: 0.9318 (m-10) cc_final: 0.9088 (m-10) REVERT: J 322 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8490 (mtm-85) REVERT: J 1100 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7767 (t80) REVERT: J 1189 MET cc_start: 0.8518 (tpt) cc_final: 0.8043 (tpp) REVERT: K 8 ASP cc_start: 0.8153 (p0) cc_final: 0.7785 (p0) REVERT: K 30 MET cc_start: 0.9193 (mtt) cc_final: 0.8970 (mtt) REVERT: K 69 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7429 (ttm110) REVERT: K 71 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8522 (pt0) REVERT: K 75 GLN cc_start: 0.9282 (tp-100) cc_final: 0.8812 (mt0) REVERT: K 76 GLU cc_start: 0.9083 (pt0) cc_final: 0.8398 (mm-30) REVERT: G 101 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8938 (p) REVERT: H 232 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8105 (p) outliers start: 70 outliers final: 54 residues processed: 259 average time/residue: 0.1571 time to fit residues: 66.3556 Evaluate side-chains 253 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 704 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 136 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 294 optimal weight: 0.0570 chunk 281 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.071015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.050997 restraints weight = 111506.777| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.44 r_work: 0.2798 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28349 Z= 0.120 Angle : 0.535 13.554 38687 Z= 0.275 Chirality : 0.040 0.384 4419 Planarity : 0.003 0.042 4753 Dihedral : 15.710 176.793 4650 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 2.59 % Allowed : 26.04 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: 1.05 (0.15), residues: 3292 helix: 2.22 (0.15), residues: 1171 sheet: 0.26 (0.24), residues: 488 loop : -0.27 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 996 TYR 0.015 0.001 TYR G 185 PHE 0.015 0.001 PHE I 389 TRP 0.018 0.001 TRP I 183 HIS 0.003 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00276 (28341) covalent geometry : angle 0.53374 (38675) hydrogen bonds : bond 0.03149 ( 1213) hydrogen bonds : angle 3.79573 ( 3368) metal coordination : bond 0.00569 ( 8) metal coordination : angle 2.26465 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 192 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 42 LYS cc_start: 0.8477 (pptt) cc_final: 0.7894 (pptt) REVERT: P 60 ASP cc_start: 0.8499 (t0) cc_final: 0.8278 (t0) REVERT: I 1 MET cc_start: 0.8042 (tmm) cc_final: 0.7512 (tmm) REVERT: I 37 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9041 (ttpp) REVERT: I 47 TYR cc_start: 0.8464 (m-80) cc_final: 0.8193 (m-80) REVERT: I 370 MET cc_start: 0.9302 (mmm) cc_final: 0.8940 (tpt) REVERT: I 374 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: I 465 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8125 (ttt-90) REVERT: I 696 ASP cc_start: 0.8620 (t0) cc_final: 0.8326 (t0) REVERT: I 825 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8396 (mm-30) REVERT: I 1107 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8819 (mpp) REVERT: J 322 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8514 (mtm-85) REVERT: J 1100 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7702 (t80) REVERT: J 1189 MET cc_start: 0.8391 (tpt) cc_final: 0.7972 (tpp) REVERT: J 1373 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7396 (ttm170) REVERT: K 8 ASP cc_start: 0.8205 (p0) cc_final: 0.7849 (p0) REVERT: K 30 MET cc_start: 0.9200 (mtt) cc_final: 0.8988 (mtt) REVERT: K 69 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7427 (ttm110) outliers start: 72 outliers final: 60 residues processed: 252 average time/residue: 0.1641 time to fit residues: 67.5565 Evaluate side-chains 256 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 189 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 95 GLN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 374 GLU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 704 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain J residue 1373 ARG Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 247 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 chunk 271 optimal weight: 0.1980 chunk 217 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 311 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 chunk 320 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN I 36 GLN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.071065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.051283 restraints weight = 97351.083| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.21 r_work: 0.2801 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 28349 Z= 0.172 Angle : 0.660 59.200 38687 Z= 0.368 Chirality : 0.042 0.753 4419 Planarity : 0.003 0.042 4753 Dihedral : 15.711 176.793 4650 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 2.59 % Allowed : 26.07 % Favored : 71.34 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: 1.04 (0.15), residues: 3292 helix: 2.21 (0.15), residues: 1171 sheet: 0.26 (0.24), residues: 488 loop : -0.27 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG G 166 TYR 0.015 0.001 TYR G 185 PHE 0.014 0.001 PHE I 389 TRP 0.018 0.001 TRP I 183 HIS 0.003 0.001 HIS P 65 Details of bonding type rmsd covalent geometry : bond 0.00374 (28341) covalent geometry : angle 0.65884 (38675) hydrogen bonds : bond 0.03142 ( 1213) hydrogen bonds : angle 3.80022 ( 3368) metal coordination : bond 0.00554 ( 8) metal coordination : angle 2.26383 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7372.07 seconds wall clock time: 126 minutes 55.48 seconds (7615.48 seconds total)