Starting phenix.real_space_refine (version: dev) on Tue May 17 15:12:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtx_10619/05_2022/6xtx_10619_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtx_10619/05_2022/6xtx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtx_10619/05_2022/6xtx_10619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtx_10619/05_2022/6xtx_10619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtx_10619/05_2022/6xtx_10619_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtx_10619/05_2022/6xtx_10619_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/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: {'PTRANS': 24, 'TRANS': 551, 'PCIS': 1} 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: {'PTRANS': 11, 'TRANS': 163, 'PCIS': 1} Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1552 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 8, 'TRANS': 184, 'PCIS': 1} 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: {'PTRANS': 12, 'TRANS': 524, 'PCIS': 1} 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: {' ZN': 1, ' MG': 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: 22.29, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 16.33 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral 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... running ksdssp... Secondary structure from input PDB file: 198 helices and 51 sheets defined 35.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain '2' and resid 182 through 186 removed outlier: 3.578A pdb=" N VAL 2 186 " --> pdb=" O VAL 2 182 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 182 through 186' Processing helix chain '2' and resid 189 through 204 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 214 through 223 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 240 Processing helix chain '2' and resid 244 through 247 No H-bonds generated for 'chain '2' and resid 244 through 247' Processing helix chain '2' and resid 252 through 270 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 274 through 276 No H-bonds generated for 'chain '2' and resid 274 through 276' Processing helix chain '2' and resid 299 through 301 No H-bonds generated for 'chain '2' and resid 299 through 301' Processing helix chain '2' and resid 400 through 402 No H-bonds generated for 'chain '2' and resid 400 through 402' Processing helix chain '2' and resid 426 through 430 Processing helix chain '2' and resid 461 through 470 removed outlier: 4.207A pdb=" N SER 2 466 " --> pdb=" O LYS 2 462 " (cutoff:3.500A) Processing helix chain '2' and resid 473 through 480 removed outlier: 3.560A pdb=" N ALA 2 479 " --> pdb=" O GLU 2 475 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER 2 480 " --> pdb=" O LYS 2 476 " (cutoff:3.500A) Processing helix chain '2' and resid 489 through 500 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 529 through 539 removed outlier: 3.534A pdb=" N ILE 2 536 " --> pdb=" O PHE 2 532 " (cutoff:3.500A) Processing helix chain '2' and resid 589 through 591 No H-bonds generated for 'chain '2' and resid 589 through 591' Processing helix chain '2' and resid 594 through 605 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 633 through 635 No H-bonds generated for 'chain '2' and resid 633 through 635' Processing helix chain '2' and resid 643 through 646 No H-bonds generated for 'chain '2' and resid 643 through 646' Processing helix chain '2' and resid 651 through 656 removed outlier: 3.710A pdb=" N SER 2 655 " --> pdb=" O GLU 2 651 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG 2 656 " --> pdb=" O PRO 2 652 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 651 through 656' Processing helix chain '2' and resid 669 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 719 through 726 Processing helix chain '2' and resid 744 through 755 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 764 through 781 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) removed outlier: 3.644A pdb=" N ALA 2 776 " --> pdb=" O ARG 2 772 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS 2 777 " --> pdb=" O MET 2 773 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA 2 778 " --> pdb=" O ALA 2 774 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG 2 779 " --> pdb=" O GLU 2 775 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE 2 780 " --> pdb=" O ALA 2 776 " (cutoff:3.500A) Processing helix chain '2' and resid 790 through 803 removed outlier: 4.078A pdb=" N PHE 2 802 " --> pdb=" O MET 2 798 " (cutoff:3.500A) Processing helix chain '2' and resid 810 through 821 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 830 through 848 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 864 through 872 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 878 through 882 Processing helix chain '3' and resid 57 through 69 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) Processing helix chain '3' and resid 78 through 85 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 96 through 102 removed outlier: 3.559A pdb=" N ARG 3 101 " --> pdb=" O ASN 3 97 " (cutoff:3.500A) Processing helix chain '3' and resid 104 through 110 Processing helix chain '3' and resid 114 through 121 removed outlier: 3.735A pdb=" N ALA 3 120 " --> pdb=" O GLU 3 116 " (cutoff:3.500A) Processing helix chain '3' and resid 123 through 130 removed outlier: 3.901A pdb=" N PHE 3 128 " --> pdb=" O ALA 3 124 " (cutoff:3.500A) Processing helix chain '3' and resid 136 through 138 No H-bonds generated for 'chain '3' and resid 136 through 138' Processing helix chain '3' and resid 250 through 252 No H-bonds generated for 'chain '3' and resid 250 through 252' Processing helix chain '3' and resid 323 through 335 removed outlier: 3.612A pdb=" N LYS 3 334 " --> pdb=" O LYS 3 330 " (cutoff:3.500A) Processing helix chain '3' and resid 341 through 346 Processing helix chain '3' and resid 356 through 367 Processing helix chain '3' and resid 396 through 406 removed outlier: 3.749A pdb=" N CYS 3 405 " --> pdb=" O ARG 3 401 " (cutoff:3.500A) Processing helix chain '3' and resid 442 through 445 No H-bonds generated for 'chain '3' and resid 442 through 445' Processing helix chain '3' and resid 461 through 467 removed outlier: 3.761A pdb=" N THR 3 465 " --> pdb=" O ASP 3 461 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA 3 466 " --> pdb=" O MET 3 462 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE 3 467 " --> pdb=" O