Starting phenix.real_space_refine on Tue Sep 15 15:17:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xtx_10619/09_2026/6xtx_10619.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xtx_10619/09_2026/6xtx_10619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xtx_10619/09_2026/6xtx_10619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xtx_10619/09_2026/6xtx_10619.map" model { file = "/net/cci-nas-00/data/ceres_data/6xtx_10619/09_2026/6xtx_10619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xtx_10619/09_2026/6xtx_10619.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xtx_10619/09_2026/6xtx_10619.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xtx_10619/09_2026/6xtx_10619.cif" } resolution = 3.29 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= -0.000 sd= 0.003 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 5 6.06 5 P 24 5.49 5 Mg 3 5.21 5 S 245 5.16 5 C 25660 2.51 5 N 7177 2.21 5 O 7720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 178 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40834 Number of models: 1 Model: "" Number of chains: 18 Chain: "2" Number of atoms: 5514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5514 Classifications: {'peptide': 691} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 662} Chain breaks: 3 Chain: "3" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4782 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 25, 'TRANS': 582} Chain breaks: 2 Chain: "4" Number of atoms: 4784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4784 Classifications: {'peptide': 598} Link IDs: {'PTRANS': 27, 'TRANS': 570} Chain breaks: 2 Chain: "5" Number of atoms: 4524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4524 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 551} Chain breaks: 6 Chain: "6" Number of atoms: 5473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5473 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 22, 'TRANS': 656} Chain breaks: 3 Chain: "7" Number of atoms: 4727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4727 Classifications: {'peptide': 598} Link IDs: {'PTRANS': 27, 'TRANS': 570} Chain breaks: 2 Chain: "A" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1613 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "B" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1431 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 163} Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1552 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "D" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1679 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "E" Number of atoms: 4380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4380 Classifications: {'peptide': 538} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 524} Chain breaks: 1 Chain: "M" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 220 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1264 SG CYS 2 329 25.980 64.896 101.686 1.00121.36 S ATOM 1287 SG CYS 2 332 24.781 64.337 105.173 1.00134.93 S ATOM 1438 SG CYS 2 352 24.126 61.801 102.893 1.00139.30 S ATOM 1460 SG CYS 2 355 22.335 64.949 102.565 1.00143.82 S ATOM 11480 SG CYS 4 306 21.796 43.361 63.914 1.00118.34 S ATOM 11502 SG CYS 4 309 20.305 42.144 61.067 1.00128.67 S ATOM 11648 SG CYS 4 328 20.040 45.639 62.264 1.00135.76 S ATOM 11669 SG CYS 4 331 18.093 43.126 63.816 1.00138.30 S ATOM 16310 SG CYS 5 172 23.355 84.616 91.679 1.00115.10 S ATOM 16333 SG CYS 5 175 20.103 85.596 92.998 1.00131.69 S ATOM 16504 SG CYS 5 197 21.161 82.316 93.428 1.00126.72 S ATOM 16518 SG CYS 5 207 20.094 83.463 90.100 1.00133.32 S ATOM 20799 SG CYS 6 158 23.731 43.490 83.561 1.00161.27 S ATOM 20821 SG CYS 6 161 20.129 42.866 84.066 1.00172.20 S ATOM 20982 SG CYS 6 180 21.574 41.913 80.507 1.00171.24 S ATOM 21021 SG CYS 6 185 21.360 45.488 81.498 1.00177.09 S ATOM 26267 SG CYS 7 184 17.501 68.998 51.549 1.00140.79 S ATOM 26290 SG CYS 7 187 15.070 71.062 49.929 1.00151.04 S ATOM 26436 SG CYS 7 206 16.512 71.830 53.438 1.00152.21 S ATOM 26473 SG CYS 7 211 13.929 69.049 52.979 1.00173.45 S Time building chain proxies: 7.87, per 1000 atoms: 0.19 Number of scatterers: 40834 At special positions: 0 Unit cell: (155.15, 159.43, 209.72, 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 5 29.99 S 245 16.00 P 24 15.00 Mg 3 11.99 O 7720 8.00 N 7177 7.00 C 25660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21000 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 352 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 355 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 329 " pdb=" ZN 4 901 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 328 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 309 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 331 " pdb=" ZN 51000 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 175 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 197 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 207 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 172 " pdb=" ZN 6 901 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 185 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 158 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 180 " pdb=" ZN 71000 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 184 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 206 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 187 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 211 " Number of angles added : 30 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9654 Finding SS restraints... Secondary structure from input PDB file: 209 helices and 60 sheets defined 42.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain '2' and resid 181 through 187 removed outlier: 3.578A pdb=" N VAL 2 186 " --> pdb=" O VAL 2 182 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER 2 187 " --> pdb=" O ARG 2 183 " (cutoff:3.500A) Processing helix chain '2' and resid 188 through 205 removed outlier: 3.538A pdb=" N LYS 2 200 " --> pdb=" O HIS 2 196 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN 2 201 " --> pdb=" O HIS 2 197 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE 2 202 " --> pdb=" O ARG 2 198 " (cutoff:3.500A) Processing helix chain '2' and resid 213 through 224 removed outlier: 4.309A pdb=" N ILE 2 219 " --> pdb=" O PHE 2 215 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER 2 220 " --> pdb=" O LYS 2 216 " (cutoff:3.500A) Processing helix chain '2' and resid 234 through 241 Processing helix chain '2' and resid 243 through 248 Processing helix chain '2' and resid 251 through 271 removed outlier: 3.706A pdb=" N LEU 2 255 " --> pdb=" O ALA 2 251 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU 2 256 " --> pdb=" O PRO 2 252 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLN 2 257 " --> pdb=" O ALA 2 253 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP 2 260 " --> pdb=" O LEU 2 256 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU 2 261 " --> pdb=" O GLN 2 257 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 277 Processing helix chain '2' and resid 298 through 302 removed outlier: 3.637A pdb=" N LEU 2 302 " --> pdb=" O GLN 2 299 " (cutoff:3.500A) Processing helix chain '2' and resid 425 through 431 Processing helix chain '2' and resid 461 through 469 removed outlier: 4.207A pdb=" N SER 2 466 " --> pdb=" O LYS 2 462 " (cutoff:3.500A) Processing helix chain '2' and resid 472 through 479 removed outlier: 4.067A pdb=" N LYS 2 476 " --> pdb=" O GLN 2 472 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA 2 479 " --> pdb=" O GLU 2 475 " (cutoff:3.500A) Processing helix chain '2' and resid 488 through 501 removed outlier: 3.688A pdb=" N ARG 2 493 " --> pdb=" O GLU 2 489 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY 2 494 " --> pdb=" O ASP 2 490 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE 2 500 " --> pdb=" O ALA 2 496 " (cutoff:3.500A) Processing helix chain '2' and resid 528 through 540 removed outlier: 3.534A pdb=" N ILE 2 536 " --> pdb=" O PHE 2 532 " (cutoff:3.500A) Processing helix chain '2' and resid 588 through 592 Processing helix chain '2' and resid 593 through 606 removed outlier: 4.341A pdb=" N GLU 2 602 " --> pdb=" O THR 2 598 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA 2 603 " --> pdb=" O SER 2 599 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET 2 604 " --> pdb=" O ILE 2 600 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU 2 605 " --> pdb=" O HIS 2 601 " (cutoff:3.500A) Processing helix chain '2' and resid 632 through 636 removed outlier: 3.551A pdb=" N GLY 2 635 " --> pdb=" O PRO 2 632 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG 2 636 " --> pdb=" O ILE 2 633 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 632 through 636' Processing helix chain '2' and resid 642 through 647 removed outlier: 3.792A pdb=" N ASN 2 646 " --> pdb=" O THR 2 642 " (cutoff:3.500A) Processing helix chain '2' and resid 650 through 655 removed outlier: 3.631A pdb=" N ILE 2 654 " --> pdb=" O THR 2 650 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER 2 655 " --> pdb=" O GLU 2 651 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 650 through 655' Processing helix chain '2' and resid 668 through 683 removed outlier: 3.742A pdb=" N GLU 2 673 " --> pdb=" O PRO 2 669 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET 2 674 " --> pdb=" O VAL 2 670 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE 2 678 " --> pdb=" O MET 2 674 " (cutoff:3.500A) Processing helix chain '2' and resid 718 through 730 removed outlier: 3.694A pdb=" N LYS 2 722 " --> pdb=" O GLU 2 718 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS 2 728 " --> pdb=" O ILE 2 724 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU 2 729 " --> pdb=" O ILE 2 725 " (cutoff:3.500A) Processing helix chain '2' and resid 743 through 756 removed outlier: 4.048A pdb=" N ASP 2 749 " --> pdb=" O LYS 2 745 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS 2 752 " --> pdb=" O SER 2 748 " (cutoff:3.500A) Processing helix chain '2' and resid 763 through 775 removed outlier: 4.019A pdb=" N SER 2 769 " --> pdb=" O ARG 2 765 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU 2 775 " --> pdb=" O ILE 2 771 " (cutoff:3.500A) Processing helix chain '2' and resid 777 through 782 Processing helix chain '2' and resid 789 through 804 removed outlier: 4.078A pdb=" N PHE 2 802 " --> pdb=" O MET 2 798 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP 2 804 " --> pdb=" O GLU 2 800 " (cutoff:3.500A) Processing helix chain '2' and resid 809 through 822 removed outlier: 4.022A pdb=" N ARG 2 815 " --> pdb=" O MET 2 811 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG 2 820 " --> pdb=" O LYS 2 816 " (cutoff:3.500A) Processing helix chain '2' and resid 829 through 849 removed outlier: 4.225A pdb=" N ILE 2 835 " --> pdb=" O LEU 2 831 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU 2 836 " --> pdb=" O LEU 2 832 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN 2 838 " --> pdb=" O PHE 2 834 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN 2 843 " --> pdb=" O LEU 2 839 " (cutoff:3.500A) Processing helix chain '2' and resid 863 through 873 removed outlier: 3.562A pdb=" N ASP 2 867 " --> pdb=" O LYS 2 863 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS 2 868 " --> pdb=" O ASP 2 864 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN 2 871 " --> pdb=" O ASP 2 867 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE 2 872 " --> pdb=" O LYS 2 868 " (cutoff:3.500A) Processing helix chain '2' and resid 877 through 883 removed outlier: 3.520A pdb=" N SER 2 883 " --> pdb=" O ALA 2 879 " (cutoff:3.500A) Processing helix chain '3' and resid 57 through 70 removed outlier: 3.848A pdb=" N GLN 3 61 " --> pdb=" O LEU 3 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP 3 66 " --> pdb=" O ARG 3 62 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP 3 70 " --> pdb=" O ASP 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 77 through 86 removed outlier: 4.144A pdb=" N ARG 3 82 " --> pdb=" O GLN 3 78 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU 3 83 " --> pdb=" O SER 3 79 " (cutoff:3.500A) Processing helix chain '3' and resid 95 through 103 removed outlier: 3.559A pdb=" N LEU 3 99 " --> pdb=" O ASN 3 95 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG 3 101 " --> pdb=" O ASN 3 97 " (cutoff:3.500A) Processing helix chain '3' and resid 103 through 111 removed outlier: 3.640A pdb=" N LEU 3 111 " --> pdb=" O ALA 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 113 through 122 removed outlier: 3.735A pdb=" N ALA 3 120 " --> pdb=" O GLU 3 116 " (cutoff:3.500A) Processing helix chain '3' and resid 122 through 131 removed outlier: 3.705A pdb=" N LYS 3 126 " --> pdb=" O GLN 3 122 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE 3 128 " --> pdb=" O ALA 3 124 " (cutoff:3.500A) Processing helix chain '3' and resid 135 through 139 removed outlier: 3.609A pdb=" N LYS 3 138 " --> pdb=" O THR 3 135 " (cutoff:3.500A) Processing helix chain '3' and resid 249 through 253 Processing helix chain '3' and resid 322 through 336 removed outlier: 3.612A pdb=" N LYS 3 334 " --> pdb=" O LYS 3 330 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG 3 336 " --> pdb=" O PHE 3 332 " (cutoff:3.500A) Processing helix chain '3' and resid 340 through 347 removed outlier: 3.788A pdb=" N SER 3 347 " --> pdb=" O GLN 3 343 " (cutoff:3.500A) Processing helix chain '3' and resid 355 through 368 Processing helix chain '3' and resid 395 through 407 removed outlier: 3.749A pdb=" N CYS 3 405 " --> pdb=" O ARG 3 401 " (cutoff:3.500A) Processing helix chain '3' and resid 441 through 446 Processing helix chain '3' and resid 460 through 465 removed outlier: 3.761A pdb=" N THR 3 465 " --> pdb=" O ASP 3 461 " (cutoff:3.500A) Processing helix chain '3' and resid 466 through 468 No H-bonds generated for 'chain '3' and resid 466 through 468' Processing helix chain '3' and resid 519 through 524 removed outlier: 4.052A pdb=" N ARG 3 523 " --> pdb=" O SER 3 519 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE 3 524 " --> pdb=" O LEU 3 520 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 519 through 524' Processing helix chain '3' and resid 535 through 550 removed outlier: 4.120A pdb=" N ASP 3 539 " --> pdb=" O ASP 3 535 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG 3 540 " --> pdb=" O PRO 3 536 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU 3 541 " --> pdb=" O GLU 3 537 " (cutoff:3.500A) Processing helix chain '3' and resid 609 through 621 removed outlier: 3.715A pdb=" N MET 3 613 " --> pdb=" O SER 3 609 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS 3 614 " --> pdb=" O ALA 3 610 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS 3 615 " --> pdb=" O ALA 3 611 " (cutoff:3.500A) Processing helix chain '3' and resid 631 through 643 removed outlier: 3.525A pdb=" N ALA 3 636 " --> pdb=" O ALA 3 632 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU 3 637 " --> pdb=" O THR 3 633 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER 3 640 " --> pdb=" O ALA 3 636 " (cutoff:3.500A) Processing helix chain '3' and resid 659 through 674 removed outlier: 3.910A pdb=" N LEU 3 663 " --> pdb=" O THR 3 659 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU 3 664 " --> pdb=" O ALA 3 660 