Starting phenix.real_space_refine on Mon Oct 14 03:40:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/10_2024/7v3v_31685.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/10_2024/7v3v_31685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/10_2024/7v3v_31685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/10_2024/7v3v_31685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/10_2024/7v3v_31685.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/10_2024/7v3v_31685.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 11 6.06 5 P 37 5.49 5 Mg 12 5.21 5 S 322 5.16 5 C 42942 2.51 5 N 11897 2.21 5 O 13135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 68356 Number of models: 1 Model: "" Number of chains: 28 Chain: "2" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4970 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 25, 'TRANS': 602} Chain breaks: 2 Chain: "3" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4987 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 4 Chain: "4" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5323 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5148 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 630} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "6" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5109 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 22, 'TRANS': 623} Chain breaks: 3 Chain: "7" Number of atoms: 5505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5505 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 2 Chain: "B" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4970 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 25, 'TRANS': 602} Chain breaks: 2 Chain: "C" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4987 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 4 Chain: "D" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5323 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5148 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 630} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5109 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 22, 'TRANS': 623} Chain breaks: 3 Chain: "G" Number of atoms: 5505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5505 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 2 Chain: "H" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3109 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 365} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2745 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 316} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "2" 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} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "5" 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} Chain: "6" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 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} Chain: "B" 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} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" 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} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" 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} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1302 SG CYS 2 341 137.797 113.558 73.619 1.00 94.42 S ATOM 1325 SG CYS 2 344 141.133 111.696 73.670 1.00 98.04 S ATOM 1483 SG CYS 2 364 139.291 112.361 70.393 1.00 97.74 S ATOM 1504 SG CYS 2 367 138.059 109.733 72.714 1.00100.50 S ATOM 11400 SG CYS 4 349 96.380 119.953 55.220 1.00 56.74 S ATOM 11421 SG CYS 4 352 94.257 118.925 52.404 1.00 58.76 S ATOM 11568 SG CYS 4 371 93.102 118.386 56.084 1.00 64.59 S ATOM 11610 SG CYS 4 376 95.851 116.230 54.313 1.00 69.30 S ATOM 16593 SG CYS 5 183 129.654 111.174 96.201 1.00 44.37 S ATOM 16618 SG CYS 5 186 131.494 107.637 96.994 1.00 46.69 S ATOM 16805 SG CYS 5 211 132.158 109.351 93.970 1.00 46.84 S ATOM 16923 SG CYS 5 236 128.644 108.127 94.330 1.00 56.79 S ATOM 21676 SG CYS 6 311 115.560 116.604 56.697 1.00 99.73 S ATOM 21698 SG CYS 6 314 116.666 114.886 53.859 1.00105.70 S ATOM 21855 SG CYS 6 333 112.718 115.515 54.216 1.00104.73 S ATOM 21889 SG CYS 6 338 114.369 112.889 56.090 1.00112.86 S ATOM 27409 SG CYS 7 262 84.631 120.447 81.144 1.00 37.89 S ATOM 27432 SG CYS 7 265 82.753 118.417 83.695 1.00 37.48 S ATOM 27586 SG CYS 7 284 86.461 119.363 84.201 1.00 41.21 S ATOM 27623 SG CYS 7 289 85.597 116.749 81.680 1.00 44.53 S ATOM 32344 SG CYS B 341 106.128 111.135 73.606 1.00 93.86 S ATOM 32367 SG CYS B 344 102.879 113.184 73.663 1.00 97.46 S ATOM 32525 SG CYS B 364 104.697 112.351 70.388 1.00 97.25 S ATOM 32546 SG CYS B 367 106.022 114.962 72.698 1.00 99.41 S ATOM 42442 SG CYS D 349 147.910 104.545 55.435 1.00 66.80 S ATOM 42463 SG CYS D 352 150.040 105.275 52.442 1.00 69.48 S ATOM 42610 SG CYS D 371 151.282 106.074 56.036 1.00 75.09 S ATOM 42652 SG CYS D 376 148.474 108.113 54.313 1.00 81.78 S ATOM 47635 SG CYS E 183 114.148 113.602 96.155 1.00 45.37 S ATOM 47660 SG CYS E 186 112.298 117.200 96.808 1.00 48.21 S ATOM 47847 SG CYS E 211 111.622 115.407 93.919 1.00 47.15 S ATOM 47965 SG CYS E 236 115.185 116.612 94.262 1.00 57.75 S ATOM 52718 SG CYS F 311 128.771 108.263 56.324 1.00103.79 S ATOM 52740 SG CYS F 314 128.072 111.327 54.284 1.00108.09 S ATOM 52897 SG CYS F 333 131.253 109.050 53.392 1.00108.22 S ATOM 52931 SG CYS F 338 131.359 111.347 55.886 1.00115.91 S ATOM 58451 SG CYS G 262 159.163 104.268 81.323 1.00 40.67 S ATOM 58474 SG CYS G 265 161.083 106.434 83.740 1.00 40.59 S ATOM 58628 SG CYS G 284 157.415 105.501 84.431 1.00 44.82 S ATOM 58665 SG CYS G 289 158.223 108.010 81.780 1.00 47.87 S ATOM 67586 SG CYS I 661 44.578 143.924 74.226 1.00 72.35 S ATOM 67609 SG CYS I 664 45.833 147.532 75.166 1.00 73.65 S Time building chain proxies: 30.88, per 1000 atoms: 0.45 Number of scatterers: 68356 At special positions: 0 Unit cell: (204.58, 225.78, 157.94, 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 11 29.99 S 322 16.00 P 37 15.00 Mg 12 11.99 O 13135 8.00 N 11897 7.00 C 42942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " distance=2.04 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 522 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.69 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 22003 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 341 " pdb=" ZN 42003 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 371 " pdb=" ZN 52003 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 186 " pdb=" ZN 62002 " pdb="ZN ZN 62002 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 62002 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 62002 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 62002 " - pdb=" SG CYS 6 333 " pdb=" ZN 72003 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 289 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 364 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 344 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 367 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 341 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 349 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 352 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 376 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 371 " pdb=" ZN E2003 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 211 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 236 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 183 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 186 " pdb=" ZN F2002 " pdb="ZN ZN F2002 " - pdb=" SG CYS F 338 " pdb="ZN ZN F2002 " - pdb=" SG CYS F 314 " pdb="ZN ZN F2002 " - pdb=" SG CYS F 333 " pdb="ZN ZN F2002 " - pdb=" SG CYS F 311 " pdb=" ZN G2003 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 262 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 265 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 284 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 289 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" NE2 HIS I 674 " pdb="ZN ZN I 801 " - pdb=" ND1 HIS I 680 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 661 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 664 " Number of angles added : 61 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16304 Finding SS restraints... Secondary structure from input PDB file: 338 helices and 96 sheets defined 45.6% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.55 Creating SS restraints... Processing helix chain '2' and resid 182 through 188 removed outlier: 3.556A pdb=" N ASN 2 188 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) Processing helix chain '2' and resid 193 through 200 removed outlier: 3.548A pdb=" N GLN 2 200 " --> pdb=" O GLU 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 