ASP 3 463 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 461 through 467' Processing helix chain '3' and resid 520 through 523 No H-bonds generated for 'chain '3' and resid 520 through 523' Processing helix chain '3' and resid 536 through 549 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 610 through 620 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 629 through 642 removed outlier: 3.795A pdb=" N THR 3 633 " --> pdb=" O GLN 3 629 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR 3 634 " --> pdb=" O GLU 3 630 " (cutoff:3.500A) 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 660 through 673 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 686 through 698 removed outlier: 4.149A pdb=" N VAL 3 691 " --> pdb=" O ALA 3 687 " (cutoff:3.500A) 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 160 through 171 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 192 through 202 Processing helix chain '4' and resid 214 through 217 No H-bonds generated for 'chain '4' and resid 214 through 217' Processing helix chain '4' and resid 223 through 226 No H-bonds generated for 'chain '4' and resid 223 through 226' Processing helix chain '4' and resid 230 through 232 No H-bonds generated for 'chain '4' and resid 230 through 232' Processing helix chain '4' and resid 234 through 245 removed outlier: 3.760A pdb=" N VAL 4 241 " --> pdb=" O PHE 4 237 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE 4 244 " --> pdb=" O ALA 4 240 " (cutoff:3.500A) Processing helix chain '4' and resid 378 through 380 No H-bonds generated for 'chain '4' and resid 378 through 380' Processing helix chain '4' and resid 443 through 454 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) removed outlier: 3.826A pdb=" N ARG 4 454 " --> pdb=" O LYS 4 450 " (cutoff:3.500A) Processing helix chain '4' and resid 459 through 465 removed outlier: 4.081A pdb=" N ALA 4 465 " --> pdb=" O ARG 4 461 " (cutoff:3.500A) Processing helix chain '4' and resid 474 through 484 removed outlier: 3.527A pdb=" N LYS 4 478 " --> pdb=" O GLU 4 474 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU 4 484 " --> pdb=" O ILE 4 480 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 523 Processing helix chain '4' and resid 540 through 543 No H-bonds generated for 'chain '4' and resid 540 through 543' Processing helix chain '4' and resid 563 through 566 No H-bonds generated for 'chain '4' and resid 563 through 566' Processing helix chain '4' and resid 581 through 584 No H-bonds generated for 'chain '4' and resid 581 through 584' Processing helix chain '4' and resid 587 through 590 No H-bonds generated for 'chain '4' and resid 587 through 590' Processing helix chain '4' and resid 620 through 622 No H-bonds generated for 'chain '4' and resid 620 through 622' Processing helix chain '4' and resid 630 through 633 No H-bonds generated for 'chain '4' and resid 630 through 633' Processing helix chain '4' and resid 638 through 641 No H-bonds generated for 'chain '4' and resid 638 through 641' Processing helix chain '4' and resid 656 through 670 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) removed outlier: 4.457A pdb=" N TYR 4 670 " --> pdb=" O LEU 4 666 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 696 removed outlier: 4.078A pdb=" N ALA 4 692 " --> pdb=" O LYS 4 688 " (cutoff:3.500A) Processing helix chain '4' and resid 704 through 710 removed outlier: 3.664A pdb=" N ALA 4 709 " --> pdb=" O GLU 4 705 " (cutoff:3.500A) Processing helix chain '4' and resid 712 through 724 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) Processing helix chain '4' and resid 731 through 748 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) removed outlier: 3.786A pdb=" N VAL 4 747 " --> pdb=" O ALA 4 743 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG 4 748 " --> pdb=" O HIS 4 744 " (cutoff:3.500A) Processing helix chain '4' and resid 756 through 766 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 31 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 36 through 39 No H-bonds generated for 'chain '5' and resid 36 through 39' Processing helix chain '5' and resid 54 through 63 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 80 Processing helix chain '5' and resid 84 through 90 removed outlier: 4.020A pdb=" N TYR 5 89 " --> pdb=" O ALA 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 106 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 108 through 111 No H-bonds generated for 'chain '5' and resid 108 through 111' Processing helix chain '5' and resid 137 through 139 No H-bonds generated for 'chain '5' and resid 137 through 139' Processing helix chain '5' and resid 142 through 144 No H-bonds generated for 'chain '5' and resid 142 through 144' Processing helix chain '5' and resid 233 through 235 No H-bonds generated for 'chain '5' and resid 233 through 235' Processing helix chain '5' and resid 316 through 327 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 331 through 337 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) Processing helix chain '5' and resid 348 through 356 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) Processing helix chain '5' and resid 386 through 396 removed outlier: 4.232A pdb=" N LEU 5 390 " --> pdb=" O ALA 5 386 " (cutoff:3.500A) Processing helix chain '5' and resid 452 through 464 Processing helix chain '5' and resid 526 through 540 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 556 through 566 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 576 through 597 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 610 through 625 removed outlier: 3.514A pdb=" N ALA 5 622 " --> pdb=" O ARG 5 618 " (cutoff:3.500A) Processing helix chain '5' and resid 634 through 655 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) Processing helix chain '6' and resid 21 through 36 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 45 through 47 No H-bonds generated for 'chain '6' and resid 45 through 47' Processing helix chain '6' and resid 52 through 54 No H-bonds generated for 'chain '6' and resid 52 through 54' Processing helix chain '6' and resid 67 through 71 Processing helix chain '6' and resid 76 through 82 removed outlier: 3.928A pdb=" N GLU 6 81 " --> pdb=" O THR 6 77 " (cutoff:3.500A) Processing helix chain '6' and resid 87 through 90 No H-bonds generated for 'chain '6' and resid 87 through 90' Processing helix chain '6' and resid 92 through 95 No H-bonds generated