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR 3 665 " --> pdb=" O ARG 3 661 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG 3 668 " --> pdb=" O GLU 3 664 " (cutoff:3.500A) Processing helix chain '3' and resid 688 through 698 removed outlier: 3.838A pdb=" N GLU 3 692 " --> pdb=" O GLU 3 688 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU 3 693 " --> pdb=" O GLU 3 689 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL 3 694 " --> pdb=" O ALA 3 690 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 172 removed outlier: 3.561A pdb=" N LYS 4 163 " --> pdb=" O VAL 4 159 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU 4 164 " --> pdb=" O ALA 4 160 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN 4 165 " --> pdb=" O ALA 4 161 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG 4 168 " --> pdb=" O GLU 4 164 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE 4 169 " --> pdb=" O ASN 4 165 " (cutoff:3.500A) Processing helix chain '4' and resid 191 through 203 Processing helix chain '4' and resid 213 through 219 Processing helix chain '4' and resid 222 through 227 removed outlier: 4.074A pdb=" N ILE 4 227 " --> pdb=" O TYR 4 223 " (cutoff:3.500A) Processing helix chain '4' and resid 229 through 232 Processing helix chain '4' and resid 233 through 243 removed outlier: 3.760A pdb=" N VAL 4 241 " --> pdb=" O PHE 4 237 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 246 No H-bonds generated for 'chain '4' and resid 244 through 246' Processing helix chain '4' and resid 442 through 453 removed outlier: 3.601A pdb=" N GLU 4 447 " --> pdb=" O GLU 4 443 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU 4 448 " --> pdb=" O LYS 4 444 " (cutoff:3.500A) Processing helix chain '4' and resid 458 through 464 Processing helix chain '4' and resid 473 through 483 removed outlier: 3.676A pdb=" N LYS 4 477 " --> pdb=" O HIS 4 473 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS 4 478 " --> pdb=" O GLU 4 474 " (cutoff:3.500A) Processing helix chain '4' and resid 516 through 524 Processing helix chain '4' and resid 539 through 544 removed outlier: 3.741A pdb=" N LEU 4 543 " --> pdb=" O SER 4 539 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR 4 544 " --> pdb=" O ALA 4 540 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 539 through 544' Processing helix chain '4' and resid 562 through 567 removed outlier: 4.293A pdb=" N ASP 4 567 " --> pdb=" O LEU 4 563 " (cutoff:3.500A) Processing helix chain '4' and resid 580 through 585 Processing helix chain '4' and resid 586 through 591 removed outlier: 4.227A pdb=" N VAL 4 590 " --> pdb=" O VAL 4 586 " (cutoff:3.500A) Processing helix chain '4' and resid 619 through 623 removed outlier: 3.998A pdb=" N GLN 4 623 " --> pdb=" O ILE 4 620 " (cutoff:3.500A) Processing helix chain '4' and resid 629 through 634 removed outlier: 3.756A pdb=" N ILE 4 634 " --> pdb=" O THR 4 630 " (cutoff:3.500A) Processing helix chain '4' and resid 637 through 642 Processing helix chain '4' and resid 655 through 669 removed outlier: 3.814A pdb=" N ALA 4 668 " --> pdb=" O HIS 4 664 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU 4 669 " --> pdb=" O HIS 4 665 " (cutoff:3.500A) Processing helix chain '4' and resid 686 through 697 removed outlier: 4.078A pdb=" N ALA 4 692 " --> pdb=" O LYS 4 688 " (cutoff:3.500A) Processing helix chain '4' and resid 703 through 711 removed outlier: 3.664A pdb=" N ALA 4 709 " --> pdb=" O GLU 4 705 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE 4 711 " --> pdb=" O SER 4 707 " (cutoff:3.500A) Processing helix chain '4' and resid 711 through 725 removed outlier: 4.088A pdb=" N MET 4 717 " --> pdb=" O ALA 4 713 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG 4 718 " --> pdb=" O TYR 4 714 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS 4 719 " --> pdb=" O VAL 4 715 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER 4 723 " --> pdb=" O LYS 4 719 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG 4 724 " --> pdb=" O ILE 4 720 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY 4 725 " --> pdb=" O GLY 4 721 " (cutoff:3.500A) Processing helix chain '4' and resid 730 through 746 removed outlier: 4.137A pdb=" N LEU 4 734 " --> pdb=" O TYR 4 730 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU 4 735 " --> pdb=" O PRO 4 731 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE 4 738 " --> pdb=" O LEU 4 734 " (cutoff:3.500A) Processing helix chain '4' and resid 747 through 749 No H-bonds generated for 'chain '4' and resid 747 through 749' Processing helix chain '4' and resid 755 through 767 removed outlier: 4.228A pdb=" N ALA 4 761 " --> pdb=" O ASP 4 757 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N HIS 4 765 " --> pdb=" O ALA 4 761 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 32 removed outlier: 3.746A pdb=" N ALA 5 26 " --> pdb=" O ASP 5 22 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN 5 30 " --> pdb=" O ALA 5 26 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 3.781A pdb=" N LEU 5 39 " --> pdb=" O PHE 5 35 " (cutoff:3.500A) Processing helix chain '5' and resid 54 through 64 removed outlier: 3.698A pdb=" N GLU 5 58 " --> pdb=" O LYS 5 54 " (cutoff:3.500A) Processing helix chain '5' and resid 74 through 81 Processing helix chain '5' and resid 83 through 91 removed outlier: 4.020A pdb=" N TYR 5 89 " --> pdb=" O ALA 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 92 through 107 removed outlier: 3.869A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU 5 98 " --> pdb=" O GLU 5 94 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU 5 105 " --> pdb=" O GLU 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 107 through 112 removed outlier: 3.935A pdb=" N THR 5 111 " --> pdb=" O ALA 5 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG 5 112 " --> pdb=" O ASP 5 108 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 107 through 112' Processing helix chain '5' and resid 136 through 140 Processing helix chain '5' and resid 141 through 145 Processing helix chain '5' and resid 232 through 236 removed outlier: 3.548A pdb=" N ALA 5 235 " --> pdb=" O LEU 5 232 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL 5 236 " --> pdb=" O PRO 5 233 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 232 through 236' Processing helix chain '5' and resid 315 through 328 removed outlier: 3.901A pdb=" N GLU 5 320 " --> pdb=" O PRO 5 316 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU 5 321 " --> pdb=" O GLN 5 317 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE 5 322 " --> pdb=" O GLU 5 318 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU 5 325 " --> pdb=" O GLU 5 321 " (cutoff:3.500A) Processing helix chain '5' and resid 330 through 338 removed outlier: 3.891A pdb=" N VAL 5 334 " --> pdb=" O ASN 5 330 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE 5 335 " --> pdb=" O VAL 5 331 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER 5 336 " --> pdb=" O TYR 5 332 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER 5 338 " --> pdb=" O VAL 5 334 " (cutoff:3.500A) Processing helix chain '5' and resid 347 through 357 removed outlier: 4.304A pdb=" N ILE 5 353 " --> pdb=" O MET 5 349 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA 5 354 " --> pdb=" O LYS 5 350 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS 5 355 " --> pdb=" O LYS 5 351 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU 5 356 " --> pdb=" O ALA 5 352 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU 5 357 " --> pdb=" O ILE 5 353 " (cutoff:3.500A) Processing helix chain '5' and resid 385 through 397 removed outlier: 3.938A pdb=" N GLN 5 389 " --> pdb=" O THR 5 385 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU 5 390 " --> pdb=" O ALA 5 386 " (cutoff:3.500A) Processing helix chain '5' and resid 451 through 465 Processing helix chain '5' and resid 525 through 541 removed outlier: 3.857A pdb=" N ILE 5 537 " --> pdb=" O ALA 5 533 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU 5 539 " --> pdb=" O HIS 5 535 " (cutoff:3.500A) Processing helix chain '5' and resid 555 through 567 removed outlier: 4.396A pdb=" N LYS 5 561 " --> pdb=" O ALA 5 557 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR 5 565 " --> pdb=" O LYS 5 561 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 598 removed outlier: 3.661A pdb=" N GLU 5 580 " --> pdb=" O ALA 5 576 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN 5 584 " --> pdb=" O GLU 5 580 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE 5 588 " --> pdb=" O ASN 5 584 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY 5 592 " --> pdb=" O ILE 5 588 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA 5 593 " --> pdb=" O MET 5 589 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG 5 594 " --> pdb=" O ARG 5 590 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN 5 595 " --> pdb=" O SER 5 591 " (cutoff:3.500A) Processing helix chain '5' and resid 609 through 624 removed outlier: 3.514A pdb=" N ALA 5 622 " --> pdb=" O ARG 5 618 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 656 removed outlier: 4.056A pdb=" N VAL 5 637 " --> pdb=" O THR 5 633 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU 5 638 " --> pdb=" O GLU 5 634 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLU 5 639 " --> pdb=" O ALA 5 635 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA 5 651 " --> pdb=" O SER 5 647 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR 5 656 " --> pdb=" O ALA 5 652 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 37 removed outlier: 3.838A pdb=" N CYS 6 26 " --> pdb=" O VAL 6 22 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU 6 35 " --> pdb=" O LEU 6 31 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 48 removed outlier: 3.549A pdb=" N LEU 6 47 " --> pdb=" O ILE 6 44 " (cutoff:3.500A) Processing helix chain '6' and resid 51 through 55 Processing helix chain '6' and resid 66 through 72 Processing helix chain '6' and resid 75 through 83 removed outlier: 3.928A pdb=" N GLU 6 81 " --> pdb=" O THR 6 77 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 91 Processing helix chain '6' and resid 91 through 96 Processing helix chain '6' and resid 98 through 102 removed outlier: 3.822A pdb=" N ARG 6 101 " --> pdb=" O VAL 6 98 " (cutoff:3.500A) Processing helix chain '6' and resid 211 through 215 removed outlier: 3.647A pdb=" N GLU 6 214 " --> pdb=" O THR 6 211 " (cutoff:3.500A) Processing helix chain '6' and resid 253 through 257 Processing helix chain '6' and resid 321 through 329 removed outlier: 3.947A pdb=" N GLN 6 328 " --> pdb=" O SER 6 324 " (cutoff:3.500A) Processing helix chain '6' and resid 330 through 343 removed outlier: 3.641A pdb=" N GLU 6 339 " --> pdb=" O GLU 6 335 " (cutoff:3.500A) Processing helix chain '6' and resid 345 through 350 Processing helix chain '6' and resid 350 through 355 Processing helix chain '6' and resid 361 through 374 removed outlier: 3.522A pdb=" N LYS 6 365 " --> pdb=" O ASN 6 361 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG 6 366 " --> pdb=" O ASP 6 362 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY 6 367 " --> pdb=" O GLU 6 363 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY 6 374 " --> pdb=" O LEU 6 370 " (cutoff:3.500A) Processing helix chain '6' and resid 402 through 413 Processing helix chain '6' and resid 425 through 430 removed outlier: 3.506A pdb=" N LEU 6 429 " --> pdb=" O SER 6 425 " (cutoff:3.500A) Processing helix chain '6' and resid 468 through 480 removed outlier: 3.813A pdb=" N ALA 6 472 " --> pdb=" O ARG 6 468 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE 6 473 " --> pdb=" O ASP 6 469 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS 6 474 " --> pdb=" O GLN 6 470 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN 6 479 " --> pdb=" O GLU 6 475 " (cutoff:3.500A) Processing helix chain '6' and resid 515 through 519 removed outlier: 3.649A pdb=" N GLN 6 518 " --> pdb=" O SER 6 515 " (cutoff:3.500A) Processing helix chain '6' and resid 525 through 529 Processing helix chain '6' and resid 543 through 558 removed outlier: 4.009A pdb=" N ALA 6 549 " --> pdb=" O ASP 6 545 " (cutoff:3.500A) Processing helix chain '6' and resid 568 through 579 removed outlier: 3.532A pdb=" N ARG 6 574 " --> pdb=" O ASP 6 570 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 582 No H-bonds generated for 'chain '6' and resid 580 through 582' Processing helix chain '6' and resid 587 through 603 removed outlier: 3.510A pdb=" N ARG 6 602 " --> pdb=" O TYR 6 598 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN 6 603 " --> pdb=" O LYS 6 599 " (cutoff:3.500A) Processing helix chain '6' and resid 604 through 606 No H-bonds generated for 'chain '6' and resid 604 through 606' Processing helix chain '6' and resid 624 through 635 removed outlier: 3.650A pdb=" N MET 6 634 " --> pdb=" O ALA 6 630 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS 6 635 " --> pdb=" O MET 6 631 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 656 removed outlier: 4.036A pdb=" N GLU 6 647 " --> pdb=" O LYS 6 643 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU 6 652 " --> pdb=" O ALA 6 648 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE 6 656 " --> pdb=" O LEU 6 652 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 728 removed outlier: 3.797A pdb=" N ASN 6 725 " --> pdb=" O CYS 6 721 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU 6 726 " --> pdb=" O ARG 6 722 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE 6 727 " --> pdb=" O ILE 6 723 " (cutoff:3.500A) Processing helix chain '6' and resid 744 through 754 removed outlier: 3.881A pdb=" N VAL 6 749 " --> pdb=" O ARG 6 745 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN 6 750 " --> pdb=" O SER 6 746 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR 6 752 " --> pdb=" O LEU 6 748 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU 6 753 " --> pdb=" O VAL 6 749 " (cutoff:3.500A) Processing helix chain '6' and resid 764 through 780 removed outlier: 3.641A pdb=" N ASN 6 768 " --> pdb=" O GLU 6 764 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE 6 772 " --> pdb=" O ASN 6 768 " (cutoff:3.500A) Processing helix chain '7' and resid 8 through 20 removed outlier: 3.694A pdb=" N LYS 7 14 " --> pdb=" O LYS 7 10 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE 7 16 " --> pdb=" O LYS 7 12 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 42 removed outlier: 3.958A pdb=" N GLN 7 36 " --> pdb=" O LYS 7 32 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL 7 38 " --> pdb=" O GLY 7 34 " (cutoff:3.500A) Processing helix chain '7' and resid 54 through 59 removed outlier: 4.183A pdb=" N ASP 7 58 " --> pdb=" O ASP 7 54 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 67 Processing helix chain '7' and resid 72 through 89 removed outlier: 4.032A pdb=" N ALA 7 78 " --> pdb=" O ALA 7 74 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN 7 82 " --> pdb=" O ALA 7 78 " (cutoff:3.500A) Proline residue: 7 86 - end of helix Processing helix chain '7' and resid 153 through 157 Processing helix chain '7' and resid 208 through 216 removed outlier: 3.541A pdb=" N ARG 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) Processing helix chain '7' and resid 320 through 328 removed outlier: 4.266A pdb=" N GLN 7 326 " --> pdb=" O GLU 7 322 " (cutoff:3.500A) Processing helix chain '7' and resid 331 