200 through 218 Processing helix chain '2' and resid 225 through 237 Processing helix chain '2' and resid 246 through 253 Processing helix chain '2' and resid 253 through 263 Processing helix chain '2' and resid 263 through 283 removed outlier: 3.955A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 290 removed outlier: 3.944A pdb=" N ILE 2 289 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 305 through 309 removed outlier: 4.029A pdb=" N LEU 2 309 " --> pdb=" O LEU 2 306 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 removed outlier: 3.683A pdb=" N LEU 2 314 " --> pdb=" O GLU 2 311 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 397 removed outlier: 3.727A pdb=" N VAL 2 397 " --> pdb=" O PRO 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 477 through 489 removed outlier: 3.670A pdb=" N ARG 2 482 " --> pdb=" O GLU 2 478 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 501 removed outlier: 3.544A pdb=" N LYS 2 496 " --> pdb=" O GLY 2 492 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 528 through 530 No H-bonds generated for 'chain '2' and resid 528 through 530' Processing helix chain '2' and resid 548 through 560 Processing helix chain '2' and resid 593 through 599 removed outlier: 3.953A pdb=" N VAL 2 597 " --> pdb=" O GLY 2 593 " (cutoff:3.500A) Processing helix chain '2' and resid 613 through 626 Processing helix chain '2' and resid 652 through 656 removed outlier: 3.981A pdb=" N ARG 2 656 " --> pdb=" O ASN 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 removed outlier: 3.581A pdb=" N ASN 2 666 " --> pdb=" O PRO 2 662 " (cutoff:3.500A) Processing helix chain '2' and resid 670 through 676 removed outlier: 3.548A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 706 Processing helix chain '2' and resid 759 through 774 removed outlier: 3.698A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE 2 774 " --> pdb=" O ALA 2 770 " (cutoff:3.500A) Processing helix chain '2' and resid 779 through 781 No H-bonds generated for 'chain '2' and resid 779 through 781' Processing helix chain '2' and resid 782 through 801 removed outlier: 3.899A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER 2 787 " --> pdb=" O MET 2 783 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG 2 788 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU 2 796 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 3.990A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET 2 823 " --> pdb=" O SER 2 819 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 847 Processing helix chain '2' and resid 850 through 861 removed outlier: 3.619A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG 2 859 " --> pdb=" O ARG 2 855 " (cutoff:3.500A) Processing helix chain '2' and resid 861 through 866 Processing helix chain '3' and resid 18 through 35 Processing helix chain '3' and resid 35 through 59 removed outlier: 4.258A pdb=" N ARG 3 39 " --> pdb=" O PHE 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 107 Processing helix chain '3' and resid 107 through 117 Processing helix chain '3' and resid 117 through 137 Proline residue: 3 123 - end of helix removed outlier: 3.657A pdb=" N MET 3 136 " --> pdb=" O LEU 3 132 " (cutoff:3.500A) Processing helix chain '3' and resid 161 through 163 No H-bonds generated for 'chain '3' and resid 161 through 163' Processing helix chain '3' and resid 172 through 176 Processing helix chain '3' and resid 279 through 283 removed outlier: 3.723A pdb=" N VAL 3 283 " --> pdb=" O ASP 3 280 " (cutoff:3.500A) Processing helix chain '3' and resid 343 through 355 removed outlier: 3.551A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 366 removed outlier: 3.514A pdb=" N GLN 3 365 " --> pdb=" O ASP 3 361 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 Processing helix chain '3' and resid 438 through 443 Processing helix chain '3' and resid 460 through 465 Processing helix chain '3' and resid 474 through 478 removed outlier: 3.524A pdb=" N MET 3 478 " --> pdb=" O PHE 3 475 " (cutoff:3.500A) Processing helix chain '3' and resid 479 through 493 removed outlier: 3.797A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 534 Processing helix chain '3' and resid 536 through 543 Processing helix chain '3' and resid 554 through 569 Processing helix chain '3' and resid 652 through 667 Processing helix chain '3' and resid 672 through 688 removed outlier: 3.761A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 716 removed outlier: 4.261A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 Processing helix chain '4' and resid 186 through 200 Processing helix chain '4' and resid 202 through 210 removed outlier: 4.010A pdb=" N ARG 4 206 " --> pdb=" O LYS 4 202 " (cutoff:3.500A) Processing helix chain '4' and resid 217 through 222 removed outlier: 3.641A pdb=" N GLU 4 222 " --> pdb=" O ASN 4 218 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 237 Processing helix chain '4' and resid 245 through 251 Processing helix chain '4' and resid 254 through 264 removed outlier: 3.796A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 286 removed outlier: 3.958A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE 4 284 " --> pdb=" O MET 4 280 " (cutoff:3.500A) Processing helix chain '4' and resid 292 through 299 removed outlier: 4.075A pdb=" N ILE 4 296 " --> pdb=" O ASP 4 292 " (cutoff:3.500A) Processing helix chain '4' and resid 318 through 322 Processing helix chain '4' and resid 422 through 424 No H-bonds generated for 'chain '4' and resid 422 through 424' Processing helix chain '4' and resid 477 through 480 Processing helix chain '4' and resid 481 through 492 Processing helix chain '4' and resid 503 through 514 Processing helix chain '4' and resid 517 through 525 Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 597 through 602 Processing helix chain '4' and resid 619 through 624 Processing helix chain '4' and resid 638 through 643 Processing helix chain '4' and resid 644 through 652 removed outlier: 3.943A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 Processing helix chain '4' and resid 695 through 700 Processing helix chain '4' and resid 714 through 726 Processing helix chain '4' and resid 727 through 729 No H-bonds generated for 'chain '4' and resid 727 through 729' Processing helix chain '4' and resid 743 through 758 Processing helix chain '4' and resid 763 through 781 Processing helix chain '4' and resid 794 through 812 removed outlier: 3.554A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 833 removed outlier: 3.689A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '5' and resid 23 through 38 Processing helix chain '5' and resid 44 through 56 Processing helix chain '5' and resid 65 through 72 Processing helix chain '5' and resid 72 through 82 Processing helix chain '5' and resid 82 through 107 Proline residue: 5 88 - end of helix removed outlier: 3.607A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU 5 104 " --> pdb=" O ARG 5 100 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA 5 107 " --> pdb=" O ILE 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 151 removed outlier: 3.712A pdb=" N LEU 5 151 " --> pdb=" O LEU 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 152 through 156 removed outlier: 3.679A pdb=" N VAL 5 156 " --> pdb=" O SER 5 153 " (cutoff:3.500A) Processing helix chain '5' and resid 212 through 217 Processing helix chain '5' and resid 281 through 283 No H-bonds generated for 'chain '5' and resid 281 through 283' Processing helix chain '5' and resid 350 through 362 removed outlier: 3.617A pdb=" N ARG 5 362 " --> pdb=" O LEU 5 358 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 374 Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 486 through 499 Processing helix chain '5' and resid 535 through 540 removed outlier: 3.645A pdb=" N ILE 5 540 " --> pdb=" O PRO 5 536 " (cutoff:3.500A) Processing helix chain '5' and resid 544 through 550 removed outlier: 3.511A pdb=" N SER 5 548 " --> pdb=" O THR 5 544 " (cutoff:3.500A) Processing helix chain '5' and resid 561 through 578 removed outlier: 4.255A pdb=" N SER 5 567 " --> pdb=" O GLU 5 563 " (cutoff:3.500A) Processing helix chain '5' and resid 578 through 591 Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 618 through 641 removed outlier: 3.890A pdb=" N LEU 5 622 " --> pdb=" O ALA 5 618 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 667 removed outlier: 3.956A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 695 removed outlier: 3.773A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA 5 691 " --> pdb=" O SER 5 687 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP 5 695 " --> pdb=" O ALA 5 691 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 122 removed