for 'chain '6' and resid 92 through 95' Processing helix chain '6' and resid 212 through 214 No H-bonds generated for 'chain '6' and resid 212 through 214' Processing helix chain '6' and resid 254 through 256 No H-bonds generated for 'chain '6' and resid 254 through 256' Processing helix chain '6' and resid 322 through 328 removed outlier: 3.947A pdb=" N GLN 6 328 " --> pdb=" O SER 6 324 " (cutoff:3.500A) Processing helix chain '6' and resid 331 through 342 removed outlier: 3.641A pdb=" N GLU 6 339 " --> pdb=" O GLU 6 335 " (cutoff:3.500A) Processing helix chain '6' and resid 346 through 349 No H-bonds generated for 'chain '6' and resid 346 through 349' Processing helix chain '6' and resid 351 through 354 No H-bonds generated for 'chain '6' and resid 351 through 354' Processing helix chain '6' and resid 362 through 373 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) Processing helix chain '6' and resid 403 through 412 Processing helix chain '6' and resid 426 through 429 No H-bonds generated for 'chain '6' and resid 426 through 429' Processing helix chain '6' and resid 469 through 479 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 526 through 528 No H-bonds generated for 'chain '6' and resid 526 through 528' Processing helix chain '6' and resid 544 through 557 removed outlier: 4.009A pdb=" N ALA 6 549 " --> pdb=" O ASP 6 545 " (cutoff:3.500A) Processing helix chain '6' and resid 569 through 581 removed outlier: 3.532A pdb=" N ARG 6 574 " --> pdb=" O ASP 6 570 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG 6 580 " --> pdb=" O LEU 6 576 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLN 6 581 " --> pdb=" O LEU 6 577 " (cutoff:3.500A) Processing helix chain '6' and resid 588 through 605 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) removed outlier: 4.202A pdb=" N ARG 6 604 " --> pdb=" O HIS 6 600 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP 6 605 " --> pdb=" O LEU 6 601 " (cutoff:3.500A) Processing helix chain '6' and resid 625 through 634 removed outlier: 3.650A pdb=" N MET 6 634 " --> pdb=" O ALA 6 630 " (cutoff:3.500A) Processing helix chain '6' and resid 642 through 655 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) Processing helix chain '6' and resid 721 through 727 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) No H-bonds generated for 'chain '6' and resid 721 through 727' Processing helix chain '6' and resid 745 through 753 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 765 through 781 removed outlier: 3.894A pdb=" N ILE 6 772 " --> pdb=" O ASN 6 768 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR 6 781 " --> pdb=" O ILE 6 777 " (cutoff:3.500A) Processing helix chain '7' and resid 9 through 19 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 41 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 55 through 58 No H-bonds generated for 'chain '7' and resid 55 through 58' Processing helix chain '7' and resid 62 through 66 Processing helix chain '7' and resid 73 through 88 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 154 through 156 No H-bonds generated for 'chain '7' and resid 154 through 156' Processing helix chain '7' and resid 209 through 215 removed outlier: 3.541A pdb=" N ARG 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) Processing helix chain '7' and resid 321 through 327 removed outlier: 4.266A pdb=" N GLN 7 326 " --> pdb=" O GLU 7 322 " (cutoff:3.500A) Processing helix chain '7' and resid 332 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 350 through 359 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 387 through 396 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 406 through 408 No H-bonds generated for 'chain '7' and resid 406 through 408' Processing helix chain '7' and resid 411 through 414 No H-bonds generated for 'chain '7' and resid 411 through 414' Processing helix chain '7' and resid 433 through 436 No H-bonds generated for 'chain '7' and resid 433 through 436' Processing helix chain '7' and resid 456 through 463 removed outlier: 3.583A pdb=" N HIS 7 459 " --> pdb=" O THR 7 456 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU 7 460 " --> pdb=" O ALA 7 457 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET 7 462 " --> pdb=" O HIS 7 459 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU 7 463 " --> pdb=" O GLU 7 460 " (cutoff:3.500A) Processing helix chain '7' and resid 509 through 514 removed outlier: 4.078A pdb=" N ARG 7 514 " --> pdb=" O ALA 7 510 " (cutoff:3.500A) Processing helix chain '7' and resid 529 through 543 removed outlier: 3.707A pdb=" N TYR 7 539 " --> pdb=" O GLN 7 535 " (cutoff:3.500A) Processing helix chain '7' and resid 556 through 567 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) Processing helix chain '7' and resid 575 through 593 removed outlier: 4.237A pdb=" N ASP 7 579 " --> pdb=" O SER 7 576 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE 7 581 " --> pdb=" O ALA 7 578 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR 7 582 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA 7 592 " --> pdb=" O ARG 7 589 " (cutoff:3.500A) Processing helix chain '7' and resid 606 through 611 Processing helix chain '7' and resid 616 through 619 No H-bonds generated for 'chain '7' and resid 616 through 619' Processing helix chain '7' and resid 627 through 636 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 642 through 644 No H-bonds generated for 'chain '7' and resid 642 through 644' Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 10 through 15 removed outlier: 4.511A pdb=" N ARG A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 51 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) removed outlier: 3.674A pdb=" N LYS A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 92 Proline residue: A 60 - end of helix removed outlier: 4.602A pdb=" N PHE A 64 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N CYS A 67 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 68 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 69 " --> pdb=" O HIS A 66 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ARG A 71 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS A 75 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA A 78 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR A 79 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 82 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG A 83 