through 339 removed outlier: 3.552A pdb=" N LEU 7 336 " --> pdb=" O PHE 7 332 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA 7 337 " --> pdb=" O TYR 7 333 " (cutoff:3.500A) Processing helix chain '7' and resid 349 through 360 removed outlier: 3.667A pdb=" N LEU 7 355 " --> pdb=" O LYS 7 351 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU 7 356 " --> pdb=" O LYS 7 352 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU 7 358 " --> pdb=" O LEU 7 354 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 397 removed outlier: 3.735A pdb=" N SER 7 392 " --> pdb=" O SER 7 388 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG 7 396 " --> pdb=" O SER 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 407 through 409 No H-bonds generated for 'chain '7' and resid 407 through 409' Processing helix chain '7' and resid 410 through 415 removed outlier: 3.729A pdb=" N THR 7 415 " --> pdb=" O GLY 7 411 " (cutoff:3.500A) Processing helix chain '7' and resid 432 through 437 Processing helix chain '7' and resid 451 through 457 removed outlier: 3.675A pdb=" N ARG 7 455 " --> pdb=" O GLU 7 452 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR 7 456 " --> pdb=" O ALA 7 453 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA 7 457 " --> pdb=" O ASP 7 454 " (cutoff:3.500A) Processing helix chain '7' and resid 458 through 464 removed outlier: 3.842A pdb=" N GLU 7 463 " --> pdb=" O HIS 7 459 " (cutoff:3.500A) Processing helix chain '7' and resid 508 through 513 Processing helix chain '7' and resid 528 through 544 removed outlier: 3.707A pdb=" N TYR 7 539 " --> pdb=" O GLN 7 535 " (cutoff:3.500A) Processing helix chain '7' and resid 555 through 568 removed outlier: 3.775A pdb=" N ARG 7 561 " --> pdb=" O LYS 7 557 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA 7 564 " --> pdb=" O ARG 7 560 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU 7 568 " --> pdb=" O ALA 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 576 No H-bonds generated for 'chain '7' and resid 574 through 576' Processing helix chain '7' and resid 577 through 592 Processing helix chain '7' and resid 605 through 612 Processing helix chain '7' and resid 615 through 620 Processing helix chain '7' and resid 626 through 637 removed outlier: 3.655A pdb=" N VAL 7 630 " --> pdb=" O GLU 7 626 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN 7 631 " --> pdb=" O LYS 7 627 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU 7 632 " --> pdb=" O GLU 7 628 " (cutoff:3.500A) Processing helix chain '7' and resid 641 through 645 removed outlier: 3.595A pdb=" N LEU 7 644 " --> pdb=" O LYS 7 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 8 Processing helix chain 'A' and resid 9 through 14 removed outlier: 3.640A pdb=" N LEU A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 50 removed outlier: 3.542A pdb=" N GLU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 58 through 83 removed outlier: 3.853A pdb=" N ARG A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 70 " --> pdb=" O HIS A 66 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR A 79 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.862A pdb=" N ARG A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 126 removed outlier: 3.690A pdb=" N ARG A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 187 removed outlier: 3.756A pdb=" N GLU A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.506A pdb=" N VAL B 6 " --> pdb=" O ASP B 2 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.758A pdb=" N ASN B 51 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 55 " --> pdb=" O ASN B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 removed outlier: 4.163A pdb=" N ASP B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 79 " --> pdb=" O ARG B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 103 removed outlier: 4.165A pdb=" N LEU B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 125 removed outlier: 4.628A pdb=" N THR B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 132 removed outlier: 3.522A pdb=" N ARG B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 149 through 156 removed outlier: 3.750A pdb=" N SER B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 172 removed outlier: 3.632A pdb=" N LEU B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 170 " --> pdb=" O HIS B 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 removed outlier: 3.592A pdb=" N LEU C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 4.235A pdb=" N GLY C 75 " --> pdb=" O TRP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 95 through 103 removed outlier: 3.860A pdb=" N VAL C 99 " --> pdb=" O GLY C 95 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 103 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 107 removed outlier: 3.776A pdb=" N VAL C 107 " --> pdb=" O PRO C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 107' Processing helix chain 'C' and resid 115 through 121 removed outlier: 3.584A pdb=" N PHE C 119 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 136 through 143 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.967A pdb=" N ALA C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 191 removed outlier: 3.630A pdb=" N GLY C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU C 175 " --> pdb=" O MET C 171 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 178 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 180 " --> pdb=" O PHE C 176 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 181 " --> pdb=" O GLN C 177 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 182 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 191 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 206 removed outlier: 3.780A pdb=" N ASN C 205 " --> pdb=" O ASN C 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 40 removed outlier: 4.076A pdb=" N ILE D 27 " --> pdb=" O PRO D 23 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS D 38 " --> pdb=" O TRP D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.513A pdb=" N VAL D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 62 Processing helix chain 'D' and resid 62 through 67 removed outlier: 3.811A pdb=" N ARG D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 95 removed outlier: 3.733A pdb=" N GLU D 81 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 103 through 113 removed outlier: 3.513A pdb=" N GLU D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 142 removed outlier: 3.750A pdb=" N ALA D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 removed outlier: 3.730A pdb=" N ASP D 193 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 216 removed outlier: 3.620A pdb=" N VAL D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 211 through 216' Processing helix chain 'E' and resid 10 through 15 Processing helix chain 'E' and resid 26 through 41 removed outlier: 3.909A pdb=" N ILE E 35 " --> pdb=" O CYS E 31 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 66 removed outlier: 3.623A pdb=" N GLU E 64 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS E 65 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 66 " --> pdb=" O PHE E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 165 through 189 removed outlier: 4.166A pdb=" N GLN E 173 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 209 removed outlier: 3.502A pdb=" N VAL E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE E 203 " --> pdb=" O ALA E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 230 removed outlier: 3.626A pdb=" N TRP E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA E 220 " --> pdb=" O MET E 216 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 255 removed outlier: 3.954A pdb=" N ARG E 247 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 removed outlier: 4.105A pdb=" N ASN E 261 " --> pdb=" O ASP E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 removed outlier: 3.972A pdb=" N ARG E 299 " --> pdb=" O TYR E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 317 removed outlier: 4.224A pdb=" N LYS E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG E 310 " --> pdb=" O HIS E 306 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN E 312 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 332 Processing helix chain 'E' and resid 339 through 347 removed outlier: 4.394A pdb=" N GLU E 345 " --> pdb=" O ARG E 341 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 384 removed outlier: 3.617A pdb=" N SER E 382 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.758A pdb=" N GLN E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER E 403 " --> pdb=" O GLN E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 407 removed outlier: 6.500A pdb=" N SER E 407 " --> pdb=" O LEU E 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 404 through 407' Processing helix chain 'E' and resid 408 through 424 removed outlier: 3.663A pdb=" N LEU E 412 " --> pdb=" O ASN E 408 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS E 414 " --> pdb=" O ASP E 410 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU E 417 " --> pdb=" O TYR E 413 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 418 " --> pdb=" O HIS E 414 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA E 419 " --> pdb=" O GLY E 415 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 420 " --> pdb=" O LEU E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 462 removed outlier: 4.400A pdb=" N ARG E 462 " --> pdb=" O LEU E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 481 removed outlier: 3.663A pdb=" N LYS E 475 " --> pdb=" O LYS E 471 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 489 Processing helix chain 'E' and resid 521 through 534 removed outlier: 3.882A pdb=" N ALA E 525 " --> pdb=" O PHE E 521 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU E 527 " --> pdb=" O GLY E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 566 removed outlier: 4.792A pdb=" N LYS E 556 " --> pdb=" O GLU E 552 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA E 560 " --> pdb=" O LYS E 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 229 through 233 removed outlier: 6.468A pdb=" N LEU 2 230 " --> pdb=" O ARG 2 284 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N SER 2 286 " --> pdb=" O LEU 2 230 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL 2 232 " --> pdb=" O SER 2 286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 393 through 398 removed outlier: 6.791A pdb=" N ARG 2 375 " --> pdb=" O CYS 2 315 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS 2 315 " --> pdb=" O ARG 2 375 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG 2 377 " --> pdb=" O THR 2 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 321 through 324 removed outlier: 6.657A pdb=" N ILE 2 369 " --> pdb=" O SER 2 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 327 through 328 removed outlier: 4.101A pdb=" N GLU 2 362 " --> pdb=" O ASN 2 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 416 through 422 removed outlier: 3.540A pdb=" N ILE 2 417 " --> pdb=" O LEU 2 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 519 through 521 removed outlier: 3.902A pdb=" N ALA 2 629 " --> pdb=" O ILE 2 586 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE 2 544 " --> pdb=" O VAL 2 583 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU 2 585 " --> pdb=" O ILE 2 544 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 559 through 562 Processing sheet with id=AA8, first strand: chain '2' and resid 608 through 612 Processing sheet with id=AA9, first strand: chain '3' and resid 91 through 92 removed outlier: 3.531A pdb=" N LEU 3 92 " --> pdb=" O TYR 3 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '3' and resid 261 through 264 Processing sheet with id=AB2, first strand: chain '3' and resid 201 through 203 removed outlier: 6.582A pdb=" N VAL 3 237 " --> pdb=" O VAL 3 187 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 284 through 289 removed outlier: 3.556A pdb=" N THR 3 285 " --> pdb=" O ILE 3 306 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG 3 302 " --> pdb=" O LEU 3 289 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE 3 301 " --> pdb=" O ALA 5 163 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA 5 163 " --> pdb=" O PHE 3 301 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE 5 170 " --> pdb=" O THR 5 180 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR 5 180 " --> pdb=" O ILE 5 170 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS 5 172 " --> pdb=" O THR 5 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR 5 178 " --> pdb=" O CYS 5 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 284 through 289 removed outlier: 3.556A pdb=" N THR 3 285 " --> pdb=" O ILE 3 306 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG 3 302 " --> pdb=" O LEU 3 289 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE 3 301 " --> pdb=" O ALA 5 163 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA 5 163 " --> pdb=" O PHE 3 301 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LYS 5 220 " --> pdb=" O THR 5 166 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE 5 168 " --> pdb=" O LYS 5 218 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N LYS 5 218 " --> pdb=" O ILE 5 168 " (cutoff:3.500A) removed outlier: 10.077A pdb=" N ILE 5 170 " --> pdb=" O PRO 5 216 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N CYS 5 172 " --> pdb=" O ILE 5 214 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE 5 214 " --> pdb=" O CYS 5 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 296 through 297 Processing sheet with id=AB6, first strand: chain '3' and resid 410 through 413 removed outlier: 6.738A pdb=" N ILE 3 411 " --> pdb=" O CYS 3 452 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP 3 454 " --> pdb=" O ILE 3 411 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR 3 413 " --> pdb=" O ASP 3 454 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL 3 451 " --> pdb=" O LEU 3 494 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA 3 496 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE 3 453 " --> pdb=" O ALA 3 496 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE 3 386 " --> pdb=" O ALA 3 495 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA 3 497 " --> pdb=" O ILE 3 386 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU 3 388 " --> pdb=" O ALA 3 497 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU 3 387 " --> pdb=" O PHE 3 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '3' and resid 425 through 428 Processing sheet with id=AB8, first strand: chain '3' and resid 475 through 479 Processing sheet with id=AB9, first strand: chain '3' and resid 652 through 654 Processing sheet with id=AC1, first strand: chain '4' and resid 283 through 284 removed outlier: 6.628A pdb=" N THR 4 391 " --> pdb=" O ILE 4 419 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N THR 4 414 " --> pdb=" O THR 4 369 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE 4 371 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL 4 370 " --> pdb=" O LEU 4 354 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 287 through 288 removed outlier: 3.572A pdb=" N VAL 4 388 " --> pdb=" O GLY 4 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '4' and resid 298 through 301 removed outlier: 6.739A pdb=" N LEU 4 345 " --> pdb=" O GLN 4 300 