outlier: 3.707A pdb=" N GLU 6 120 " --> pdb=" O GLU 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 147 removed outlier: 3.542A pdb=" N ILE 6 145 " --> pdb=" O GLU 6 141 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 160 Processing helix chain '6' and resid 164 through 173 Processing helix chain '6' and resid 173 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 194 through 199 removed outlier: 4.144A pdb=" N ASN 6 198 " --> pdb=" O PRO 6 194 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR 6 199 " --> pdb=" O GLU 6 195 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 194 through 199' Processing helix chain '6' and resid 280 through 284 removed outlier: 3.578A pdb=" N ILE 6 284 " --> pdb=" O SER 6 281 " (cutoff:3.500A) Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '6' and resid 407 through 411 removed outlier: 4.019A pdb=" N GLY 6 411 " --> pdb=" O THR 6 408 " (cutoff:3.500A) Processing helix chain '6' and resid 500 through 508 removed outlier: 3.828A pdb=" N PHE 6 504 " --> pdb=" O ASP 6 500 " (cutoff:3.500A) Processing helix chain '6' and resid 509 through 522 Processing helix chain '6' and resid 524 through 533 removed outlier: 3.514A pdb=" N ILE 6 533 " --> pdb=" O LEU 6 529 " (cutoff:3.500A) Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 580 through 592 removed outlier: 3.613A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 604 through 609 Processing helix chain '6' and resid 626 through 631 Processing helix chain '6' and resid 645 through 658 removed outlier: 3.837A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 708 removed outlier: 3.963A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 738 Processing helix chain '6' and resid 747 through 759 Processing helix chain '6' and resid 766 through 788 removed outlier: 3.856A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) Processing helix chain '6' and resid 789 through 791 No H-bonds generated for 'chain '6' and resid 789 through 791' Processing helix chain '6' and resid 796 through 814 removed outlier: 3.654A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 835 removed outlier: 3.590A pdb=" N ILE 6 835 " --> pdb=" O LEU 6 831 " (cutoff:3.500A) Processing helix chain '7' and resid 15 through 28 Processing helix chain '7' and resid 61 through 72 removed outlier: 3.748A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 96 Processing helix chain '7' and resid 101 through 109 Processing helix chain '7' and resid 109 through 124 removed outlier: 3.527A pdb=" N PHE 7 113 " --> pdb=" O ASN 7 109 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 165 removed outlier: 3.645A pdb=" N ASN 7 165 " --> pdb=" O ILE 7 161 " (cutoff:3.500A) Processing helix chain '7' and resid 174 through 189 Processing helix chain '7' and resid 193 through 198 removed outlier: 3.739A pdb=" N ARG 7 198 " --> pdb=" O ASN 7 195 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 215 Processing helix chain '7' and resid 231 through 235 removed outlier: 3.623A pdb=" N LEU 7 235 " --> pdb=" O GLY 7 232 " (cutoff:3.500A) Processing helix chain '7' and resid 286 through 292 Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 394 through 407 removed outlier: 3.556A pdb=" N GLU 7 398 " --> pdb=" O THR 7 394 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU 7 399 " --> pdb=" O SER 7 395 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG 7 400 " --> pdb=" O ASP 7 396 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 417 removed outlier: 3.522A pdb=" N SER 7 417 " --> pdb=" O ARG 7 413 " (cutoff:3.500A) Processing helix chain '7' and resid 425 through 438 Processing helix chain '7' and resid 465 through 477 Processing helix chain '7' and resid 511 through 516 Processing helix chain '7' and resid 525 through 529 removed outlier: 3.605A pdb=" N LYS 7 528 " --> pdb=" O GLU 7 525 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET 7 529 " --> pdb=" O PHE 7 526 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 525 through 529' Processing helix chain '7' and resid 530 through 544 removed outlier: 4.141A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 584 Processing helix chain '7' and resid 587 through 594 removed outlier: 3.532A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 623 removed outlier: 3.545A pdb=" N ASP 7 609 " --> pdb=" O SER 7 605 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 647 Processing helix chain '7' and resid 653 through 674 Processing helix chain '7' and resid 685 through 703 Processing helix chain '7' and resid 709 through 730 removed outlier: 3.557A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 188 removed outlier: 3.693A pdb=" N ASN B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 removed outlier: 3.533A pdb=" N TRP B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 218 Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 263 through 281 removed outlier: 3.742A pdb=" N LEU B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.573A pdb=" N ILE B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.858A pdb=" N LEU B 309 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.503A pdb=" N ASN B 313 " --> pdb=" O ARG B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.938A pdb=" N VAL B 415 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 528 through 530 No H-bonds generated for 'chain 'B' and resid 528 through 530' Processing helix chain 'B' and resid 548 through 560 removed outlier: 3.537A pdb=" N ILE B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 599 removed outlier: 3.950A pdb=" N VAL B 597 " --> pdb=" O GLY B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 626 Processing helix chain 'B' and resid 652 through 656 removed outlier: 4.034A pdb=" N ARG B 656 " --> pdb=" O ASN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 Processing helix chain 'B' and resid 688 through 706 Processing helix chain 'B' and resid 759 through 774 removed outlier: 4.276A pdb=" N LYS B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 781 No H-bonds generated for 'chain 'B' and resid 779 through 781' Processing helix chain 'B' and resid 782 through 801 removed outlier: 4.313A pdb=" N VAL B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 787 " --> pdb=" O MET B 783 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 788 " --> pdb=" O ASP B 784 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 824 removed outlier: 3.892A pdb=" N LEU B 810 " --> pdb=" O THR B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 847 Processing helix chain 'B' and resid 850 through 861 removed outlier: 3.844A pdb=" N GLN B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG B 859 " --> pdb=" O ARG B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'C' and resid 18 through 35 Processing helix chain 'C' and resid 36 through 59 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 107 through 117 Processing helix chain 'C' and resid 117 through 136 removed outlier: 3.565A pdb=" N PHE C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Proline residue: C 123 - end of helix 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 172 through 176 removed outlier: 3.529A pdb=" N LEU C 176 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 removed outlier: 3.608A pdb=" N LYS C 355 " --> pdb=" O ASN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 366 removed outlier: 3.630A pdb=" N SER C 364 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 365 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 414 through 426 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 479 through 493 removed outlier: 3.792A pdb=" N GLU C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C 491 " --> pdb=" O HIS C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.509A pdb=" N PHE C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 570 Processing helix chain 'C' and resid 652 through 667 removed outlier: 3.644A pdb=" N VAL C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 688 removed outlier: 4.019A pdb=" N VAL C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 716 removed outlier: 4.195A pdb=" N LEU C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 703 " --> pdb=" O ALA C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 738 Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 202 through 210 removed outlier: 4.013A pdb=" N ARG D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 237 Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.798A pdb=" N HIS D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 287 removed outlier: 3.901A pdb=" N SER D 270 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 284 " --> pdb=" O MET D 280 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 3.838A