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG A 86 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 127 removed outlier: 3.690A pdb=" N ARG A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 186 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 3 through 12 removed outlier: 3.920A pdb=" N PHE B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS B 12 " --> pdb=" O PHE B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.758A pdb=" N ASN B 51 " --> pdb=" O TRP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 80 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 92 through 102 removed outlier: 4.165A pdb=" N LEU B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 124 removed outlier: 4.628A pdb=" N THR B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.507A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 137 No H-bonds generated for 'chain 'B' and resid 134 through 137' Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 157 through 172 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 22 through 28 removed outlier: 3.592A pdb=" N LEU C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 94 through 102 removed outlier: 3.790A pdb=" N THR C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) 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) Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 129 through 134 removed outlier: 4.411A pdb=" N ALA C 132 " --> pdb=" O PRO C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 170 through 186 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) Processing helix chain 'C' and resid 202 through 205 No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'D' and resid 23 through 39 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 48 through 54 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 63 through 66 No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'D' and resid 74 through 96 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) removed outlier: 3.569A pdb=" N ARG D 96 " --> pdb=" O TYR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.513A pdb=" N GLU D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 143 removed outlier: 3.750A pdb=" N ALA D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 212 through 215 No H-bonds generated for 'chain 'D' and resid 212 through 215' Processing helix chain 'E' and resid 11 through 16 removed outlier: 5.685A pdb=" N SER E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 40 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 56 through 64 removed outlier: 3.623A pdb=" N GLU E 64 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 109 No H-bonds generated for 'chain 'E' and resid 107 through 109' Processing helix chain 'E' and resid 165 through 188 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 198 through 208 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 235 through 254 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) Processing helix chain 'E' and resid 259 through 261 No H-bonds generated for 'chain 'E' and resid 259 through 261' Processing helix chain 'E' and resid 296 through 299 No H-bonds generated for 'chain 'E' and resid 296 through 299' Processing helix chain 'E' and resid 305 through 318 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) removed outlier: 3.901A pdb=" N MET E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 340 through 346 removed outlier: 4.394A pdb=" N GLU E 345 " --> pdb=" O ARG E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 383 removed outlier: 3.617A pdb=" N SER E 382 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 404 removed outlier: 3.746A pdb=" N SER E 403 " --> pdb=" O GLN E 399 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU E 404 " --> pdb=" O ALA E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 425 removed outlier: 3.874A pdb=" N LEU E 409 " --> pdb=" O ARG E 406 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP E 410 " --> pdb=" O SER E 407 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU E 412 " --> pdb=" O LEU E 409 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR E 413 " --> pdb=" O ASP E 410 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU E 416 " --> pdb=" O TYR E 413 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU E 418 " --> pdb=" O GLY E 415 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA E 419 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS E 420 " --> pdb=" O GLU E 417 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN E 422 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG E 424 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 461 No H-bonds generated for 'chain 'E' and resid 459 through 461' Processing helix chain 'E' and resid 467 through 480 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 486 through 488 No H-bonds generated for 'chain 'E' and resid 486 through 488' Processing helix chain 'E' and resid 522 through 533 removed outlier: 3.766A pdb=" N GLU E 527 " --> pdb=" O GLY E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 565 removed outlier: 3.889A pdb=" N ALA E 560 " --> pdb=" O LYS E 556 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 229 through 233 removed outlier: 6.454A pdb=" N HIS 2 282 " --> pdb=" O LEU 2 230 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL 2 232 " --> pdb=" O HIS 2 282 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG 2 284 " --> pdb=" O VAL 2 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 374 through 379 Processing sheet with id= C, 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= D, 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: 7.088A pdb=" N ILE 2 544 " --> pdb=" O LEU 2 585 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ASP 2 587 " --> pdb=" O ILE 2 544 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR 2 546 " --> pdb=" O ASP 2 587 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 559 through 562 Processing sheet with id= F, first strand: chain '2' and resid 608 through 612 Processing sheet with id= G, 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= H, first strand: chain '3' and resid 169 through 174 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) Processing sheet with id= I, 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= J, first strand: chain '3' and resid 244 through 247 Processing sheet with id= K, first strand: chain '3' and resid 526 through 529 Processing sheet with