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 304 through 306 Processing sheet with id=AC5, first strand: chain '4' and resid 408 through 409 Processing sheet with id=AC6, first strand: chain '4' and resid 531 through 533 removed outlier: 6.312A pdb=" N CYS 4 571 " --> pdb=" O LEU 4 614 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ALA 4 616 " --> pdb=" O CYS 4 571 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE 4 573 " --> pdb=" O ALA 4 616 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE 4 506 " --> pdb=" O ALA 4 615 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ALA 4 617 " --> pdb=" O ILE 4 506 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU 4 508 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU 4 650 " --> pdb=" O LEU 4 507 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS 4 509 " --> pdb=" O LEU 4 650 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '4' and resid 547 through 549 Processing sheet with id=AC8, first strand: chain '4' and resid 595 through 599 removed outlier: 3.608A pdb=" N LEU 4 596 " --> pdb=" O LEU 4 607 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain '5' and resid 71 through 73 removed outlier: 6.399A pdb=" N VAL 5 72 " --> pdb=" O LYS 5 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain '5' and resid 262 through 265 removed outlier: 3.500A pdb=" N VAL 5 263 " --> pdb=" O GLY 5 153 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY 5 153 " --> pdb=" O VAL 5 263 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS 5 228 " --> pdb=" O ILE 5 156 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU 5 227 " --> pdb=" O LEU 5 247 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU 5 247 " --> pdb=" O LEU 5 227 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N HIS 5 244 " --> pdb=" O SER 5 292 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N ILE 5 294 " --> pdb=" O HIS 5 244 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN 5 246 " --> pdb=" O ILE 5 294 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL 5 296 " --> pdb=" O GLN 5 246 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR 5 248 " --> pdb=" O VAL 5 296 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '5' and resid 401 through 404 removed outlier: 3.885A pdb=" N ASP 5 445 " --> pdb=" O THR 5 404 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ARG 5 481 " --> pdb=" O ASP 5 438 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY 5 440 " --> pdb=" O ARG 5 481 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU 5 377 " --> pdb=" O ALA 5 486 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N PHE 5 518 " --> pdb=" O ASN 5 376 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU 5 378 " --> pdb=" O PHE 5 518 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '5' and resid 417 through 420 Processing sheet with id=AD5, first strand: chain '5' and resid 466 through 471 removed outlier: 3.559A pdb=" N ILE 5 469 " --> pdb=" O THR 5 476 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR 5 476 " --> pdb=" O ILE 5 469 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '5' and resid 573 through 574 removed outlier: 7.033A pdb=" N ARG 5 573 " --> pdb=" O ALA 5 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '6' and resid 60 through 62 removed outlier: 6.289A pdb=" N LEU 6 61 " --> pdb=" O ALA 6 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '6' and resid 137 through 138 removed outlier: 6.359A pdb=" N ASP 6 243 " --> pdb=" O VAL 6 303 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL 6 303 " --> pdb=" O ASP 6 243 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR 6 245 " --> pdb=" O CYS 6 301 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '6' and resid 143 through 144 removed outlier: 3.752A pdb=" N ARG 6 143 " --> pdb=" O ARG 6 207 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG 6 207 " --> pdb=" O ARG 6 143 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG 6 199 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '6' and resid 143 through 144 removed outlier: 3.752A pdb=" N ARG 6 143 " --> pdb=" O ARG 6 207 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG 6 207 " --> pdb=" O ARG 6 143 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '6' and resid 156 through 158 removed outlier: 3.505A pdb=" N LEU 6 192 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '6' and resid 416 through 419 removed outlier: 6.251A pdb=" N CYS 6 457 " --> pdb=" O LEU 6 500 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA 6 502 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE 6 459 " --> pdb=" O ALA 6 502 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY 6 396 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS 6 393 " --> pdb=" O PHE 6 534 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU 6 536 " --> pdb=" O CYS 6 393 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL 6 395 " --> pdb=" O LEU 6 536 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '6' and resid 431 through 436 Processing sheet with id=AE5, first strand: chain '6' and resid 481 through 485 Processing sheet with id=AE6, first strand: chain '6' and resid 585 through 586 removed outlier: 6.675A pdb=" N LYS 6 585 " --> pdb=" O VAL 6 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain '7' and resid 21 through 22 removed outlier: 3.637A pdb=" N GLN 7 30 " --> pdb=" O GLN 7 22 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '7' and resid 47 through 51 removed outlier: 5.966A pdb=" N LEU 7 48 " --> pdb=" O TYR 7 137 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN 7 139 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL 7 50 " --> pdb=" O GLN 7 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain '7' and resid 160 through 168 removed outlier: 9.330A pdb=" N SER 7 252 " --> pdb=" O THR 7 296 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N LEU 7 298 " --> pdb=" O SER 7 252 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR 7 254 " --> pdb=" O LEU 7 298 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA 7 300 " --> pdb=" O THR 7 254 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU 7 256 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ARG 7 302 " --> pdb=" O LEU 7 256 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N GLU 7 258 " --> pdb=" O ARG 7 302 " (cutoff:3.500A) removed outlier: 12.544A pdb=" N VAL 7 304 " --> pdb=" O GLU 7 258 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR 7 274 " --> pdb=" O HIS 7 301 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE 7 303 " --> pdb=" O SER 7 272 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER 7 272 " --> pdb=" O ILE 7 303 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS 7 305 " --> pdb=" O HIS 7 270 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N HIS 7 270 " --> pdb=" O LYS 7 305 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY 7 275 " --> pdb=" O VAL 7 161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL 7 161 " --> pdb=" O GLY 7 275 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '7' and resid 191 through 194 removed outlier: 6.822A pdb=" N ARG 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA 7 180 " --> pdb=" O GLY 7 226 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N GLY 7 226 " --> pdb=" O ALA 7 180 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N TYR 7 182 " --> pdb=" O THR 7 224 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N THR 7 224 " --> pdb=" O TYR 7 182 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '7' and resid 401 through 405 removed outlier: 6.466A pdb=" N ILE 7 377 " --> pdb=" O ALA 7 486 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N CYS 7 378 " --> pdb=" O TRP 7 519 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE 7 521 " --> pdb=" O CYS 7 378 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N MET 7 380 " --> pdb=" O ILE 7 521 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '7' and resid 416 through 420 Processing sheet with id=AF4, first strand: chain '7' and resid 466 through 469 Processing sheet with id=AF5, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AF6, first strand: chain 'A' and resid 156 through 159 removed outlier: 5.850A pdb=" N GLY A 157 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU A 169 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 174 through 175 removed outlier: 3.660A pdb=" N GLN A 174 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE E 95 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AF9, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AG1, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.713A pdb=" N GLN D 203 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 65 through 69 Processing sheet with id=AG3, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.360A pdb=" N ILE D 196 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU D 183 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR D 194 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 101 through 102 removed outlier: 3.528A pdb=" N TYR E 193 " --> pdb=" O ARG E 102 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 269 through 276 Processing sheet with id=AG6, first strand: chain 'E' and resid 440 through 441 removed outlier: 3.547A pdb=" N VAL E 492 " --> pdb=" O LEU E 446 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA E 494 " --> pdb=" O CYS E 448 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU E 491 " --> pdb=" O ILE E 509 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET E 493 " --> pdb=" O VAL E 507 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR E 503 " --> pdb=" O LEU E 497 " (cutoff:3.500A) 1268 hydrogen bonds defined for protein. 3561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.54 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 13699 1.35 - 1.48: 9943 1.48 - 1.62: 17540 1.62 - 1.76: 0 1.76 - 1.90: 392 Bond restraints: 41574 Sorted by residual: bond pdb=" CA ALA 5 85 " pdb=" C ALA 5 85 " ideal model delta sigma weight residual 1.522 1.452 0.070 1.72e-02 3.38e+03 1.66e+01 bond pdb=" CA LEU D 97 " pdb=" C LEU D 97 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.72e-02 3.38e+03 1.43e+01 bond pdb=" CA LEU 6 299 " pdb=" CB LEU 6 299 " ideal model delta sigma weight residual 1.528 1.450 0.079 2.61e-02 1.47e+03 9.05e+00 bond pdb=" CA GLN 3 506 " pdb=" C GLN 3 506 " ideal model delta sigma weight residual 1.523 1.470 0.054 1.80e-02 3.09e+03 8.89e+00 bond pdb=" C3' DT M 7 " pdb=" O3' DT M 7 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.52e+00 ... (remaining 41569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 55441 2.68 - 5.36: 660 5.36 - 8.04: 61 8.04 - 10.72: 4 10.72 - 13.40: 7 Bond angle restraints: 56173 Sorted by residual: angle pdb=" N ILE 4 458 " pdb=" CA ILE 4 458 " pdb=" C ILE 4 458 " ideal model delta sigma weight residual 113.39 105.92 7.47 1.47e+00 4.63e-01 2.58e+01 angle pdb=" N ILE 5 156 " pdb=" CA ILE 5 156 " pdb=" C ILE 5 156 " ideal model delta sigma weight residual 113.71 109.32 4.39 9.50e-01 1.11e+00 2.13e+01 angle pdb=" N3 DT M 6 " pdb=" C4 DT M 6 " pdb=" O4 DT M 6 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" O3G AGS 4 904 " pdb=" PG AGS 4 904 " pdb=" S1G AGS 4 904 " ideal model delta sigma weight residual 109.29 122.69 -13.40 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O2G AGS 4 902 " pdb=" PG AGS 4 902 " pdb=" O3G AGS 4 902 " ideal model delta sigma weight residual 109.23 96.04 13.19 3.00e+00 1.11e-01 1.93e+01 ... (remaining 56168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.21: 24924 32.21 - 64.42: 589 64.42 - 96.63: 54 96.63 - 128.83: 2 128.83 - 161.04: 3 Dihedral angle restraints: 25572 sinusoidal: 10734 harmonic: 14838 Sorted by residual: dihedral pdb=" O2A ADP 21001 " pdb=" O3A ADP 21001 " pdb=" PA ADP 21001 " pdb=" PB ADP 21001 " ideal model delta sinusoidal sigma weight residual -60.00 71.24 -131.24 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" C5' ADP 21001 " pdb=" O5' ADP 21001 " pdb=" PA ADP 21001 " pdb=" O2A ADP 21001 " ideal model delta sinusoidal sigma weight residual -60.00 58.50 -118.49 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O1B ADP 21001 " pdb=" O3A ADP 21001 " pdb=" PB ADP 21001 " pdb=" PA ADP 21001 " ideal model delta sinusoidal sigma weight residual -60.00 -176.89 116.89 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 25569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4265 0.048 - 0.095: 1694 0.095 - 0.142: 322 0.142 - 0.190: 25 0.190 - 0.237: 2 Chirality restraints: 6308 Sorted by residual: chirality pdb=" CA HIS 2 287 " pdb=" N HIS 2 287 " pdb=" C HIS 2 287 " pdb=" CB HIS 2 287 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL 6 226 " pdb=" CA VAL 6 226 " pdb=" CG1 VAL 6 226 " pdb=" CG2 VAL 6 226 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CA PRO 7 490 " pdb=" N PRO 7 490 " pdb=" C PRO 7 490 " pdb=" CB PRO 7 490 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 6305 not shown) Planarity restraints: 7229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY 5 571 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO 5 572 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO 5 572 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO 5 572 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 3 5 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO 3 6 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO 3 6 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO 3 6 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG 5 594 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ARG 5 594 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG 5 594 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN 5 595 " 0.012 2.00e-02 2.50e+03 ... (remaining 7226 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 419 2.59 - 3.16: 35733 3.16 - 3.74: 56453 3.74 - 4.32: 82957 4.32 - 4.90: 138061 Nonbonded interactions: 313623 Sorted by model distance: nonbonded pdb=" O2B AGS 4 902 " pdb="MG MG 4 903 " model vdw 2.008 2.170 nonbonded pdb=" OG SER 4 517 " pdb="MG MG 4 903 " model vdw 2.026 2.170 nonbonded pdb=" O2G AGS 4 902 " pdb="MG MG 4 903 " model vdw 2.047 2.170 nonbonded pdb=" OG SER 7 388 " pdb="MG MG 71002 " model vdw 2.061 2.170 nonbonded pdb=" O2B AGS 4 904 " pdb="MG MG 6 902 " model vdw 2.077 2.170 ... (remaining 313618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 47.030 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.130 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: 0.030 Load rotamer database and sin/cos tables:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 0.009 0.202 41594 Z= 0.399 Angle : 0.799 13.400 56203 Z= 0.439 Chirality : 0.049 0.237 6308 Planarity : 0.004 0.055 7229 Dihedral : 14.412 161.043 15918 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.89 % Favored : 89.07 % Rotamer: Outliers : 0.11 % Allowed : 7.05 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 are not related in a simple way. whole: -5.12 (0.09), residues: 4996 helix: -3.50 (0.08), residues: 1890 sheet: -3.11 (0.16), residues: 816 loop : -3.32 (0.11), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 114 TYR 0.024 0.002 TYR 4 671 PHE 0.025 0.002 PHE 6 156 TRP 0.023 0.002 TRP 6 614 HIS 0.010 0.001 HIS 2 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00892 / 0.39 (41574) covalent geometry : angle 0.79343 / 0.44 (56173) hydrogen bonds : bond 0.19587 / 13.48 ( 1264) hydrogen bonds : angle 8.05436 / 5.47 ( 3561) metal coordination : bond 0.10611 / 6.47 ( 20) metal coordination : angle 4.04813 / 2.31 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 456 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 183 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7345 (ttp-110) REVERT: 2 572 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6862 (mm-30) REVERT: 2 595 GLN cc_start: 0.8624 (tp40) cc_final: 0.8394 (pm20) REVERT: 2 726 TYR cc_start: 0.7692 (t80) cc_final: 0.7213 (m-80) REVERT: 2 746 MET cc_start: 0.7779 (tmm) cc_final: 0.7546 (ppp) REVERT: 2 798 MET cc_start: 0.8269 (ppp) cc_final: 0.7954 (ptm) REVERT: 3 338 LYS cc_start: 0.8565 (mttt) cc_final: 0.8218 (tptt) REVERT: 3 503 ARG cc_start: 0.8393 (mtt180) cc_final: 0.8160 (ttm110) REVERT: 4 283 ILE cc_start: 0.8689 (mt) cc_final: 0.8487 (mt) REVERT: 4 726 MET cc_start: 0.6401 (ptp) cc_final: 0.6101 (ptp) REVERT: 5 332 TYR cc_start: 0.7753 (t80) cc_final: 0.7527 (t80) REVERT: 5 391 LEU cc_start: 0.8162 (mt) cc_final: 0.7912 (pp) REVERT: 5 425 ARG cc_start: 0.6443 (mtm180) cc_final: 0.6137 (mtm180) REVERT: 5 434 MET cc_start: 0.8472 (mtp) cc_final: 0.8260 (mtm) REVERT: 5 621 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7533 (mm-30) REVERT: 6 193 LEU cc_start: 0.7619 (pt) cc_final: 0.7113 (pt) REVERT: 6 340 MET cc_start: 0.9192 (mtm) cc_final: 0.8956 (mtp) REVERT: 6 440 HIS cc_start: 0.7803 (t70) cc_final: 0.7478 (t70) REVERT: 6 751 TRP cc_start: 0.5671 (t60) cc_final: 0.5435 (t60) REVERT: 6 778 HIS cc_start: 0.7336 (m-70) cc_final: 0.6760 (t-170) REVERT: A 30 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7566 (mmt180) REVERT: A 80 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8417 (mm) REVERT: A 196 SER cc_start: 0.7289 (p) cc_final: 0.7060 (m) REVERT: B 67 ASP cc_start: 0.8227 (t0) cc_final: 0.7573 (p0) REVERT: B 151 MET cc_start: 0.8509 (tpt) cc_final: 0.7980 (tpt) REVERT: C 35 ARG cc_start: 0.7640 (ptm-80) cc_final: 0.7422 (ttp-110) REVERT: D 187 ASP cc_start: 0.8533 (t0) cc_final: 0.8285 (t0) REVERT: D 189 ASP cc_start: 0.8282 (t0) cc_final: 0.7723 (t0) REVERT: D 192 ARG cc_start: 0.8761 (mtp85) cc_final: 0.8389 (mtm-85) REVERT: E 284 TRP cc_start: 0.8944 (OUTLIER) cc_final: 0.7868 (m-10) REVERT: E 332 MET cc_start: 0.8664 (ttm) cc_final: 0.8452 (ttm) REVERT: E 389 LYS cc_start: 0.6608 (mmtt) cc_final: 0.6407 (mmtm) outliers start: 5 outliers final: 2 residues processed: 461 average time/residue: 0.2977 time to fit residues: 214.6487 Evaluate side-chains 342 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 338 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 284 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 494 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 196 HIS 2 226 ASN 2 282 HIS 2 328 ASN 2 563 HIS 2 607 GLN 2 838 GLN 2 843 GLN 2 875 HIS 2 893 HIS 2 902 GLN 3 318 GLN 3 398 GLN 3 431 GLN 4 171 GLN 4 195 GLN ** 4 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 342 ASN 4 389 ASN 4 415 HIS 4 594 GLN 4 633 ASN ** 4 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 733 GLN ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 181 ASN 5 244 HIS 5 426 ASN 5 459 HIS 5 464 GLN 5 629 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 342 GLN 6 349 ASN 6 509 HIS 6 635 HIS 6 725 ASN 7 36 GLN 7 186 GLN 7 223 GLN 7 543 HIS A 20 GLN B 102 HIS C 136 GLN C 177 GLN C 180 GLN D 78 HIS E 15 GLN E 37 GLN E 248 HIS E 253 ASN E 324 GLN E 364 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.115608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086049 restraints weight = 83476.914| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.74 r_work: 0.3069 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41594 Z= 0.128 Angle : 0.608 13.222 56203 Z= 0.309 Chirality : 0.043 0.329 6308 Planarity : 0.004 0.056 7229 Dihedral : 8.686 172.590 5709 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.90 % Favored : 94.06 % Rotamer: Outliers : 1.36 % Allowed : 10.70 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 are not related in a simple way. whole: -3.81 (0.10), residues: 4996 helix: -2.31 (0.10), residues: 1971 sheet: -2.46 (0.17), residues: 808 loop : -2.64 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 101 TYR 0.018 0.001 TYR 6 347 PHE 0.018 0.001 PHE 5 644 TRP 0.025 0.001 TRP 6 614 HIS 0.008 0.001 HIS 5 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (41574) covalent geometry : angle 0.59556 / 0.31 (56173) hydrogen bonds : bond 0.04178 / 2.85 ( 1264) hydrogen bonds : angle 5.38943 / 3.69 ( 3561) metal coordination : bond 0.01040 / 0.64 ( 20) metal coordination : angle 5.42479 / 3.40 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 414 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 183 ARG cc_start: 0.7710 (ttm-80) cc_final: 0.7294 (ttp-110) REVERT: 2 572 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6962 (mm-30) REVERT: 2 674 MET cc_start: 0.8012 (mtp) cc_final: 0.7325 (tpt) REVERT: 2 726 TYR cc_start: 0.7424 (t80) cc_final: 0.7146 (m-80) REVERT: 2 746 MET cc_start: 0.7883 (tmm) cc_final: 0.7498 (ppp) REVERT: 2 834 PHE cc_start: 0.7406 (m-80) cc_final: 0.6941 (m-80) REVERT: 3 338 LYS cc_start: 0.8452 (mttt) cc_final: 0.8117 (tptt) REVERT: 4 249 TYR cc_start: 0.6100 (OUTLIER) cc_final: 0.5800 (m-80) REVERT: 4 372 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8971 (mt) REVERT: 4 726 MET cc_start: 0.5986 (ptp) cc_final: 0.5751 (ptp) REVERT: 5 621 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7466 (mm-30) REVERT: 6 340 MET cc_start: 0.9073 (mtm) cc_final: 0.8849 (mtp) REVERT: 6 440 HIS cc_start: 0.8018 (t70) cc_final: 0.7337 (t70) REVERT: 6 751 TRP cc_start: 0.5558 (t60) cc_final: 0.5137 (t60) REVERT: 6 778 HIS cc_start: 0.7193 (m-70) cc_final: 0.6685 (t-170) REVERT: A 141 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8768 (tttm) REVERT: A 196 SER cc_start: 0.7145 (p) cc_final: 0.6735 (m) REVERT: B 2 ASP cc_start: 0.8371 (p0) cc_final: 0.8039 (p0) REVERT: B 151 MET cc_start: 0.8776 (tpt) cc_final: 0.8228 (tpt) REVERT: C 35 ARG cc_start: 0.8176 (ptm-80) cc_final: 0.7906 (ttp80) REVERT: C 40 MET cc_start: 0.6420 (tpt) cc_final: 0.5730 (tmm) REVERT: D 189 ASP cc_start: 0.8265 (t0) cc_final: 0.7870 (t0) REVERT: D 192 ARG cc_start: 0.8910 (mtp85) cc_final: 0.8640 (ttp-110) REVERT: E 284 TRP cc_start: 0.8915 (OUTLIER) cc_final: 0.7820 (m-10) REVERT: E 389 LYS cc_start: 0.6713 (mmtt) cc_final: 0.4468 (tptp) outliers start: 61 outliers final: 27 residues processed: 454 average time/residue: 0.2530 time to fit residues: 189.8727 Evaluate side-chains 368 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 338 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 214 VAL Chi-restraints excluded: chain 2 residue 216 LYS Chi-restraints excluded: chain 2 residue 270 MET Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 577 VAL Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 617 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 789 ASP Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 459 MET Chi-restraints excluded: chain 3 residue 471 MET Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 372 LEU Chi-restraints excluded: chain 5 residue 325 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 62 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 7 residue 530 ASP Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain E residue 284 TRP Chi-restraints excluded: chain E residue 360 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 491 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 358 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 469 optimal weight: 0.8980 chunk 331 optimal weight: 3.9990 chunk 465 optimal weight: 3.9990 chunk 493 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 449 optimal weight: 1.9990 chunk 398 optimal weight: 0.3980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 318 GLN ** 4 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 335 HIS ** 4 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 540 HIS 5 629 GLN 7 30 GLN ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN E 111 ASN E 364 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.116210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086653 restraints weight = 83577.527| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.65 r_work: 0.3078 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41594 Z= 0.122 Angle : 0.563 12.206 56203 Z= 0.283 Chirality : 0.042 0.282 6308 Planarity : 0.004 0.056 7229 Dihedral : 8.405 174.473 5705 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.66 % Favored : 94.30 % Rotamer: Outliers : 1.70 % Allowed : 12.58 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 are not related in a simple way. whole: -3.19 (0.11), residues: 4996 helix: -1.76 (0.11), residues: 1999 sheet: -2.21 (0.17), residues: 808 loop : -2.30 (0.12), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 401 TYR 0.019 0.001 TYR 3 64 PHE 0.014 0.001 PHE 7 16 TRP 0.022 0.001 TRP 6 614 HIS 0.024 0.001 HIS 4 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (41574) covalent geometry : angle 0.55109 / 0.28 (56173) hydrogen bonds : bond 0.03737 / 2.55 ( 1264) hydrogen bonds : angle 4.91676 / 3.36 ( 3561) metal coordination : bond 0.00868 / 0.54 ( 20) metal coordination : angle 5.00832 / 3.20 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 373 time to evaluate : 1.730 Fit side-chains REVERT: 2 183 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7227 (ttp-110) REVERT: 2 572 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6879 (mm-30) REVERT: 2 674 MET cc_start: 0.8005 (mtp) cc_final: 0.7149 (tpt) REVERT: 2 726 TYR cc_start: 0.7398 (t80) cc_final: 0.7110 (m-80) REVERT: 2 746 MET cc_start: 0.7920 (tmm) cc_final: 0.7636 (ppp) REVERT: 2 761 PRO cc_start: 0.7147 (Cg_endo) cc_final: 0.6929 (Cg_exo) REVERT: 2 770 MET cc_start: 0.7446 (ttp) cc_final: 0.7091 (ttp) REVERT: 2 785 TYR cc_start: 0.8024 (t80) cc_final: 0.7757 (t80) REVERT: 2 798 MET cc_start: 0.7956 (ppp) cc_final: 0.7568 (ppp) REVERT: 2 834 PHE cc_start: 0.7400 (m-80) cc_final: 0.6915 (m-10) REVERT: 3 247 GLN cc_start: 0.8095 (tt0) cc_final: 0.7831 (tm-30) REVERT: 3 338 LYS cc_start: 0.8467 (mttt) cc_final: 0.8155 (tptt) REVERT: 3 455 GLU cc_start: 0.8110 (tp30) cc_final: 0.7889 (tp30) REVERT: 4 249 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5818 (m-80) REVERT: 4 337 MET cc_start: 0.7794 (mmm) cc_final: 0.7423 (mmm) REVERT: 4 372 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8954 (mt) REVERT: 4 726 MET cc_start: 0.6087 (ptp) cc_final: 0.5805 (ptp) REVERT: 5 184 MET cc_start: 0.9065 (mmt) cc_final: 0.8838 (mmm) REVERT: 5 391 LEU cc_start: 0.7927 (mt) cc_final: 0.7663 (pp) REVERT: 5 621 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7458 (mm-30) REVERT: 6 440 HIS cc_start: 0.8031 (t70) cc_final: 0.7306 (t70) REVERT: 6 751 TRP cc_start: 0.5486 (t60) cc_final: 0.5029 (t60) REVERT: 6 778 HIS cc_start: 0.7269 (m-70) cc_final: 0.6687 (t-170) REVERT: 7 474 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8523 (tt) REVERT: B 2 ASP cc_start: 0.8432 (p0) cc_final: 0.8166 (p0) REVERT: B 87 MET cc_start: 0.8797 (mmp) cc_final: 0.8541 (tpp) REVERT: B 151 MET cc_start: 0.8893 (tpt) cc_final: 0.8620 (tpt) REVERT: D 187 ASP cc_start: 0.8563 (t0) cc_final: 0.8286 (t0) REVERT: D 189 ASP cc_start: 0.8142 (t0) cc_final: 0.7673 (t0) REVERT: D 192 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8599 (ttp-110) REVERT: E 284 TRP cc_start: 0.8885 (OUTLIER) cc_final: 0.7696 (m-10) REVERT: E 389 LYS cc_start: 0.6554 (mmtt) cc_final: 0.4564 (tptp) REVERT: E 458 MET cc_start: 0.8044 (mmt) cc_final: 0.7830 (tmm) outliers start: 76 outliers final: 37 residues processed: 431 average time/residue: 0.2320 time to fit residues: 168.9979 Evaluate side-chains 382 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 577 VAL Chi-restraints excluded: chain 2 residue 617 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 719 VAL Chi-restraints excluded: chain 3 residue 459 MET Chi-restraints excluded: chain 3 residue 471 MET Chi-restraints excluded: chain 3 residue 633 THR Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 361 MET Chi-restraints excluded: chain 4 residue 372 LEU Chi-restraints excluded: chain 4 residue 639 THR Chi-restraints excluded: chain 4 residue 727 VAL Chi-restraints excluded: chain 5 residue 325 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 62 VAL Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 467 VAL Chi-restraints excluded: chain 6 residue 490 LYS Chi-restraints excluded: chain 6 residue 728 VAL Chi-restraints excluded: chain 7 residue 152 VAL Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 427 LEU Chi-restraints excluded: chain 7 residue 474 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 284 TRP Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 360 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 229 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 383 optimal weight: 8.9990 chunk 473 optimal weight: 2.9990 chunk 491 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 275 optimal weight: 0.3980 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 393 optimal weight: 0.5980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 540 HIS 5 629 GLN ** 7 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 376 ASN ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.115537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.085292 restraints weight = 83068.217| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.89 r_work: 0.3076 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41594 Z= 0.132 Angle : 0.559 19.856 56203 Z= 0.278 Chirality : 0.042 0.252 6308 Planarity : 0.004 0.097 7229 Dihedral : 8.262 175.977 5705 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.66 % Favored : 94.32 % Rotamer: Outliers : 1.92 % Allowed : 13.18 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 are not related in a simple way. whole: -2.77 (0.11), residues: 4996 helix: -1.37 (0.11), residues: 1977 sheet: -2.04 (0.17), residues: 820 loop : -2.08 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 219 TYR 0.033 0.001 TYR 3 64 PHE 0.013 0.001 PHE 6 203 TRP 0.021 0.001 TRP 6 614 HIS 0.009 0.001 HIS 5 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (41574) covalent geometry : angle 0.54913 / 0.28 (56173) hydrogen bonds : bond 0.03481 / 2.37 ( 1264) hydrogen bonds : angle 4.69921 / 3.21 ( 3561) metal coordination : bond 0.00732 / 0.45 ( 20) metal coordination : angle 4.59701 / 2.96 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 370 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 183 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.7187 (ttp-110) REVERT: 2 561 GLN cc_start: 0.7166 (tm-30) cc_final: 0.6740 (tm-30) REVERT: 2 572 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6942 (mm-30) REVERT: 2 592 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7931 (ttp) REVERT: 2 674 MET cc_start: 0.8000 (mtp) cc_final: 0.7213 (tpt) REVERT: 2 726 TYR cc_start: 0.7359 (t80) cc_final: 0.7115 (m-80) REVERT: 2 746 MET cc_start: 0.7916 (tmm) cc_final: 0.7676 (ppp) REVERT: 2 770 MET cc_start: 0.7392 (ttp) cc_final: 0.7040 (ttp) REVERT: 2 798 MET cc_start: 0.7857 (ppp) cc_final: 0.7537 (ppp) REVERT: 2 799 LEU cc_start: 0.8961 (tp) cc_final: 