pdb=" N ILE D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 removed outlier: 3.642A pdb=" N GLU D 316 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.537A pdb=" N ILE D 322 " --> pdb=" O PRO D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 481 through 492 Processing helix chain 'D' and resid 502 through 514 removed outlier: 3.557A pdb=" N LEU D 506 " --> pdb=" O THR D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 525 Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 597 through 602 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 638 through 643 Processing helix chain 'D' and resid 644 through 652 removed outlier: 3.996A pdb=" N VAL D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 693 Processing helix chain 'D' and resid 695 through 701 removed outlier: 3.867A pdb=" N ARG D 701 " --> pdb=" O PRO D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 726 removed outlier: 3.618A pdb=" N ASP D 717 " --> pdb=" O ASP D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 729 No H-bonds generated for 'chain 'D' and resid 727 through 729' Processing helix chain 'D' and resid 743 through 758 Processing helix chain 'D' and resid 763 through 781 Processing helix chain 'D' and resid 794 through 812 removed outlier: 3.537A pdb=" N LYS D 812 " --> pdb=" O HIS D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 834 removed outlier: 3.529A pdb=" N VAL D 822 " --> pdb=" O GLU D 818 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 833 " --> pdb=" O ILE D 829 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 38 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 82 through 107 Proline residue: E 88 - end of helix removed outlier: 3.569A pdb=" N ARG E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.667A pdb=" N LEU E 151 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 350 through 362 removed outlier: 3.542A pdb=" N SER E 361 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG E 362 " --> pdb=" O LEU E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 374 Processing helix chain 'E' and resid 381 through 394 Processing helix chain 'E' and resid 421 through 433 Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 486 through 499 Processing helix chain 'E' and resid 535 through 540 removed outlier: 3.706A pdb=" N ILE E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 549 removed outlier: 3.899A pdb=" N SER E 548 " --> pdb=" O THR E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 578 removed outlier: 3.958A pdb=" N SER E 567 " --> pdb=" O GLU E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 591 Processing helix chain 'E' and resid 595 through 610 Processing helix chain 'E' and resid 618 through 641 removed outlier: 3.566A pdb=" N LEU E 622 " --> pdb=" O ALA E 618 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG E 630 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 667 removed outlier: 3.908A pdb=" N GLU E 667 " --> pdb=" O LEU E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 695 removed outlier: 3.591A pdb=" N VAL E 677 " --> pdb=" O GLN E 673 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 689 " --> pdb=" O GLN E 685 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP E 690 " --> pdb=" O ALA E 686 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA E 691 " --> pdb=" O SER E 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 122 Processing helix chain 'F' and resid 134 through 147 removed outlier: 3.878A pdb=" N ILE F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR F 146 " --> pdb=" O PHE F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 161 removed outlier: 3.733A pdb=" N ARG F 161 " --> pdb=" O HIS F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 173 Processing helix chain 'F' and resid 173 through 193 Proline residue: F 179 - end of helix Processing helix chain 'F' and resid 194 through 199 removed outlier: 4.128A pdb=" N ASN F 198 " --> pdb=" O PRO F 194 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 194 through 199' Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.626A pdb=" N ILE F 279 " --> pdb=" O ILE F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 407 through 411 removed outlier: 4.329A pdb=" N GLY F 411 " --> pdb=" O THR F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 508 removed outlier: 3.773A pdb=" N PHE F 504 " --> pdb=" O ASP F 500 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER F 507 " --> pdb=" O VAL F 503 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 522 removed outlier: 3.533A pdb=" N ASP F 522 " --> pdb=" O GLU F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 532 Processing helix chain 'F' and resid 540 through 553 Processing helix chain 'F' and resid 580 through 592 removed outlier: 3.722A pdb=" N PHE F 584 " --> pdb=" O SER F 580 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 Processing helix chain 'F' and resid 626 through 631 Processing helix chain 'F' and resid 645 through 659 removed outlier: 3.910A pdb=" N ALA F 655 " --> pdb=" O ALA F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 699 Processing helix chain 'F' and resid 702 through 708 removed outlier: 3.857A pdb=" N ARG F 708 " --> pdb=" O PRO F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 738 Processing helix chain 'F' and resid 747 through 759 Processing helix chain 'F' and resid 766 through 788 removed outlier: 3.883A pdb=" N SER F 771 " --> pdb=" O LYS F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 789 through 791 No H-bonds generated for 'chain 'F' and resid 789 through 791' Processing helix chain 'F' and resid 796 through 814 Processing helix chain 'F' and resid 820 through 833 Processing helix chain 'G' and resid 13 through 28 Processing helix chain 'G' and resid 61 through 72 Processing helix chain 'G' and resid 82 through 96 Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 109 through 124 removed outlier: 3.511A pdb=" N PHE G 113 " --> pdb=" O ASN G 109 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 165 removed outlier: 3.684A pdb=" N ASN G 165 " --> pdb=" O ILE G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 189 Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.057A pdb=" N ARG G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 215 Processing helix chain 'G' and resid 231 through 235 removed outlier: 3.665A pdb=" N LEU G 235 " --> pdb=" O GLY G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 292 Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 394 through 408 removed outlier: 3.565A pdb=" N GLU G 398 " --> pdb=" O THR G 394 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU G 399 " --> pdb=" O SER G 395 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG G 400 " --> pdb=" O ASP G 396 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY G 408 " --> pdb=" O LEU G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 417 Processing helix chain 'G' and resid 425 through 438 Processing helix chain 'G' and resid 466 through 477 Processing helix chain 'G' and resid 489 through 494 Processing helix chain 'G' and resid 511 through 516 Processing helix chain 'G' and resid 525 through 529 removed outlier: 3.556A pdb=" N LYS G 528 " --> pdb=" O GLU G 525 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET G 529 " --> pdb=" O PHE G 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 525 through 529' Processing helix chain 'G' and resid 530 through 544 removed outlier: 4.425A pdb=" N GLU G 542 " --> pdb=" O HIS G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 579 through 584 Processing helix chain 'G' and resid 587 through 594 removed outlier: 3.544A pdb=" N PHE G 594 " --> pdb=" O LEU G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 623 removed outlier: 3.585A pdb=" N ASP G 609 " --> pdb=" O SER G 605 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 647 removed outlier: 3.663A pdb=" N THR G 647 " --> pdb=" O ALA G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 675 Processing helix chain 'G' and resid 685 through 703 Processing helix chain 'G' and resid 709 through 730 removed outlier: 4.077A pdb=" N LYS G 724 " --> pdb=" O VAL G 720 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER G 726 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU G 727 " --> pdb=" O SER G 723 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU G 730 " --> pdb=" O SER G 726 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 26 removed outlier: 4.041A pdb=" N GLU H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 33 Processing helix chain 'H' and resid 55 through 62 removed outlier: 4.092A pdb=" N LYS H 59 " --> pdb=" O GLY H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 98 removed outlier: 3.531A pdb=" N MET