id= L, first strand: chain '3' and resid 425 through 428 Processing sheet with id= M, first strand: chain '3' and resid 475 through 480 removed outlier: 3.759A pdb=" N ILE 3 483 " --> pdb=" O LYS 3 480 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '3' and resid 652 through 654 Processing sheet with id= O, first strand: chain '4' and resid 304 through 306 Processing sheet with id= P, first strand: chain '4' and resid 351 through 355 removed outlier: 3.641A pdb=" N VAL 4 370 " --> pdb=" O LEU 4 354 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 646 through 650 removed outlier: 3.732A pdb=" N GLY 4 510 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) 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: 6.346A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 547 through 549 Processing sheet with id= S, 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= T, 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= U, first strand: chain '4' and resid 391 through 397 removed outlier: 5.878A pdb=" N ILE 4 393 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL 4 418 " --> pdb=" O ILE 4 393 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG 4 395 " --> pdb=" O ILE 4 416 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE 4 416 " --> pdb=" O ARG 4 395 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL 4 397 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR 4 414 " --> pdb=" O VAL 4 397 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '5' and resid 71 through 73 removed outlier: 6.530A pdb=" N MET 5 127 " --> pdb=" O VAL 5 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain '5' and resid 292 through 296 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) Processing sheet with id= X, first strand: chain '5' and resid 170 through 172 Processing sheet with id= Y, first strand: chain '5' and resid 517 through 519 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) removed outlier: 6.653A pdb=" N VAL 5 484 " --> pdb=" O LEU 5 377 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N MET 5 379 " --> pdb=" O VAL 5 484 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA 5 486 " --> pdb=" O MET 5 379 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP 5 445 " --> pdb=" O THR 5 404 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '5' and resid 417 through 420 Processing sheet with id= AA, 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= AB, first strand: chain '5' and resid 162 through 168 removed outlier: 6.792A pdb=" N LYS 5 220 " --> pdb=" O THR 5 166 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '6' and resid 60 through 64 removed outlier: 6.542A pdb=" N TYR 6 111 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL 6 63 " --> pdb=" O TYR 6 111 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA 6 113 " --> pdb=" O VAL 6 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain '6' and resid 204 through 209 Processing sheet with id= AE, first strand: chain '6' and resid 533 through 536 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) removed outlier: 3.877A pdb=" N GLY 6 396 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain '6' and resid 431 through 436 Processing sheet with id= AG, first strand: chain '6' and resid 481 through 485 Processing sheet with id= AH, first strand: chain '6' and resid 148 through 153 removed outlier: 7.176A pdb=" N ARG 6 199 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '6' and resid 242 through 251 removed outlier: 3.557A pdb=" N ALA 6 304 " --> pdb=" O ASP 6 243 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR 6 247 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ALA 6 300 " --> pdb=" O THR 6 247 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE 6 249 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE 6 298 " --> pdb=" O ILE 6 249 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL 6 251 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU 6 296 " --> pdb=" O VAL 6 251 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '7' and resid 47 through 51 removed outlier: 7.333A pdb=" N GLU 7 135 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL 7 50 " --> pdb=" O GLU 7 135 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR 7 137 " --> pdb=" O VAL 7 50 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain '7' and resid 252 through 258 removed outlier: 3.517A pdb=" N VAL 7 161 " --> pdb=" O GLY 7 275 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY 7 275 " --> pdb=" O VAL 7 161 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE 7 276 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ALA 7 300 " --> pdb=" O ILE 7 276 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU 7 278 " --> pdb=" O LEU 7 298 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU 7 298 " --> pdb=" O LEU 7 278 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '7' and resid 191 through 194 removed outlier: 4.542A pdb=" N THR 7 181 " --> pdb=" O GLN 7 223 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 377 through 381 removed outlier: 6.540A pdb=" N LEU 7 517 " --> pdb=" O CYS 7 378 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N MET 7 380 " --> pdb=" O LEU 7 517 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TRP 7 519 " --> pdb=" O MET 7 380 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain '7' and resid 401 through 405 removed outlier: 6.819A pdb=" N VAL 7 441 " --> pdb=" O GLN 7 402 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N THR 7 404 " --> pdb=" O VAL 7 441 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N CYS 7 443 " --> pdb=" O THR 7 404 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N SER 7 483 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE 7 444 " --> pdb=" O SER 7 483 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU 7 485 " --> pdb=" O ILE 7 444 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain '7' and resid 416 through 420 Processing sheet with id= AP, first strand: chain '7' and resid 466 through 469 Processing sheet with id= AQ, first strand: chain '7' and resid 176 through 179 removed outlier: 6.822A pdb=" N ARG 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'B' and resid 14 through 18 Processing sheet with id= AS, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= AT, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= AU, first strand: chain 'D' and resid 170 through 174 Processing sheet