0.8700 (mm) REVERT: 2 834 PHE cc_start: 0.7352 (m-80) cc_final: 0.6822 (m-80) REVERT: 3 64 TYR cc_start: 0.8525 (m-80) cc_final: 0.8209 (m-80) REVERT: 3 247 GLN cc_start: 0.8227 (tt0) cc_final: 0.7932 (tm-30) REVERT: 3 338 LYS cc_start: 0.8473 (mttt) cc_final: 0.8189 (tptt) REVERT: 4 249 TYR cc_start: 0.6243 (OUTLIER) cc_final: 0.5895 (m-80) REVERT: 4 337 MET cc_start: 0.7765 (mmm) cc_final: 0.7367 (mmm) REVERT: 4 726 MET cc_start: 0.6105 (ptp) cc_final: 0.5873 (ptp) REVERT: 5 325 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8406 (mt) REVERT: 5 332 TYR cc_start: 0.7784 (t80) cc_final: 0.7509 (t80) REVERT: 5 391 LEU cc_start: 0.8011 (mt) cc_final: 0.7735 (pp) REVERT: 5 621 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7516 (mm-30) REVERT: 6 440 HIS cc_start: 0.8045 (t70) cc_final: 0.7305 (t70) REVERT: 6 751 TRP cc_start: 0.5445 (t60) cc_final: 0.4955 (t60) REVERT: 6 778 HIS cc_start: 0.7203 (m-70) cc_final: 0.6664 (t-170) REVERT: 7 474 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8534 (tt) REVERT: A 111 MET cc_start: 0.8842 (mpp) cc_final: 0.8283 (mpp) REVERT: A 141 LYS cc_start: 0.9120 (mtpp) cc_final: 0.8757 (tttm) REVERT: B 87 MET cc_start: 0.8738 (mmp) cc_final: 0.8187 (tpp) REVERT: B 151 MET cc_start: 0.8868 (tpt) cc_final: 0.8603 (tpt) REVERT: C 40 MET cc_start: 0.6884 (tpt) cc_final: 0.6514 (tmm) REVERT: C 43 LEU cc_start: 0.7445 (tp) cc_final: 0.7159 (pp) REVERT: D 187 ASP cc_start: 0.8521 (t0) cc_final: 0.8263 (t0) REVERT: D 189 ASP cc_start: 0.8127 (t0) cc_final: 0.7680 (t0) REVERT: D 192 ARG cc_start: 0.8863 (mtp85) cc_final: 0.8574 (ttp-110) REVERT: E 284 TRP cc_start: 0.8839 (OUTLIER) cc_final: 0.7649 (m-10) REVERT: E 389 LYS cc_start: 0.6513 (mmtt) cc_final: 0.4524 (tptp) REVERT: E 458 MET cc_start: 0.8104 (mmt) cc_final: 0.7855 (tmm) outliers start: 86 outliers final: 54 residues processed: 432 average time/residue: 0.2358 time to fit residues: 170.7767 Evaluate side-chains 409 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 350 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 214 VAL Chi-restraints excluded: chain 2 residue 236 ASP Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 306 ILE Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 617 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 719 VAL Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 459 MET Chi-restraints excluded: chain 3 residue 471 MET Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 361 MET Chi-restraints excluded: chain 4 residue 382 VAL Chi-restraints excluded: chain 4 residue 639 THR Chi-restraints excluded: chain 4 residue 727 VAL Chi-restraints excluded: chain 5 residue 325 LEU Chi-restraints excluded: chain 5 residue 375 ILE Chi-restraints excluded: chain 5 residue 582 LEU Chi-restraints excluded: chain 6 residue 16 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain 6 residue 62 VAL Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 6 residue 131 ILE Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 467 VAL Chi-restraints excluded: chain 6 residue 490 LYS Chi-restraints excluded: chain 6 residue 728 VAL Chi-restraints excluded: chain 7 residue 152 VAL Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 271 VAL Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 427 LEU Chi-restraints excluded: chain 7 residue 474 ILE Chi-restraints excluded: chain 7 residue 530 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 284 TRP Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 360 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 89 optimal weight: 5.9990 chunk 316 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 382 optimal weight: 5.9990 chunk 247 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 151 optimal weight: 0.0770 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 318 GLN ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 540 HIS 5 584 ASN 5 629 GLN ** 7 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN C 105 ASN E 254 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.117189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087745 restraints weight = 82996.886| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.92 r_work: 0.3086 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 41594 Z= 0.101 Angle : 0.546 20.034 56203 Z= 0.268 Chirality : 0.041 0.217 6308 Planarity : 0.004 0.055 7229 Dihedral : 8.058 175.755 5705 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.18 % Favored : 94.80 % Rotamer: Outliers : 1.99 % Allowed : 14.25 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 are not related in a simple way. whole: -2.38 (0.11), residues: 4996 helix: -1.05 (0.11), residues: 1982 sheet: -1.87 (0.17), residues: 833 loop : -1.84 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 7 TYR 0.027 0.001 TYR 3 64 PHE 0.011 0.001 PHE D 104 TRP 0.022 0.001 TRP 6 614 HIS 0.010 0.001 HIS 5 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (41574) covalent geometry : angle 0.53636 / 0.27 (56173) hydrogen bonds : bond 0.03135 / 2.14 ( 1264) hydrogen bonds : angle 4.46214 / 3.05 ( 3561) metal coordination : bond 0.00622 / 0.38 ( 20) metal coordination : angle 4.39973 / 2.92 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 380 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: 2 183 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.7206 (ttp-110) REVERT: 2 463 MET cc_start: 0.6313 (pmm) cc_final: 0.6028 (pmm) REVERT: 2 572 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6909 (mm-30) REVERT: 2 592 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8019 (ttp) REVERT: 2 595 GLN cc_start: 0.7685 (pm20) cc_final: 0.7064 (tm-30) REVERT: 2 674 MET cc_start: 0.8017 (mtp) cc_final: 0.7212 (tpt) REVERT: 2 746 MET cc_start: 0.7819 (tmm) cc_final: 0.7599 (ppp) REVERT: 2 770 MET cc_start: 0.7414 (ttp) cc_final: 0.7189 (ttp) REVERT: 2 798 MET cc_start: 0.7985 (ppp) cc_final: 0.7528 (ppp) REVERT: 2 799 LEU cc_start: 0.8871 (tp) cc_final: 0.8624 (mm) REVERT: 2 834 PHE cc_start: 0.7359 (m-80) cc_final: 0.6738 (m-10) REVERT: 3 206 ASP cc_start: 0.6970 (t70) cc_final: 0.6592 (t0) REVERT: 3 247 GLN cc_start: 0.8178 (tt0) cc_final: 0.7935 (tm-30) REVERT: 3 338 LYS cc_start: 0.8439 (mttt) cc_final: 0.8166 (tptt) REVERT: 4 249 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.5806 (m-80) REVERT: 4 337 MET cc_start: 0.7752 (mmm) cc_final: 0.7329 (mmm) REVERT: 4 726 MET cc_start: 0.6104 (ptp) cc_final: 0.5865 (ptp) REVERT: 5 325 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8413 (mt) REVERT: 5 332 TYR cc_start: 0.7841 (t80) cc_final: 0.7589 (t80) REVERT: 5 391 LEU cc_start: 0.8011 (mt) cc_final: 0.7709 (pp) REVERT: 5 621 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7499 (mm-30) REVERT: 5 626 MET cc_start: 0.8749 (mtm) cc_final: 0.7766 (ptp) REVERT: 6 440 HIS cc_start: 0.8038 (t70) cc_final: 0.7325 (t70) REVERT: 6 490 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8424 (tppt) REVERT: 6 751 TRP cc_start: 0.5447 (t60) cc_final: 0.4959 (t60) REVERT: 6 778 HIS cc_start: 0.7221 (m-70) cc_final: 0.6636 (t-170) REVERT: 7 474 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8554 (tt) REVERT: A 141 LYS cc_start: 0.9084 (mtpp) cc_final: 0.8703 (tttm) REVERT: B 151 MET cc_start: 0.8859 (tpt) cc_final: 0.8626 (tpt) REVERT: C 40 MET cc_start: 0.6816 (tpt) cc_final: 0.6516 (tmm) REVERT: D 187 ASP cc_start: 0.8506 (t0) cc_final: 0.8183 (t0) REVERT: D 189 ASP cc_start: 0.8175 (t0) cc_final: 0.7537 (t0) REVERT: D 192 ARG cc_start: 0.8865 (mtp85) cc_final: 0.8461 (ttp-110) REVERT: E 208 MET cc_start: 0.8951 (mtt) cc_final: 0.8741 (mtm) REVERT: E 284 TRP cc_start: 0.8810 (OUTLIER) cc_final: 0.7592 (m-10) REVERT: E 389 LYS cc_start: 0.6488 (mmtt) cc_final: 0.4596 (tptp) REVERT: E 458 MET cc_start: 0.8107 (mmt) cc_final: 0.7858 (tmm) outliers start: 89 outliers final: 61 residues processed: 445 average time/residue: 0.2368 time to fit residues: 178.1955 Evaluate side-chains 416 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 349 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 214 VAL Chi-restraints excluded: chain 2 residue 216 LYS Chi-restraints excluded: chain 2 residue 236 ASP Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 306 ILE Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 577 VAL Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 617 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 719 VAL Chi-restraints excluded: chain 3 residue 84 LEU Chi-restraints excluded: chain 3 residue 335 THR Chi-restraints excluded: chain 3 residue 388 LEU Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 451 VAL Chi-restraints excluded: chain 3 residue 459 MET Chi-restraints excluded: chain 3 residue 471 MET Chi-restraints excluded: chain 3 residue 633 THR Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 361 MET Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 639 THR Chi-restraints excluded: chain 4 residue 686 VAL Chi-restraints excluded: chain 4 residue 727 VAL Chi-restraints excluded: chain 5 residue 325 LEU Chi-restraints excluded: chain 5 residue 375 ILE Chi-restraints excluded: chain 5 residue 582 LEU Chi-restraints excluded: chain 6 residue 16 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 62 VAL Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 6 residue 131 ILE Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 444 ILE Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 467 VAL Chi-restraints excluded: chain 6 residue 490 LYS Chi-restraints excluded: chain 6 residue 728 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 271 VAL Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 427 LEU Chi-restraints excluded: chain 7 residue 474 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 254 HIS Chi-restraints excluded: chain E residue 284 TRP Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 360 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 404 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 471 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 414 optimal weight: 3.9990 chunk 449 optimal weight: 0.7980 chunk 323 optimal weight: 0.9990 chunk 483 optimal weight: 0.9990 chunk 427 optimal weight: 2.9990 chunk 209 optimal weight: 0.5980 chunk 262 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 242 ASN 4 505 ASN ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 540 HIS 5 629 GLN ** 7 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 254 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.116911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087144 restraints weight = 83615.920| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.88 r_work: 0.3094 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41594 Z= 0.115 Angle : 0.547 19.356 56203 Z= 0.270 Chirality : 0.041 0.184 6308 Planarity : 0.004 0.054 7229 Dihedral : 8.001 177.229 5705 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.24 % Favored : 94.74 % Rotamer: Outliers : 2.35 % Allowed : 14.34 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 are not related in a simple way. whole: -2.18 (0.11), residues: 4996 helix: -0.85 (0.11), residues: 1980 sheet: -1.78 (0.17), residues: 853 loop : -1.75 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 7 TYR 0.033 0.001 TYR 3 64 PHE 0.011 0.001 PHE 6 203 TRP 0.021 0.001 TRP 6 614 HIS 0.021 0.001 HIS E 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (41574) covalent geometry : angle 0.53840 / 0.27 (56173) hydrogen bonds : bond 0.03124 / 2.13 ( 1264) hydrogen bonds : angle 4.39932 / 3.00 ( 3561) metal coordination : bond 0.00599 / 0.37 ( 20) metal coordination : angle 4.15881 / 2.72 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 365 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 183 ARG cc_start: 0.7653 (ttm-80) cc_final: 0.7205 (ttp-110) REVERT: 2 463 MET cc_start: 0.6465 (pmm) cc_final: 0.6075 (pmm) REVERT: 2 561 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6816 (tm-30) REVERT: 2 592 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7983 (ttp) REVERT: 2 595 GLN cc_start: 0.7678 (pm20) cc_final: 0.7056 (tm-30) REVERT: 2 674 MET cc_start: 0.7941 (mtp) cc_final: 0.7220 (tpt) REVERT: 2 799 LEU cc_start: 0.8853 (tp) cc_final: 0.8636 (mm) REVERT: 2 834 PHE cc_start: 0.7169 (m-80) cc_final: 0.6569 (m-80) REVERT: 3 206 ASP cc_start: 0.6981 (t70) cc_final: 0.6554 (t0) REVERT: 3 247 GLN cc_start: 0.8167 (tt0) cc_final: 0.7928 (tm-30) REVERT: 3 338 LYS cc_start: 0.8443 (mttt) cc_final: 0.8167 (tptt) REVERT: 3 437 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.8096 (ttp80) REVERT: 4 249 TYR cc_start: 0.6145 (OUTLIER) cc_final: 0.5805 (m-80) REVERT: 4 337 MET cc_start: 0.7763 (mmm) cc_final: 0.7366 (mmm) REVERT: 4 592 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: 4 726 MET cc_start: 0.6077 (ptp) cc_final: 0.5823 (ptp) REVERT: 5 325 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8426 (mt) REVERT: 5 332 TYR cc_start: 0.7812 (t80) cc_final: 0.7565 (t80) REVERT: 5 391 LEU cc_start: 0.7964 (mt) cc_final: 0.7658 (pp) REVERT: 5 621 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7450 (mm-30) REVERT: 5 626 MET cc_start: 0.8745 (mtm) cc_final: 0.7741 (ptp) REVERT: 6 57 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8451 (pt0) REVERT: 6 440 HIS cc_start: 0.8029 (t70) cc_final: 0.7322 (t70) REVERT: 6 751 TRP cc_start: 0.5432 (t60) cc_final: 0.4940 (t60) REVERT: 6 778 HIS cc_start: 0.7213 (m-70) cc_final: 0.6635 (t-170) REVERT: 7 151 GLU cc_start: 0.8347 (tp30) cc_final: 0.8041 (mt-10) REVERT: 7 474 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8516 (tt) REVERT: A 141 LYS cc_start: 0.9094 (mtpp) cc_final: 0.8697 (tttm) REVERT: B 151 MET cc_start: 0.8871 (tpt) cc_final: 0.8634 (tpt) REVERT: C 43 LEU cc_start: 0.7649 (tt) cc_final: 0.6892 (pt) REVERT: D 187 ASP cc_start: 0.8455 (t0) cc_final: 0.8211 (t0) REVERT: D 189 ASP cc_start: 0.8420 (t0) cc_final: 0.7494 (t0) REVERT: D 192 ARG cc_start: 0.8878 (mtp85) cc_final: 0.8455 (ttp-110) REVERT: E 208 MET cc_start: 0.8977 (mtt) cc_final: 0.8772 (mtm) REVERT: E 284 TRP cc_start: 0.8807 (OUTLIER) cc_final: 0.7600 (m-10) REVERT: E 389 LYS cc_start: 0.6407 (mmtt) cc_final: 0.5999 (mptt) REVERT: E 458 MET cc_start: 0.8056 (mmt) cc_final: 0.7825 (tmm) outliers start: 105 outliers final: 75 residues processed: 441 average time/residue: 0.2358 time to fit residues: 175.7415 Evaluate side-chains 427 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 345 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 214 VAL Chi-restraints excluded: chain 2 residue 216 LYS Chi-restraints excluded: chain 2 residue 236 ASP Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 306 ILE Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 577 VAL Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 617 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 650 THR Chi-restraints excluded: chain 2 residue 719 VAL Chi-restraints excluded: chain 3 residue 84 LEU Chi-restraints excluded: chain 3 residue 289 LEU Chi-restraints excluded: chain 3 residue 335 THR Chi-restraints excluded: chain 3 residue 388 LEU Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 459 MET Chi-restraints excluded: chain 3 residue 471 MET Chi-restraints excluded: chain 3 residue 633 THR Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 361 MET Chi-restraints excluded: chain 4 residue 382 VAL Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 590 VAL Chi-restraints excluded: chain 4 residue 592 GLU Chi-restraints excluded: chain 4 residue 639 THR Chi-restraints excluded: chain 4 residue 686 VAL Chi-restraints excluded: chain 4 residue 727 VAL Chi-restraints excluded: chain 5 residue 325 LEU Chi-restraints excluded: chain 5 residue 375 ILE Chi-restraints excluded: chain 5 residue 582 LEU Chi-restraints excluded: chain 6 residue 16 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain 6 residue 62 VAL Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 6 residue 131 ILE Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 250 VAL Chi-restraints excluded: chain 6 residue 303 VAL Chi-restraints excluded: chain 6 residue 444 ILE Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 467 VAL Chi-restraints excluded: chain 6 residue 490 LYS Chi-restraints excluded: chain 6 residue 535 ILE Chi-restraints excluded: chain 6 residue 728 VAL Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 271 VAL Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 427 LEU Chi-restraints excluded: chain 7 residue 474 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 254 HIS Chi-restraints excluded: chain E residue 284 TRP Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 360 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 370 optimal weight: 4.9990 chunk 384 optimal weight: 0.7980 chunk 329 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 248 optimal weight: 0.0570 chunk 178 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 289 optimal weight: 8.9990 chunk 322 optimal weight: 8.