H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR H 98 " --> pdb=" O LEU H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 104 removed outlier: 3.789A pdb=" N VAL H 103 " --> pdb=" O SER H 100 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA H 104 " --> pdb=" O SER H 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 100 through 104' Processing helix chain 'H' and resid 136 through 157 Processing helix chain 'H' and resid 260 through 264 removed outlier: 3.820A pdb=" N LYS H 263 " --> pdb=" O ASP H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 291 Processing helix chain 'H' and resid 299 through 315 removed outlier: 3.669A pdb=" N TRP H 303 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 337 removed outlier: 3.847A pdb=" N ILE H 335 " --> pdb=" O GLU H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 349 removed outlier: 3.666A pdb=" N LEU H 347 " --> pdb=" O LYS H 343 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS H 348 " --> pdb=" O CYS H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 384 removed outlier: 4.538A pdb=" N PHE H 372 " --> pdb=" O GLY H 368 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU H 380 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY H 384 " --> pdb=" O GLU H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 405 Processing helix chain 'H' and resid 426 through 450 removed outlier: 3.803A pdb=" N PHE H 443 " --> pdb=" O HIS H 439 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN H 448 " --> pdb=" O GLN H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 465 Processing helix chain 'H' and resid 466 through 470 removed outlier: 3.605A pdb=" N ASN H 470 " --> pdb=" O PRO H 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 123 Processing helix chain 'I' and resid 137 through 158 removed outlier: 3.613A pdb=" N LYS I 143 " --> pdb=" O TYR I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.509A pdb=" N ILE I 182 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR I 183 " --> pdb=" O GLU I 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 179 through 183' Processing helix chain 'I' and resid 189 through 197 removed outlier: 3.522A pdb=" N ARG I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 Processing helix chain 'I' and resid 233 through 245 Processing helix chain 'I' and resid 284 through 289 removed outlier: 3.553A pdb=" N LEU I 288 " --> pdb=" O LYS I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 344 removed outlier: 4.630A pdb=" N LYS I 335 " --> pdb=" O LYS I 331 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR I 336 " --> pdb=" O ALA I 332 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN I 339 " --> pdb=" O LYS I 335 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU I 340 " --> pdb=" O TYR I 336 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE I 344 " --> pdb=" O LEU I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 386 Processing helix chain 'I' and resid 521 through 527 Processing helix chain 'I' and resid 670 through 676 removed outlier: 3.574A pdb=" N VAL I 676 " --> pdb=" O GLU I 672 " (cutoff:3.500A) Processing helix chain 'I' and resid 677 through 686 removed outlier: 3.572A pdb=" N ASN I 686 " --> pdb=" O SER I 682 " (cutoff:3.500A) Processing helix chain 'I' and resid 690 through 702 Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 245 removed outlier: 6.203A pdb=" N LEU 2 242 " --> pdb=" O ARG 2 296 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SER 2 298 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL 2 244 " --> pdb=" O SER 2 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 351 through 352 removed outlier: 6.757A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N THR 2 449 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU 2 407 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA 2 448 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ARG 2 458 " --> pdb=" O GLU 2 423 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLU 2 423 " --> pdb=" O ARG 2 458 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER 2 316 " --> pdb=" O TYR 2 430 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 339 through 341 Processing sheet with id=AA4, first strand: chain '2' and resid 525 through 527 Processing sheet with id=AA5, first strand: chain '2' and resid 563 through 567 removed outlier: 6.542A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA 2 566 " --> pdb=" O ASP 2 607 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU 2 542 " --> pdb=" O VAL 2 683 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 579 through 582 Processing sheet with id=AA7, first strand: chain '2' and resid 628 through 633 Processing sheet with id=AA8, first strand: chain '3' and resid 95 through 99 Processing sheet with id=AA9, first strand: chain '3' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 178 through 189 current: chain '3' and resid 208 through 213 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 208 through 213 current: chain '3' and resid 273 through 278 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 273 through 278 current: chain '3' and resid 318 through 330 Processing sheet with id=AB1, first strand: chain '3' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain '3' and resid 429 through 433 removed outlier: 6.643A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET 3 407 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 444 through 448 Processing sheet with id=AB4, first strand: chain '3' and resid 494 through 498 Processing sheet with id=AB5, first strand: chain '3' and resid 670 through 671 removed outlier: 6.906A pdb=" N GLN 3 670 " --> pdb=" O VAL 3 721 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '4' and resid 178 through 180 Processing sheet with id=AB7, first strand: chain '4' and resid 240 through 244 removed outlier: 6.527A pdb=" N LEU 4 241 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR 4 306 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU 4 243 " --> pdb=" O TYR 4 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '4' and resid 339 through 342 removed outlier: 9.410A pdb=" N THR 4 459 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER 4 416 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N TYR 4 420 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N HIS 4 465 " --> pdb=" O TYR 4 420 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR 4 436 " --> pdb=" O VAL 4 464 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL 4 466 " --> pdb=" O GLU 4 434 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU 4 434 " --> pdb=" O VAL 4 466 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER 4 335 " --> pdb=" O VAL 4 396 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL 4 396 " --> pdb=" O SER 4 335 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 355 through 359 Processing sheet with id=AC1, first strand: chain '4' and resid 364 through 367 Processing sheet with id=AC2, first strand: chain '4' and resid 453 through 454 Processing sheet with id=AC3, first strand: chain '4' and resid 550 through 551 Processing sheet with id=AC4, first strand: chain '4' and resid 589 through 592 removed outlier: 3.674A pdb=" N VAL 4 589 " --> pdb=" O VAL 4 628 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS 4 629 " --> pdb=" O LEU 4 672 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N SER 4 674 " --> pdb=" O CYS 4 629 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE 4 631 " --> pdb=" O SER 4 674 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE 4 564 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA 4 675 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU 4 566 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '4' and resid 603 through 607 Processing sheet with id=AC6, first strand: chain '4' and resid 653 through 657 Processing sheet with id=AC7, first strand: chain '4' and resid 761 through 762 removed outlier: 6.365A pdb=" N ILE 4 761 " --> pdb=" O VAL 4 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '5' and resid 8 through 12 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 8 through 12 current: chain 'G' and resid 238 through 248 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 238 through 248 current: chain 'G' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 267 through 272 current: chain 'G' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 330 through 336 current: chain 'G' and resid 372 through 383 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '5' and resid 60 through 64 removed outlier: 5.681A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN 5 140 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL 5 63 " --> pdb=" O ASN 5 