with id= AV, first strand: chain 'D' and resid 182 through 184 removed outlier: 3.666A pdb=" N VAL D 184 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR D 194 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'E' and resid 49 through 51 removed outlier: 6.418A pdb=" N LEU E 21 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N PHE E 22 " --> pdb=" O TYR E 71 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE E 73 " --> pdb=" O PHE E 22 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE E 94 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU E 74 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE E 96 " --> pdb=" O LEU E 74 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'E' and resid 269 through 276 Processing sheet with id= AY, first strand: chain 'E' and resid 547 through 550 removed outlier: 5.357A pdb=" N THR E 505 " --> pdb=" O PRO E 496 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL E 507 " --> pdb=" O ALA E 494 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA E 494 " --> pdb=" O VAL E 507 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE E 509 " --> pdb=" O VAL E 492 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL E 492 " --> pdb=" O ILE E 509 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2736 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: 14.73 Time building geometry restraints manager: 17.64 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=" CA THR 3 671 " pdb=" C THR 3 671 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.72e-02 3.38e+03 7.00e+00 ... (remaining 41569 not shown) Histogram of bond angle deviations from ideal: 96.04 - 104.09: 699 104.09 - 112.14: 20700 112.14 - 120.19: 18153 120.19 - 128.24: 16340 128.24 - 136.29: 281 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=" 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 angle pdb=" O3G AGS 4 902 " pdb=" PG AGS 4 902 " pdb=" S1G AGS 4 902 " ideal model delta sigma weight residual 109.29 122.09 -12.80 3.00e+00 1.11e-01 1.82e+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: 4268 0.048 - 0.095: 1697 0.095 - 0.142: 317 0.142 - 0.190: 24 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: 430 2.59 - 3.16: 35858 3.16 - 3.74: 56703 3.74 - 4.32: 83540 4.32 - 4.90: 138224 Nonbonded interactions: 314755 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 314750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 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. 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 13.620 Check model and map are aligned: 0.560 Convert atoms to be neutral: 0.290 Process input model: 107.980 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.200 ------------------------------------------------------------------------------- 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 0.079 41574 Z= 0.585 Angle : 0.790 13.400 56173 Z= 0.428 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 : 10.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.89 % Favored : 89.07 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 456 time to evaluate : 5.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 461 average time/residue: 0.5936 time to fit residues: 428.9982 Evaluate side-chains 331 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 329 time to evaluate : 5.092 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3594 time to fit residues: 8.2489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 422 optimal weight: 0.8980 chunk 378 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 255 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 391 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 454 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 206 HIS 2 282 HIS 2 328 ASN ** 2 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 563 HIS 2 607 GLN 2 838 GLN 2 843 GLN 2 875 HIS 2 893 HIS ** 2 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 112 ASN ** 3 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 398 GLN 3 431 GLN 3 513 ASN ** 4 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 171 GLN 4 195 GLN 4 214 HIS 4 332 HIS 4 342 ASN 4 415 HIS 4 521 GLN 4 525 ASN 4 594 GLN 4 633 ASN 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 5 540 HIS 5 629 GLN 6 342 GLN 6 349 ASN 6 509 HIS 6 635 HIS 6 725 ASN 6 778 HIS 7 30 GLN 7 36 GLN 7 186 GLN 7 193 GLN 7 223 GLN 7 503 GLN ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 543 HIS ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 ASN B 51 ASN B 102 HIS B 138 GLN C 136 GLN C 177 GLN D 78 HIS E 15 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 HIS E 253 ASN E 324 GLN E 364 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 41574 Z= 0.261 Angle : 0.588 10.676 56173 Z= 0.300 Chirality : 0.043 0.322 6308 Planarity : 0.004 0.063 7229 Dihedral : 8.706 177.859 5702 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.97 % Favored : 92.99 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.10), residues: 4996 helix: -2.54 (0.10), residues: 1910 sheet: -2.63 (0.16), residues: 824 loop : -2.69 (0.12), residues: 2262 *********************** 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 457 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 382 time to evaluate : 5.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 40 residues processed: 429 average time/residue: 0.5363 time to fit residues: 384.7385 Evaluate side-chains 371 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 331 time to evaluate : 4.995 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3889 time to fit residues: 35.3279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 252 optimal weight: 0.9990 chunk 140 optimal weight: 0.1980 chunk 377 optimal weight: 0.7980 chunk 309 optimal weight: 4.9990 chunk 125 optimal weight: 0.0870 chunk 454 optimal weight: 1.9990 chunk 491 optimal weight: 7.9990 chunk 405 optimal weight: 0.9980 chunk 451 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 364 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 196 HIS ** 2 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 318 GLN ** 4 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 459 HIS 5 540 HIS 5 584 ASN 5 629 GLN ** 7 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN C 180 GLN E 37 GLN E 364 HIS E 396 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 41574 Z= 0.139 Angle : 0.528 20.230 56173 Z= 0.266 Chirality : 0.041 0.279 6308 Planarity : 0.004 0.051 7229 Dihedral : 8.181 172.382 5702 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.34 % Favored : 94.62 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.11), residues: 4996 helix: -1.90 (0.11), residues: 1921 sheet: -2.25 (0.17), residues: 828 loop : -2.21 (0.12), residues: 2247 *********************** 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 454 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 398 time to evaluate : 5.