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 595 GLN 3 318 GLN 4 171 GLN 4 195 GLN ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 540 HIS 5 629 GLN ** 7 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN E 254 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.117549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087523 restraints weight = 83662.286| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.92 r_work: 0.3104 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 41594 Z= 0.101 Angle : 0.541 18.601 56203 Z= 0.265 Chirality : 0.041 0.168 6308 Planarity : 0.003 0.054 7229 Dihedral : 7.891 177.569 5705 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.08 % Favored : 94.90 % Rotamer: Outliers : 2.33 % Allowed : 14.61 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 are not related in a simple way. whole: -1.98 (0.12), residues: 4996 helix: -0.66 (0.12), residues: 1984 sheet: -1.69 (0.17), residues: 867 loop : -1.65 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 7 TYR 0.030 0.001 TYR 3 64 PHE 0.025 0.001 PHE 5 644 TRP 0.029 0.001 TRP 6 614 HIS 0.031 0.001 HIS E 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (41574) covalent geometry : angle 0.53276 / 0.26 (56173) hydrogen bonds : bond 0.02951 / 2.02 ( 1264) hydrogen bonds : angle 4.29736 / 2.93 ( 3561) metal coordination : bond 0.00566 / 0.36 ( 20) metal coordination : angle 4.05050 / 2.66 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 371 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: 2 183 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7212 (ttp-110) REVERT: 2 463 MET cc_start: 0.6458 (pmm) cc_final: 0.5435 (ppp) REVERT: 2 592 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7970 (ttp) REVERT: 2 594 ASP cc_start: 0.7666 (t70) cc_final: 0.7452 (t70) REVERT: 2 595 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: 2 674 MET cc_start: 0.7922 (mtp) cc_final: 0.7221 (tpt) REVERT: 2 746 MET cc_start: 0.7273 (ppp) cc_final: 0.6629 (ttt) REVERT: 2 799 LEU cc_start: 0.8866 (tp) cc_final: 0.8644 (mm) REVERT: 2 834 PHE cc_start: 0.7050 (m-80) cc_final: 0.6376 (m-80) REVERT: 3 64 TYR cc_start: 0.8221 (m-80) cc_final: 0.7848 (m-80) REVERT: 3 247 GLN cc_start: 0.8171 (tt0) cc_final: 0.7948 (tm-30) REVERT: 3 338 LYS cc_start: 0.8444 (mttt) cc_final: 0.8159 (tptt) REVERT: 3 437 ARG cc_start: 0.8367 (ttp-110) cc_final: 0.8135 (ttp80) REVERT: 4 249 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.5723 (m-80) REVERT: 4 337 MET cc_start: 0.7814 (mmm) cc_final: 0.7430 (mmm) REVERT: 4 592 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7536 (tp30) REVERT: 4 726 MET cc_start: 0.5982 (ptp) cc_final: 0.5700 (ptp) REVERT: 5 325 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8390 (mt) REVERT: 5 332 TYR cc_start: 0.7786 (t80) cc_final: 0.7586 (t80) REVERT: 5 621 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7433 (mm-30) REVERT: 5 626 MET cc_start: 0.8750 (mtm) cc_final: 0.7810 (ptp) REVERT: 6 440 HIS cc_start: 0.8027 (t70) cc_final: 0.7320 (t70) REVERT: 6 490 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8407 (tppt) REVERT: 6 751 TRP cc_start: 0.5383 (t60) cc_final: 0.4881 (t60) REVERT: 6 778 HIS cc_start: 0.7230 (m-70) cc_final: 0.6630 (t-170) REVERT: 7 474 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8515 (tt) REVERT: A 141 LYS cc_start: 0.9082 (mtpp) cc_final: 0.8688 (tttm) REVERT: B 87 MET cc_start: 0.8777 (mmp) cc_final: 0.8367 (tpp) REVERT: B 151 MET cc_start: 0.8891 (tpt) cc_final: 0.8668 (tpt) REVERT: D 187 ASP cc_start: 0.8443 (t0) cc_final: 0.8170 (t0) REVERT: D 189 ASP cc_start: 0.8413 (t0) cc_final: 0.7499 (t0) REVERT: D 192 ARG cc_start: 0.8841 (mtp85) cc_final: 0.8312 (ttp-110) REVERT: E 208 MET cc_start: 0.8956 (mtt) cc_final: 0.8715 (mtm) REVERT: E 284 TRP cc_start: 0.8788 (OUTLIER) cc_final: 0.7597 (m-10) REVERT: E 389 LYS cc_start: 0.6437 (mmtt) cc_final: 0.6060 (mptt) REVERT: E 458 MET cc_start: 0.8025 (mmt) cc_final: 0.7810 (tmm) outliers start: 104 outliers final: 78 residues processed: 446 average time/residue: 0.2318 time to fit residues: 176.3837 Evaluate side-chains 434 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 348 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 214 VAL Chi-restraints excluded: chain 2 residue 216 LYS Chi-restraints excluded: chain 2 residue 236 ASP Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 306 ILE Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 577 VAL Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 595 GLN Chi-restraints excluded: chain 2 residue 616 ILE Chi-restraints excluded: chain 2 residue 617 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 650 THR Chi-restraints excluded: chain 3 residue 84 LEU Chi-restraints excluded: chain 3 residue 289 LEU Chi-restraints excluded: chain 3 residue 318 GLN Chi-restraints excluded: chain 3 residue 335 THR Chi-restraints excluded: chain 3 residue 388 LEU Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 421 VAL Chi-restraints excluded: chain 3 residue 428 THR Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 471 MET Chi-restraints excluded: chain 3 residue 633 THR Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 222 LEU Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 361 MET Chi-restraints excluded: chain 4 residue 382 VAL Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 592 GLU Chi-restraints excluded: chain 4 residue 639 THR Chi-restraints excluded: chain 4 residue 686 VAL Chi-restraints excluded: chain 4 residue 727 VAL Chi-restraints excluded: chain 5 residue 325 LEU Chi-restraints excluded: chain 5 residue 375 ILE Chi-restraints excluded: chain 5 residue 582 LEU Chi-restraints excluded: chain 6 residue 16 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 62 VAL Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 6 residue 131 ILE Chi-restraints excluded: chain 6 residue 144 THR Chi-restraints excluded: chain 6 residue 174 TYR Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 250 VAL Chi-restraints excluded: chain 6 residue 303 VAL Chi-restraints excluded: chain 6 residue 340 MET Chi-restraints excluded: chain 6 residue 444 ILE Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 467 VAL Chi-restraints excluded: chain 6 residue 490 LYS Chi-restraints excluded: chain 6 residue 535 ILE Chi-restraints excluded: chain 6 residue 728 VAL Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 271 VAL Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 474 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 254 HIS Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain E residue 284 TRP Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 360 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 80 optimal weight: 4.9990 chunk 224 optimal weight: 30.0000 chunk 113 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 374 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 367 optimal weight: 3.9990 chunk 433 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 413 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 889 ASN 3 318 GLN 4 171 GLN 4 214 HIS ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 540 HIS 5 629 GLN 6 785 HIS ** 7 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 243 GLN A 115 ASN B 138 GLN E 254 HIS E 364 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.115019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.085266 restraints weight = 83868.336| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.76 r_work: 0.3051 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 41594 Z= 0.222 Angle : 0.613 18.054 56203 Z= 0.304 Chirality : 0.044 0.186 6308 Planarity : 0.004 0.054 7229 Dihedral : 8.122 177.946 5705 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.02 % Favored : 93.94 % Rotamer: Outliers : 2.44 % Allowed : 14.79 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 are not related in a simple way. whole: -2.10 (0.12), residues: 4996 helix: -0.76 (0.11), residues: 1990 sheet: -1.77 (0.17), residues: 890 loop : -1.70 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 597 TYR 0.034 0.001 TYR 3 64 PHE 0.018 0.002 PHE A 64 TRP 0.022 0.002 TRP 6 614 HIS 0.022 0.001 HIS E 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (41574) covalent geometry : angle 0.60616 / 0.30 (56173) hydrogen bonds : bond 0.03634 / 2.46 ( 1264) hydrogen bonds : angle 4.56760 / 3.11 ( 3561) metal coordination : bond 0.00755 / 0.46 ( 20) metal coordination : angle 4.11350 / 2.61 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 346 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: 2 183 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7268 (ttp-110) REVERT: 2 595 GLN cc_start: 0.7945 (pm20) cc_final: 0.7635 (tp40) REVERT: 2 674 MET cc_start: 0.7975 (mtp) cc_final: 0.7271 (tpt) REVERT: 2 746 MET cc_start: 0.7403 (ppp) cc_final: 0.6713 (ttt) REVERT: 2 834 PHE cc_start: 0.7163 (m-80) cc_final: 0.6482 (m-80) REVERT: 3 64 TYR cc_start: 0.8390 (m-80) cc_final: 0.8056 (m-80) REVERT: 3 247 GLN cc_start: 0.8158 (tt0) cc_final: 0.7929 (tm-30) REVERT: 3 338 LYS cc_start: 0.8489 (mttt) cc_final: 0.8111 (tptt) REVERT: 3 437 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.8145 (ttp80) REVERT: 4 249 TYR cc_start: 0.6286 (OUTLIER) cc_final: 0.5879 (m-80) REVERT: 4 372 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8826 (mt) REVERT: 4 554 ARG cc_start: 0.8407 (mmp-170) cc_final: 0.8143 (mmp-170) REVERT: 4 592 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: 4 726 MET cc_start: 0.6290 (ptp) cc_final: 0.6036 (ptp) REVERT: 5 325 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8409 (mt) REVERT: 5 332 TYR cc_start: 0.7816 (t80) cc_final: 0.7578 (t80) REVERT: 5 621 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7576 (mm-30) REVERT: 5 626 MET cc_start: 0.8702 (mtm) cc_final: 0.7796 (ptp) REVERT: 6 340 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8518 (mtp) REVERT: 6 440 HIS cc_start: 0.8067 (t70) cc_final: 0.7328 (t70) REVERT: 6 751 TRP cc_start: 0.5463 (t60) cc_final: 0.4980 (t60) REVERT: 6 778 HIS cc_start: 0.7262 (m-70) cc_final: 0.6673 (t-170) REVERT: A 141 LYS cc_start: 0.9115 (mtpp) cc_final: 0.8764 (tttm) REVERT: B 87 MET cc_start: 0.8866 (mmp) cc_final: 0.8525 (tpp) REVERT: B 151 MET cc_start: 0.8876 (tpt) cc_final: 0.8586 (tpt) REVERT: D 187 ASP cc_start: 0.8520 (t0) cc_final: 0.8239 (t0) REVERT: D 189 ASP cc_start: 0.8444 (t0) cc_final: 0.7579 (t0) REVERT: D 192 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8348 (ttp-110) REVERT: E 284 TRP cc_start: 0.8885 (OUTLIER) cc_final: 0.8075 (m-10) REVERT: E 389 LYS cc_start: 0.6543 (mmtt) cc_final: 0.5477 (mmtt) REVERT: E 458 MET cc_start: 0.8055 (mmt) cc_final: 0.7823 (tmm) outliers start: 109 outliers final: 82 residues processed: 425 average time/residue: 0.2352 time to fit residues: 169.2288 Evaluate side-chains 424 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 336 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 214 VAL Chi-restraints excluded: chain 2 residue 216 LYS Chi-restraints excluded: chain 2 residue 236 ASP Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 306 ILE Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 577 VAL Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 616 ILE Chi-restraints excluded: chain 2 residue 617 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 650 THR Chi-restraints excluded: chain 2 residue 719 VAL Chi-restraints excluded: chain 3 residue 84 LEU Chi-restraints excluded: chain 3 residue 289 LEU Chi-restraints excluded: chain 3 residue 318 GLN Chi-restraints excluded: chain 3 residue 347 SER Chi-restraints excluded: chain 3 residue 388 LEU Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 421 VAL Chi-restraints excluded: chain 3 residue 428 THR Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 459 MET Chi-restraints excluded: chain 3 residue 471 MET Chi-restraints excluded: chain 3 residue 633 THR Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 222 LEU Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 260 VAL Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 372 LEU Chi-restraints excluded: chain 4 residue 382 VAL Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 590 VAL Chi-restraints excluded: chain 4 residue 592 GLU Chi-restraints excluded: chain 4 residue 639 THR Chi-restraints excluded: chain 4 residue 727 VAL Chi-restraints excluded: chain 5 residue 325 LEU Chi-restraints excluded: chain 5 residue 375 ILE Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 582 LEU Chi-restraints excluded: chain 6 residue 16 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain 6 residue 62 VAL Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 6 residue 144 THR Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 250 VAL Chi-restraints excluded: chain 6 residue 340 MET Chi-restraints excluded: chain 6 residue 417 VAL Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 467 VAL Chi-restraints excluded: chain 6 residue 490 LYS Chi-restraints excluded: chain 6 residue 728 VAL Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 271 VAL Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 427 LEU Chi-restraints excluded: chain 7 residue 474 ILE Chi-restraints excluded: chain 7 residue 530 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 254 HIS Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain E residue 284 TRP Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 360 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 404 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 326 optimal weight: 7.9990 chunk 486 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 337 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 475 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 595 GLN 3 318 GLN 4 171 GLN ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 