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '5' and resid 189 through 193 removed outlier: 5.525A pdb=" N SER 5 174 " --> pdb=" O GLN 5 253 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN 5 253 " --> pdb=" O SER 5 174 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA 5 176 " --> pdb=" O ILE 5 251 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE 5 251 " --> pdb=" O ALA 5 176 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER 5 180 " --> pdb=" O SER 5 247 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER 5 247 " --> pdb=" O SER 5 180 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N MET 5 182 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 9.843A pdb=" N HIS 5 245 " --> pdb=" O MET 5 182 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE 5 330 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ASP 5 279 " --> pdb=" O GLY 5 332 " (cutoff:3.500A) removed outlier: 12.740A pdb=" N GLN 5 334 " --> pdb=" O ASP 5 279 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '5' and resid 398 through 399 Processing sheet with id=AD3, first strand: chain '5' and resid 436 through 440 removed outlier: 6.694A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP 5 480 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR 5 439 " --> pdb=" O ASP 5 480 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY 5 475 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU 5 520 " --> pdb=" O GLY 5 475 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '5' and resid 452 through 455 removed outlier: 6.532A pdb=" N SER 5 452 " --> pdb=" O GLU 5 465 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '5' and resid 501 through 505 Processing sheet with id=AD6, first strand: chain '5' and resid 613 through 614 removed outlier: 6.725A pdb=" N ARG 5 613 " --> pdb=" O ALA 5 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '6' and resid 124 through 125 Processing sheet with id=AD8, first strand: chain '6' and resid 150 through 154 Processing sheet with id=AD9, first strand: chain '6' and resid 287 through 297 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 287 through 297 current: chain '6' and resid 317 through 322 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 317 through 322 current: chain '6' and resid 376 through 382 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 376 through 382 current: chain '6' and resid 450 through 460 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain '6' and resid 557 through 558 Processing sheet with id=AE2, first strand: chain '6' and resid 595 through 599 removed outlier: 6.346A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE 6 571 " --> pdb=" O ALA 6 680 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ALA 6 682 " --> pdb=" O ILE 6 571 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL 6 573 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '6' and resid 610 through 614 Processing sheet with id=AE4, first strand: chain '6' and resid 660 through 663 Processing sheet with id=AE5, first strand: chain '6' and resid 764 through 765 removed outlier: 6.867A pdb=" N ILE 6 764 " --> pdb=" O ILE 6 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain '7' and resid 77 through 81 removed outlier: 6.497A pdb=" N VAL 7 78 " --> pdb=" O TYR 7 203 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS 7 205 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE 7 80 " --> pdb=" O LYS 7 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain '7' and resid 224 through 225 removed outlier: 6.251A pdb=" N LEU 7 225 " --> pdb=" O ARG 7 242 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ILE 7 244 " --> pdb=" O LEU 7 225 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '7' and resid 238 through 248 current: chain '7' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 267 through 272 current: chain '7' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 330 through 336 current: chain '7' and resid 372 through 383 No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain '7' and resid 442 through 443 Processing sheet with id=AE9, first strand: chain '7' and resid 481 through 484 removed outlier: 6.234A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL 7 456 " --> pdb=" O ALA 7 565 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ALA 7 567 " --> pdb=" O VAL 7 456 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU 7 458 " --> pdb=" O ALA 7 567 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N CYS 7 457 " --> pdb=" O PHE 7 598 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N MET 7 600 " --> pdb=" O CYS 7 457 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET 7 459 " --> pdb=" O MET 7 600 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain '7' and resid 495 through 500 Processing sheet with id=AF2, first strand: chain '7' and resid 545 through 549 Processing sheet with id=AF3, first strand: chain 'B' and resid 241 through 245 removed outlier: 6.332A pdb=" N LEU B 242 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER B 298 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 244 " --> pdb=" O SER B 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'B' and resid 351 through 352 removed outlier: 6.711A pdb=" N VAL B 381 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N HIS B 405 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ILE B 451 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU B 407 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ALA B 453 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 409 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER B 455 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR B 449 " --> pdb=" O ASN B 433 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN B 433 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE B 451 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS B 431 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ALA B 453 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 429 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B 316 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B 389 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG B 327 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG B 387 " --> pdb=" O ARG B 327 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AF6, first strand: chain 'B' and resid 525 through 527 Processing sheet with id=AF7, first strand: chain 'B' and resid 563 through 567 removed outlier: 6.104A pdb=" N LEU B 540 " --> pdb=" O CYS B 681 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL B 683 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 542 " --> pdb=" O VAL B 683 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 579 through 582 Processing sheet with id=AF9, first strand: chain 'B' and resid 628 through 633 Processing sheet with id=AG1, first strand: chain 'C' and resid 95 through 99 Processing sheet with id=AG2, first strand: chain 'C' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 178 through 189 current: chain 'C' and resid 208 through 213 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 208 through 213 current: chain 'C' and resid 273 through 278 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 278 current: chain 'C' and resid 318 through 330 Processing sheet with id=AG3, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AG4, first strand: chain 'C' and resid 429 through 433 removed outlier: 6.432A pdb=" N ILE C 430 " --> pdb=" O CYS C 471 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASP C 473 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR C 432 " --> pdb=" O ASP C 473 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 409 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU C 406 " --> pdb=" O PHE C 547 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL C 549 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL C 408 " --> pdb=" O VAL C 549 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 444 through 448 Processing sheet with id=AG6, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AG7, first strand: chain 'D' and resid 240 through 244 removed outlier: 6.856A pdb=" N LEU D 241 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR D 306 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 243 " --> pdb=" O TYR D 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'D' and resid 339 through 342 removed outlier: 10.057A pdb=" N SER D 414 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N VAL D 461 " --> pdb=" O SER D 414 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N SER D 416 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL D 463 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS D 418 