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 18 residues processed: 440 average time/residue: 0.5059 time to fit residues: 374.3975 Evaluate side-chains 364 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 346 time to evaluate : 4.983 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3986 time to fit residues: 19.8837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 449 optimal weight: 2.9990 chunk 341 optimal weight: 0.4980 chunk 236 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 217 optimal weight: 0.0070 chunk 305 optimal weight: 3.9990 chunk 456 optimal weight: 9.9990 chunk 483 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 432 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.7004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 335 HIS ** 5 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 459 HIS 5 540 HIS 5 629 GLN ** 7 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 41574 Z= 0.215 Angle : 0.545 20.087 56173 Z= 0.272 Chirality : 0.042 0.248 6308 Planarity : 0.004 0.096 7229 Dihedral : 8.122 175.864 5702 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.76 % Favored : 94.20 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.11), residues: 4996 helix: -1.61 (0.11), residues: 1914 sheet: -2.12 (0.17), residues: 836 loop : -2.01 (0.12), residues: 2246 *********************** 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 437 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 364 time to evaluate : 5.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 38 residues processed: 414 average time/residue: 0.5133 time to fit residues: 360.3670 Evaluate side-chains 380 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 342 time to evaluate : 4.941 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.3832 time to fit residues: 33.4240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 402 optimal weight: 0.9980 chunk 274 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 359 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 412 optimal weight: 7.9990 chunk 334 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 433 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 318 GLN ** 4 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 HIS 5 540 HIS 5 629 GLN ** 7 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 503 GLN ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.095 41574 Z= 0.185 Angle : 0.534 19.733 56173 Z= 0.265 Chirality : 0.041 0.216 6308 Planarity : 0.004 0.069 7229 Dihedral : 7.993 173.642 5702 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.66 % Favored : 94.32 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.11), residues: 4996 helix: -1.33 (0.11), residues: 1903 sheet: -1.94 (0.17), residues: 828 loop : -1.86 (0.13), residues: 2265 *********************** 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 404 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 357 time to evaluate : 5.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 20 residues processed: 391 average time/residue: 0.5157 time to fit residues: 341.2529 Evaluate side-chains 359 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 339 time to evaluate : 5.050 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4062 time to fit residues: 21.9636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 4.9990 chunk 435 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 283 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 483 optimal weight: 0.6980 chunk 401 optimal weight: 2.9990 chunk 223 optimal weight: 30.0000 chunk 40 optimal weight: 0.0570 chunk 160 optimal weight: 2.9990 chunk 253 optimal weight: 0.0870 overall best weight: 1.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 664 HIS 5 540 HIS 5 629 GLN ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 188 GLN B 138 GLN C 105 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.115 41574 Z= 0.185 Angle : 0.531 19.542 56173 Z= 0.263 Chirality : 0.041 0.184 6308 Planarity : 0.004 0.069 7229 Dihedral : 7.912 173.627 5702 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.48 % Favored : 94.50 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.11), residues: 4996 helix: -1.15 (0.12), residues: 1915 sheet: -1.81 (0.17), residues: 834 loop : -1.77 (0.13), residues: 2247 *********************** 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 400 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 355 time to evaluate : 4.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 24 residues processed: 384 average time/residue: 0.5436 time to fit residues: 356.5429 Evaluate side-chains 363 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 339 time to evaluate : 5.078 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4094 time to fit residues: 25.2290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 466 optimal weight: 0.0770 chunk 54 optimal weight: 6.9990 chunk 275 optimal weight: 0.8980 chunk 353 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 407 optimal weight: 0.8980 chunk 270 optimal weight: 4.9990 chunk 481 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 222 optimal weight: 20.0000 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 318 GLN ** 4 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 540 HIS 5 629 GLN ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 188 GLN B 138 GLN D 179 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.123 41574 Z= 0.163 Angle : 0.526 17.764 56173 Z= 0.262 Chirality : 0.041 0.173 6308 Planarity : 0.004 0.116 7229 Dihedral : 7.771 172.512 5702 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.10 % Favored : 94.88 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.12), residues: 4996 helix: -0.89 (0.12), residues: 1902 sheet: -1.65 (0.18), residues: 834 loop : -1.64 (0.13), residues: 2260 *********************** 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 397 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 363 time to evaluate : 5.