540 HIS 5 629 GLN ** 7 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN E 254 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.116785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.086846 restraints weight = 83857.382| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.99 r_work: 0.3075 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41594 Z= 0.117 Angle : 0.562 18.610 56203 Z= 0.277 Chirality : 0.042 0.167 6308 Planarity : 0.004 0.053 7229 Dihedral : 7.944 179.656 5705 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.20 % Favored : 94.78 % Rotamer: Outliers : 2.06 % Allowed : 15.24 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 are not related in a simple way. whole: -1.88 (0.12), residues: 4996 helix: -0.56 (0.12), residues: 1988 sheet: -1.64 (0.17), residues: 864 loop : -1.62 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 7 TYR 0.028 0.001 TYR 3 64 PHE 0.012 0.001 PHE 3 121 TRP 0.025 0.001 TRP 6 614 HIS 0.014 0.001 HIS E 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (41574) covalent geometry : angle 0.55419 / 0.28 (56173) hydrogen bonds : bond 0.03126 / 2.13 ( 1264) hydrogen bonds : angle 4.34855 / 2.97 ( 3561) metal coordination : bond 0.00577 / 0.36 ( 20) metal coordination : angle 4.09829 / 2.68 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 359 time to evaluate : 1.662 Fit side-chains revert: symmetry clash REVERT: 2 183 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.7255 (ttp-110) REVERT: 2 463 MET cc_start: 0.7822 (pmm) cc_final: 0.6711 (ppp) REVERT: 2 572 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6891 (mm-30) REVERT: 2 592 MET cc_start: 0.8390 (mtm) cc_final: 0.7999 (ttp) REVERT: 2 594 ASP cc_start: 0.7910 (t70) cc_final: 0.7502 (t70) REVERT: 2 595 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: 2 674 MET cc_start: 0.7932 (mtp) cc_final: 0.7203 (tpt) REVERT: 2 746 MET cc_start: 0.7465 (ppp) cc_final: 0.6659 (ttt) REVERT: 2 834 PHE cc_start: 0.7066 (m-80) cc_final: 0.6345 (m-80) REVERT: 3 247 GLN cc_start: 0.8152 (tt0) cc_final: 0.7923 (tm-30) REVERT: 3 338 LYS cc_start: 0.8469 (mttt) cc_final: 0.8086 (tptt) REVERT: 3 437 ARG cc_start: 0.8373 (ttp-110) cc_final: 0.8143 (ttp80) REVERT: 4 249 TYR cc_start: 0.6181 (OUTLIER) cc_final: 0.5852 (m-80) REVERT: 4 554 ARG cc_start: 0.8391 (mmp-170) cc_final: 0.8121 (mmp-170) REVERT: 4 592 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: 4 726 MET cc_start: 0.6050 (ptp) cc_final: 0.5775 (ptp) REVERT: 5 266 MET cc_start: 0.8611 (ttm) cc_final: 0.8399 (ttm) REVERT: 5 325 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8408 (mt) REVERT: 5 349 MET cc_start: 0.8162 (mtp) cc_final: 0.7756 (mmp) REVERT: 5 419 MET cc_start: 0.6546 (mmm) cc_final: 0.6235 (mmm) REVERT: 5 621 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7468 (mm-30) REVERT: 5 626 MET cc_start: 0.8655 (mtm) cc_final: 0.7851 (ptp) REVERT: 5 629 GLN cc_start: 0.6723 (tt0) cc_final: 0.6399 (tt0) REVERT: 6 440 HIS cc_start: 0.8076 (t70) cc_final: 0.7332 (t70) REVERT: 6 751 TRP cc_start: 0.5463 (t60) cc_final: 0.5005 (t60) REVERT: 6 778 HIS cc_start: 0.7243 (m-70) cc_final: 0.6632 (t-170) REVERT: 7 427 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8190 (mp) REVERT: 7 474 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8345 (tt) REVERT: A 141 LYS cc_start: 0.9120 (mtpp) cc_final: 0.8728 (tttm) REVERT: B 151 MET cc_start: 0.8859 (tpt) cc_final: 0.8651 (tpt) REVERT: C 191 LYS cc_start: 0.9095 (mtmt) cc_final: 0.8811 (mtmt) REVERT: D 187 ASP cc_start: 0.8498 (t0) cc_final: 0.8279 (t0) REVERT: D 189 ASP cc_start: 0.8496 (t0) cc_final: 0.8139 (t0) REVERT: D 192 ARG cc_start: 0.8916 (mtp85) cc_final: 0.8579 (ttp-110) REVERT: E 284 TRP cc_start: 0.8819 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: E 389 LYS cc_start: 0.6431 (mmtt) cc_final: 0.5866 (mptt) REVERT: E 458 MET cc_start: 0.8091 (mmt) cc_final: 0.7825 (tmm) outliers start: 92 outliers final: 74 residues processed: 424 average time/residue: 0.2419 time to fit residues: 172.6534 Evaluate side-chains 432 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 351 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 214 VAL Chi-restraints excluded: chain 2 residue 216 LYS Chi-restraints excluded: chain 2 residue 236 ASP Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 577 VAL Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 595 GLN Chi-restraints excluded: chain 2 residue 616 ILE Chi-restraints excluded: chain 2 residue 617 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 650 THR Chi-restraints excluded: chain 2 residue 719 VAL Chi-restraints excluded: chain 3 residue 84 LEU Chi-restraints excluded: chain 3 residue 289 LEU Chi-restraints excluded: chain 3 residue 318 GLN Chi-restraints excluded: chain 3 residue 347 SER Chi-restraints excluded: chain 3 residue 388 LEU Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 421 VAL Chi-restraints excluded: chain 3 residue 428 THR Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 471 MET Chi-restraints excluded: chain 3 residue 633 THR Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 222 LEU Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 260 VAL Chi-restraints excluded: chain 4 residue 382 VAL Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 590 VAL Chi-restraints excluded: chain 4 residue 592 GLU Chi-restraints excluded: chain 4 residue 639 THR Chi-restraints excluded: chain 4 residue 727 VAL Chi-restraints excluded: chain 5 residue 325 LEU Chi-restraints excluded: chain 5 residue 375 ILE Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 582 LEU Chi-restraints excluded: chain 6 residue 16 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain 6 residue 62 VAL Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 6 residue 174 TYR Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 250 VAL Chi-restraints excluded: chain 6 residue 303 VAL Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 467 VAL Chi-restraints excluded: chain 6 residue 490 LYS Chi-restraints excluded: chain 6 residue 728 VAL Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 271 VAL Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 404 THR Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 427 LEU Chi-restraints excluded: chain 7 residue 474 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 254 HIS Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain E residue 284 TRP Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 360 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 193 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 356 optimal weight: 2.9990 chunk 453 optimal weight: 5.9990 chunk 396 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 393 optimal weight: 9.9990 chunk 471 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 466 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 4 335 HIS ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 540 HIS ** 7 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.116721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.086754 restraints weight = 83490.683| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.02 r_work: 0.3069 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 41594 Z= 0.147 Angle : 0.666 59.177 56203 Z= 0.356 Chirality : 0.042 0.258 6308 Planarity : 0.004 0.122 7229 Dihedral : 7.942 179.483 5705 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 1.90 % Allowed : 15.64 % Favored : 82.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.92 % 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 are not related in a simple way. whole: -1.87 (0.12), residues: 4996 helix: -0.55 (0.12), residues: 1988 sheet: -1.62 (0.17), residues: 866 loop : -1.61 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 124 TYR 0.028 0.001 TYR 5 332 PHE 0.017 0.001 PHE 4 246 TRP 0.023 0.001 TRP 6 614 HIS 0.114 0.001 HIS E 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (41574) covalent geometry : angle 0.65899 / 0.36 (56173) hydrogen bonds : bond 0.03151 / 2.15 ( 1264) hydrogen bonds : angle 4.35614 / 2.97 ( 3561) metal coordination : bond 0.00593 / 0.37 ( 20) metal coordination : angle 4.09035 / 2.68 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9992 Ramachandran restraints generated. 4996 Oldfield, 0 Emsley, 4996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 351 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: 2 183 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7243 (ttp-110) REVERT: 2 463 MET cc_start: 0.7841 (pmm) cc_final: 0.6754 (ppp) REVERT: 2 572 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6882 (mm-30) REVERT: 2 594 ASP cc_start: 0.7924 (t70) cc_final: 0.7534 (t70) REVERT: 2 595 GLN cc_start: 0.7963 (pm20) cc_final: 0.7359 (pp30) REVERT: 2 674 MET cc_start: 0.7921 (mtp) cc_final: 0.7193 (tpt) REVERT: 2 746 MET cc_start: 0.7503 (ppp) cc_final: 0.6687 (ttt) REVERT: 2 834 PHE cc_start: 0.7065 (m-80) cc_final: 0.6348 (m-80) REVERT: 3 247 GLN cc_start: 0.8171 (tt0) cc_final: 0.7927 (tm-30) REVERT: 3 338 LYS cc_start: 0.8514 (mttt) cc_final: 0.8094 (tptt) REVERT: 3 437 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.8126 (ttp80) REVERT: 4 249 TYR cc_start: 0.6386 (OUTLIER) cc_final: 0.5889 (m-80) REVERT: 4 554 ARG cc_start: 0.8431 (mmp-170) cc_final: 0.8136 (mmp-170) REVERT: 4 592 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: 4 726 MET cc_start: 0.6045 (ptp) cc_final: 0.5775 (ptp) REVERT: 5 266 MET cc_start: 0.8634 (ttm) cc_final: 0.8421 (ttm) REVERT: 5 325 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8404 (mt) REVERT: 5 349 MET cc_start: 0.8155 (mtp) cc_final: 0.7743 (mmp) REVERT: 5 419 MET cc_start: 0.6551 (mmm) cc_final: 0.6240 (mmm) REVERT: 5 621 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7464 (mm-30) REVERT: 5 626 MET cc_start: 0.8543 (mtm) cc_final: 0.7843 (ptp) REVERT: 5 629 GLN cc_start: 0.6720 (tt0) cc_final: 0.6393 (tt0) REVERT: 6 340 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8563 (mtp) REVERT: 6 440 HIS cc_start: 0.8096 (t70) cc_final: 0.7334 (t70) REVERT: 6 751 TRP cc_start: 0.5351 (t60) cc_final: 0.4854 (t60) REVERT: 6 778 HIS cc_start: 0.7209 (m-70) cc_final: 0.6626 (t-170) REVERT: 7 427 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8190 (mp) REVERT: 7 474 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8350 (tt) REVERT: A 141 LYS cc_start: 0.9127 (mtpp) cc_final: 0.8729 (tttm) REVERT: B 87 MET cc_start: 0.8849 (mmt) cc_final: 0.8172 (mmt) REVERT: B 151 MET cc_start: 0.8882 (tpt) cc_final: 0.8669 (tpt) REVERT: C 191 LYS cc_start: 0.9100 (mtmt) cc_final: 0.8828 (mtmt) REVERT: D 187 ASP cc_start: 0.8514 (t0) cc_final: 0.8279 (t0) REVERT: D 189 ASP cc_start: 0.8532 (t0) cc_final: 0.8149 (t0) REVERT: D 192 ARG cc_start: 0.8964 (mtp85) cc_final: 0.8598 (ttp-110) REVERT: E 284 TRP cc_start: 0.8823 (OUTLIER) cc_final: 0.7629 (m-10) REVERT: E 389 LYS cc_start: 0.6437 (mmtt) cc_final: 0.5868 (mptt) REVERT: E 458 MET cc_start: 0.8100 (mmt) cc_final: 0.7820 (tmm) outliers start: 85 outliers final: 75 residues processed: 412 average time/residue: 0.2448 time to fit residues: 169.9949 Evaluate side-chains 431 residues out of total 4469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 349 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 214 VAL Chi-restraints excluded: chain 2 residue 216 LYS Chi-restraints excluded: chain 2 residue 236 ASP Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 577 VAL Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 616 ILE Chi-restraints excluded: chain 2 residue 617 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 650 THR Chi-restraints excluded: chain 2 residue 719 VAL Chi-restraints excluded: chain 3 residue 84 LEU Chi-restraints excluded: chain 3 residue 289 LEU Chi-restraints excluded: chain 3 residue 388 LEU Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 421 VAL Chi-restraints excluded: chain 3 residue 428 THR Chi-restraints excluded: chain 3 residue 433 THR Chi-restraints excluded: chain 3 residue 471 MET Chi-restraints excluded: chain 3 residue 633 THR Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 222 LEU Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 260 VAL Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 335 HIS Chi-restraints excluded: chain 4 residue 382 VAL Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 590 VAL Chi-restraints excluded: chain 4 residue 592 GLU Chi-restraints excluded: chain 4 residue 639 THR Chi-restraints excluded: chain 4 residue 727 VAL Chi-restraints excluded: chain 5 residue 325 LEU Chi-restraints excluded: chain 5 residue 375 ILE Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 582 LEU Chi-restraints excluded: chain 6 residue 16 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain 6 residue 62 VAL Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 6 residue 131 ILE Chi-restraints excluded: chain 6 residue 174 TYR Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 250 VAL Chi-restraints excluded: chain 6 residue 303 VAL Chi-restraints excluded: chain 6 residue 340 MET Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 467 VAL Chi-restraints excluded: chain 6 residue 490 LYS Chi-restraints excluded: chain 6 residue 728 VAL Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 271 VAL Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 404 THR Chi-restraints excluded: chain 7 residue 419 LEU Chi-restraints excluded: chain 7 residue 427 LEU Chi-restraints excluded: chain 7 residue 474 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain E residue 284 TRP Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 360 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 13 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 437 optimal weight: 5.9990 chunk 469 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 429 optimal weight: 2.9990 chunk 394 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 4 335 HIS ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 540 HIS ** 7 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN B 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.116092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.086732 restraints weight = 84318.103| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.85 r_work: 0.3071 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41594 Z= 0.161 Angle : 0.584 18.824 56203 Z= 0.287 Chirality : 0.043 0.169 6308 Planarity : 0.004 0.053 7229 Dihedral : 7.952 177.383 5705 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.82 % Favored : 94.16 % Rotamer: Outliers : 1.99 % Allowed : 15.57 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 are not related in a simple way. whole: -1.88 (0.12), residues: 4996 helix: -0.53 (0.12), residues: 1986 sheet: -1.63 (0.17), residues: 869 loop : -1.64 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 7 TYR 0.031 0.001 TYR 3 64 PHE 0.024 0.001 PHE 5 644 TRP 0.023 0.001 TRP 6 614 HIS 0.050 0.001 HIS 4 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (41574) covalent geometry : angle 0.57604 / 0.29 (56173) hydrogen bonds : bond 0.03283 / 2.23 ( 1264) hydrogen bonds : angle 4.40707 / 3.01 ( 3561) metal coordination : bond 0.00657 / 0.41 ( 20) metal coordination : angle 4.15555 / 2.67 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9494.05 seconds wall clock time: 163 minutes 50.20 seconds (9830.20 seconds total)