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N HIS D 465 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N TYR D 420 " --> pdb=" O HIS D 465 " (cutoff:3.500A) removed outlier: 13.155A pdb=" N LYS D 467 " --> pdb=" O TYR D 420 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR D 436 " --> pdb=" O VAL D 464 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL D 466 " --> pdb=" O GLU D 434 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU D 434 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS D 398 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER D 335 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 396 " --> pdb=" O SER D 335 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 355 through 359 Processing sheet with id=AH1, first strand: chain 'D' and resid 364 through 368 Processing sheet with id=AH2, first strand: chain 'D' and resid 453 through 454 Processing sheet with id=AH3, first strand: chain 'D' and resid 550 through 551 Processing sheet with id=AH4, first strand: chain 'D' and resid 589 through 592 removed outlier: 3.533A pdb=" N VAL D 589 " --> pdb=" O VAL D 628 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N CYS D 629 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER D 674 " --> pdb=" O CYS D 629 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE D 631 " --> pdb=" O SER D 674 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE D 564 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA D 675 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 566 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU D 565 " --> pdb=" O TYR D 706 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL D 708 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N CYS D 567 " --> pdb=" O VAL D 708 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 603 through 607 Processing sheet with id=AH6, first strand: chain 'D' and resid 653 through 657 Processing sheet with id=AH7, first strand: chain 'D' and resid 761 through 762 removed outlier: 6.493A pdb=" N ILE D 761 " --> pdb=" O VAL D 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'E' and resid 60 through 64 removed outlier: 5.801A pdb=" N LEU E 61 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN E 140 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL E 63 " --> pdb=" O ASN E 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'E' and resid 189 through 193 removed outlier: 5.452A pdb=" N SER E 174 " --> pdb=" O GLN E 253 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN E 253 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA E 176 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE E 251 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER E 180 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER E 247 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 11.385A pdb=" N MET E 182 " --> pdb=" O HIS E 245 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N HIS E 245 " --> pdb=" O MET E 182 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR E 275 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP E 279 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLY E 332 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL E 295 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE E 333 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR E 293 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER E 335 " --> pdb=" O ARG E 291 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ARG E 291 " --> pdb=" O SER E 335 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS E 158 " --> pdb=" O TYR E 298 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS E 257 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR E 169 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE E 255 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 436 through 439 removed outlier: 3.517A pdb=" N GLY E 416 " --> pdb=" O ALA E 523 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 452 through 455 removed outlier: 6.817A pdb=" N SER E 452 " --> pdb=" O GLU E 465 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 501 through 505 Processing sheet with id=AI4, first strand: chain 'E' and resid 613 through 614 removed outlier: 6.749A pdb=" N ARG E 613 " --> pdb=" O ALA E 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=AI6, first strand: chain 'F' and resid 150 through 154 removed outlier: 6.255A pdb=" N ILE F 151 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE F 268 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE F 153 " --> pdb=" O PHE F 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'F' and resid 287 through 297 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 287 through 297 current: chain 'F' and resid 317 through 322 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 317 through 322 current: chain 'F' and resid 376 through 382 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 376 through 382 current: chain 'F' and resid 450 through 460 No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'F' and resid 557 through 558 Processing sheet with id=AI9, first strand: chain 'F' and resid 595 through 599 removed outlier: 3.879A pdb=" N GLY F 575 " --> pdb=" O ALA F 682 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 610 through 614 Processing sheet with id=AJ2, first strand: chain 'F' and resid 660 through 663 Processing sheet with id=AJ3, first strand: chain 'F' and resid 764 through 765 removed outlier: 7.010A pdb=" N ILE F 764 " --> pdb=" O ILE F 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'G' and resid 77 through 81 Processing sheet with id=AJ5, first strand: chain 'G' and resid 442 through 443 Processing sheet with id=AJ6, first strand: chain 'G' and resid 480 through 484 removed outlier: 6.389A pdb=" N VAL G 481 " --> pdb=" O CYS G 522 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASP G 524 " --> pdb=" O VAL G 481 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR G 483 " --> pdb=" O ASP G 524 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N CYS G 521 " --> pdb=" O LEU G 564 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ALA G 566 " --> pdb=" O CYS G 521 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE G 523 " --> pdb=" O ALA G 566 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS G 457 " --> pdb=" O PHE G 598 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N MET G 600 " --> pdb=" O CYS G 457 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET G 459 " --> pdb=" O MET G 600 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 495 through 500 Processing sheet with id=AJ8, first strand: chain 'G' and resid 545 through 549 Processing sheet with id=AJ9, first strand: chain 'G' and resid 651 through 652 removed outlier: 7.154A pdb=" N VAL G 651 " --> pdb=" O VAL G 708 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'H' and resid 34 through 41 removed outlier: 3.828A pdb=" N LYS H 34 " --> pdb=" O LYS H 51 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS H 49 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LYS H 38 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLY H 40 " --> pdb=" O SER H 45 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER H 45 " --> pdb=" O GLY H 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE H 78 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL H 116 " --> pdb=" O ILE H 78 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP H 108 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'H' and resid 159 through 160 Processing sheet with id=AK3, first strand: chain 'H' and resid 169 through 172 Processing sheet with id=AK4, first strand: chain 'H' and resid 352 through 354 removed outlier: 4.104A pdb=" N GLU H 353 " --> pdb=" O TYR I 267 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR I 267 " --> pdb=" O GLU H 353 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'I' and resid 126 through 128 Processing sheet with id=AK6, first strand: chain 'I' and resid 659 through 661 2874 hydrogen bonds defined for protein. 8346 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: 33.95 Time building geometry restraints manager: 15.