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 384 average time/residue: 0.5185 time to fit residues: 338.8513 Evaluate side-chains 362 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 342 time to evaluate : 5.174 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3654 time to fit residues: 19.8093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 298 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 306 optimal weight: 2.9990 chunk 328 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 378 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 540 HIS 5 629 GLN 7 243 GLN ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN C 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.119 41574 Z= 0.278 Angle : 0.569 17.906 56173 Z= 0.282 Chirality : 0.043 0.214 6308 Planarity : 0.004 0.085 7229 Dihedral : 7.905 174.241 5702 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.72 % Favored : 94.22 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.12), residues: 4996 helix: -0.87 (0.12), residues: 1910 sheet: -1.69 (0.17), residues: 848 loop : -1.67 (0.13), residues: 2238 *********************** 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 380 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 344 time to evaluate : 5.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 364 average time/residue: 0.5099 time to fit residues: 313.5371 Evaluate side-chains 356 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 335 time to evaluate : 5.038 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4166 time to fit residues: 22.5165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 438 optimal weight: 2.9990 chunk 461 optimal weight: 2.9990 chunk 421 optimal weight: 4.9990 chunk 449 optimal weight: 0.8980 chunk 270 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 352 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 405 optimal weight: 0.5980 chunk 424 optimal weight: 1.9990 chunk 447 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 318 GLN ** 4 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 459 HIS 5 540 HIS 5 629 GLN ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.148 41574 Z= 0.195 Angle : 0.549 18.514 56173 Z= 0.271 Chirality : 0.041 0.210 6308 Planarity : 0.004 0.087 7229 Dihedral : 7.783 171.438 5702 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.40 % Favored : 94.58 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.12), residues: 4996 helix: -0.76 (0.12), residues: 1913 sheet: -1.57 (0.18), residues: 837 loop : -1.61 (0.13), residues: 2246 *********************** 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 380 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 357 time to evaluate : 5.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 8 residues processed: 371 average time/residue: 0.5246 time to fit residues: 328.8872 Evaluate side-chains 347 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 339 time to evaluate : 4.832 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4066 time to fit residues: 12.3173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 294 optimal weight: 3.9990 chunk 474 optimal weight: 2.9990 chunk 289 optimal weight: 7.9990 chunk 225 optimal weight: 0.9990 chunk 330 optimal weight: 0.0270 chunk 498 optimal weight: 6.9990 chunk 458 optimal weight: 1.9990 chunk 396 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 306 optimal weight: 0.0370 chunk 243 optimal weight: 9.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 365 GLN 5 459 HIS 5 540 HIS 5 629 GLN 7 465 GLN ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.312 41574 Z= 0.198 Angle : 0.547 18.801 56173 Z= 0.274 Chirality : 0.041 0.387 6308 Planarity : 0.004 0.126 7229 Dihedral : 7.636 170.655 5702 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.20 % Favored : 94.78 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.12), residues: 4996 helix: -0.59 (0.12), residues: 1917 sheet: -1.46 (0.18), residues: 835 loop : -1.55 (0.13), residues: 2244 ********************** 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 362 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 356 time to evaluate : 5.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 359 average time/residue: 0.5458 time to fit residues: 330.6441 Evaluate side-chains 350 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 347 time to evaluate : 4.662 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3875 time to fit residues: 9.2195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 315 optimal weight: 7.9990 chunk 422 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 365 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 397 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 407 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 318 GLN ** 4 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 459 HIS 5 540 HIS 5 629 GLN ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.116180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087449 restraints weight = 83148.133| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.80 r_work: 0.3250 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work: 0.3222 rms_B_bonded: 2.54 restraints_weight: 0.1250 r_work: 0.3208 rms_B_bonded: 2.61 restraints_weight: 0.0625 r_work: 0.3193 rms_B_bonded: 2.71 restraints_weight: 0.0312 r_work: 0.3177 rms_B_bonded: 2.85 restraints_weight: 0.0156 r_work: 0.3161 rms_B_bonded: 3.03 restraints_weight: 0.0078 r_work: 0.3143 rms_B_bonded: 3.25 restraints_weight: 0.0039 r_work: 0.3124 rms_B_bonded: 3.51 restraints_weight: 0.0020 r_work: 0.3103 rms_B_bonded: 3.82 restraints_weight: 0.0010 r_work: 0.3081 rms_B_bonded: 4.18 restraints_weight: 0.0005 r_work: 0.3056 rms_B_bonded: 4.61 restraints_weight: 0.0002 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.327 41574 Z= 0.253 Angle : 0.589 18.215 56173 Z= 0.294 Chirality : 0.042 0.288 6308 Planarity : 0.004 0.108 7229 Dihedral : 7.723 172.784 5702 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.82 % Favored : 94.16 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.12), residues: 4996 helix: -0.61 (0.12), residues: 1927 sheet: -1.48 (0.18), residues: 847 loop : -1.53 (0.13), residues: 2222 =============================================================================== Job complete usr+sys time: 7639.75 seconds wall clock time: 140 minutes 15.47 seconds (8415.47 seconds total)