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 23017 1.36 - 1.51: 18116 1.51 - 1.65: 27831 1.65 - 1.80: 349 1.80 - 1.95: 163 Bond restraints: 69476 Sorted by residual: bond pdb=" CA ASN G 575 " pdb=" CB ASN G 575 " ideal model delta sigma weight residual 1.534 1.568 -0.035 1.57e-02 4.06e+03 4.87e+00 bond pdb=" CB PRO G 359 " pdb=" CG PRO G 359 " ideal model delta sigma weight residual 1.492 1.598 -0.106 5.00e-02 4.00e+02 4.50e+00 bond pdb=" CG LEU H 147 " pdb=" CD1 LEU H 147 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" C SER D 414 " pdb=" N ILE D 415 " ideal model delta sigma weight residual 1.331 1.308 0.023 1.20e-02 6.94e+03 3.83e+00 bond pdb=" CB ASP D 693 " pdb=" CG ASP D 693 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.60e+00 ... (remaining 69471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 93021 3.20 - 6.40: 851 6.40 - 9.60: 105 9.60 - 12.80: 16 12.80 - 16.00: 3 Bond angle restraints: 93996 Sorted by residual: angle pdb=" CB ARG H 316 " pdb=" CG ARG H 316 " pdb=" CD ARG H 316 " ideal model delta sigma weight residual 111.30 126.86 -15.56 2.30e+00 1.89e-01 4.58e+01 angle pdb=" N GLU H 402 " pdb=" CA GLU H 402 " pdb=" CB GLU H 402 " ideal model delta sigma weight residual 110.16 119.46 -9.30 1.48e+00 4.57e-01 3.95e+01 angle pdb=" N GLU F 116 " pdb=" CA GLU F 116 " pdb=" CB GLU F 116 " ideal model delta sigma weight residual 110.28 119.06 -8.78 1.55e+00 4.16e-01 3.21e+01 angle pdb=" CA GLU H 126 " pdb=" CB GLU H 126 " pdb=" CG GLU H 126 " ideal model delta sigma weight residual 114.10 125.27 -11.17 2.00e+00 2.50e-01 3.12e+01 angle pdb=" N GLU 7 91 " pdb=" CA GLU 7 91 " pdb=" CB GLU 7 91 " ideal model delta sigma weight residual 110.40 119.13 -8.73 1.63e+00 3.76e-01 2.87e+01 ... (remaining 93991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.76: 41905 32.76 - 65.52: 798 65.52 - 98.28: 82 98.28 - 131.04: 4 131.04 - 163.80: 4 Dihedral angle restraints: 42793 sinusoidal: 17665 harmonic: 25128 Sorted by residual: dihedral pdb=" CB CYS 7 474 " pdb=" SG CYS 7 474 " pdb=" SG CYS 7 522 " pdb=" CB CYS 7 522 " ideal model delta sinusoidal sigma weight residual -86.00 -146.09 60.09 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" O2A ADP C2001 " pdb=" O3A ADP C2001 " pdb=" PA ADP C2001 " pdb=" PB ADP C2001 " ideal model delta sinusoidal sigma weight residual -60.00 66.87 -126.87 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" O2A ADP 32001 " pdb=" O3A ADP 32001 " pdb=" PA ADP 32001 " pdb=" PB ADP 32001 " ideal model delta sinusoidal sigma weight residual -60.00 65.89 -125.89 1 2.00e+01 2.50e-03 3.81e+01 ... (remaining 42790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 9869 0.091 - 0.182: 917 0.182 - 0.274: 37 0.274 - 0.365: 8 0.365 - 0.456: 3 Chirality restraints: 10834 Sorted by residual: chirality pdb=" CG LEU I 268 " pdb=" CB LEU I 268 " pdb=" CD1 LEU I 268 " pdb=" CD2 LEU I 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" CB ILE I 126 " pdb=" CA ILE I 126 " pdb=" CG1 ILE I 126 " pdb=" CG2 ILE I 126 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB ILE H 53 " pdb=" CA ILE H 53 " pdb=" CG1 ILE H 53 " pdb=" CG2 ILE H 53 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 10831 not shown) Planarity restraints: 12062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS 6 390 " -0.092 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO 6 391 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO 6 391 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO 6 391 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE H 398 " -0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C PHE H 398 " 0.083 2.00e-02 2.50e+03 pdb=" O PHE H 398 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU H 399 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 358 " 0.080 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO G 359 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO G 359 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO G 359 " 0.062 5.00e-02 4.00e+02 ... (remaining 12059 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 713 2.61 - 3.19: 57459 3.19 - 3.76: 107226 3.76 - 4.33: 149235 4.33 - 4.90: 244383 Nonbonded interactions: 559016 Sorted by model distance: nonbonded pdb=" OG SER 7 467 " pdb="MG MG 72002 " model vdw 2.042 2.170 nonbonded pdb=" O3B AGS 52001 " pdb="MG MG 52002 " model vdw 2.044 2.170 nonbonded pdb=" OG SER B 550 " pdb="MG MG B2002 " model vdw 2.044 2.170 nonbonded pdb=" O3B AGS E2001 " pdb="MG MG E2002 " model vdw 2.044 2.170 nonbonded pdb=" OG SER G 467 " pdb="MG MG G2002 " model vdw 2.050 2.170 ... (remaining 559011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '2' selection = chain 'B' } ncs_group { reference = chain '3' selection = chain 'C' } ncs_group { reference = chain '4' selection = chain 'D' } ncs_group { reference = chain '5' selection = chain 'E' } ncs_group { reference = chain '6' selection = chain 'F' } ncs_group { reference = chain '7' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 5.850 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: 0.100 Extract box with map and model: 2.010 Check model and map are aligned: 0.400 Set scattering table: 0.480 Process input model: 137.480 Find NCS groups from input model: 4.280 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 69476 Z= 0.275 Angle : 0.819 16.003 93996 Z= 0.437 Chirality : 0.052 0.456 10834 Planarity : 0.007 0.138 12062 Dihedral : 13.446 163.798 26483 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.31 % Rotamer: Outliers : 0.07 % Allowed : 0.38 % Favored : 99.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.08), residues: 8483 helix: -0.22 (0.08), residues: 3448 sheet: -0.14 (0.12), residues: 1589 loop : -0.41 (0.10), residues: 3446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP H 436 HIS 0.016 0.001 HIS H 24 PHE 0.071 0.002 PHE H 169 TYR 0.033 0.002 TYR 4 519 ARG 0.020 0.001 ARG I 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1951 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1946 time to evaluate : 5.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 210 GLU cc_start: 0.5400 (mm-30) cc_final: 0.5136 (mm-30) REVERT: 2 232 ARG cc_start: 0.6378 (mmm-85) cc_final: 0.5721 (mtp180) REVERT: 2 258 LEU cc_start: 0.6859 (tt) cc_final: 0.6444 (mt) REVERT: 2 269 LYS cc_start: 0.6553 (ttmm) cc_final: 0.6303 (ttmt) REVERT: 2 651 ASN cc_start: 0.8164 (m-40) cc_final: 0.7704 (m-40) REVERT: 2 686 LEU cc_start: 0.4893 (pt) cc_final: 0.4210 (mt) REVERT: 2 798 ILE cc_start: 0.5147 (mt) cc_final: 0.4679 (pt) REVERT: 3 27 ARG cc_start: 0.7314 (tpt170) cc_final: 0.6979 (ttp80) REVERT: 3 97 ILE cc_start: 0.7400 (mm) cc_final: 0.7056 (mt) REVERT: 3 188 LYS cc_start: 0.7737 (mtmm) cc_final: 0.7292 (ttpt) REVERT: 3 261 MET cc_start: 0.7809 (mtp) cc_final: 0.7528 (mtt) REVERT: 3 274 ILE cc_start: 0.8757 (pt) cc_final: 0.8156 (tp) REVERT: 3 556 ILE cc_start: 0.6723 (tp) cc_final: 0.6509 (mm) REVERT: 3 682 ASN cc_start: 0.8107 (m110) cc_final: 0.7898 (m-40) REVERT: 4 178 ARG cc_start: 0.7188 (mmm160) cc_final: 0.6948 (mmm-85) REVERT: 4 266 GLN cc_start: 0.7670 (tp40) cc_final: 0.7440 (tp-100) REVERT: 4 375 ASP cc_start: 0.6733 (m-30) cc_final: 0.6448 (m-30) REVERT: 4 404 ASP cc_start: 0.6688 (m-30) cc_final: 0.6434 (m-30) REVERT: 4 583 LYS cc_start: 0.7868 (mmpt) cc_final: 0.7568 (mtmm) REVERT: 4 666 ASN cc_start: 0.7934 (m-40) cc_final: 0.7700 (m110) REVERT: 4 715 LYS cc_start: 0.6891 (pttp) cc_final: 0.6250 (tptm) REVERT: 4 811 MET cc_start: 0.8496 (ttp) cc_final: 0.8245 (ttm) REVERT: 5 25 THR cc_start: 0.7159 (m) cc_final: 0.6927 (p) REVERT: 5 249 LYS cc_start: 0.7848 (mmmm) cc_final: 0.7562 (mttp) REVERT: 5 279 ASP cc_start: 0.6707 (p0) cc_final: 0.6418 (p0) REVERT: 5 358 LEU cc_start: 0.5114 (mt) cc_final: 0.4898 (tm) REVERT: 5 379 PHE cc_start: 0.7439 (t80) cc_final: 0.7050 (t80) REVERT: 5 556 VAL cc_start: 0.6463 (t) cc_final: 0.6210 (p) REVERT: 5 581 ASN cc_start: 0.5674 (t0) cc_final: 0.4623 (m-40) REVERT: 5 625 ASN cc_start: 0.6223 (m110) cc_final: 0.5301 (t0) REVERT: 5 671 ILE cc_start: 0.7111 (mm) cc_final: 0.6754 (mp) REVERT: 6 105 ASP cc_start: 0.7283 (m-30) cc_final: 0.6785 (t0) REVERT: 6 116 GLU cc_start: 0.6774 (pt0) cc_final: 0.6559 (mt-10) REVERT: 6 156 GLN cc_start: 0.6841 (mm-40) cc_final: 0.6457 (mt0) REVERT: 6 174 TYR cc_start: 0.7836 (t80) cc_final: 0.7438 (t80) REVERT: 6 299 GLU cc_start: 0.6890 (pm20) cc_final: 0.6494 (pt0) REVERT: 6 328 THR cc_start: 0.6302 (p) cc_final: 0.5819 (t) REVERT: 6 347 ASN cc_start: 0.6590 (t0) cc_final: 0.5719 (m-40) REVERT: 6 367 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7538 (mt-10) REVERT: 6 724 ASP cc_start: 0.6317 (m-30) cc_final: 0.6106 (m-30) REVERT: 6 764 ILE cc_start: 0.7120 (mt) cc_final: 0.6669 (pp) REVERT: 6 776 LYS cc_start: 0.7270 (mmtt) cc_final: 0.7017 (mmtp) REVERT: 6 794 ARG cc_start: 0.5272 (mtp-110) cc_final: 0.4604 (mtm110) REVERT: 6 798 ARG cc_start: 0.6894 (mtt90) cc_final: 0.6648 (ttp-170) REVERT: 6 829 ASP cc_start: 0.6740 (t0) cc_final: 0.6271 (t70) REVERT: 7 64 MET cc_start: 0.8712 (mmt) cc_final: 0.8262 (mmt) REVERT: 7 69 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7734 (mtpt) REVERT: 7 76 ASN cc_start: 0.7276 (t0) cc_final: 0.7020 (m110) REVERT: 7 81 ASP cc_start: 0.7603 (m-30) cc_final: 0.7174 (t0) REVERT: 7 159 ASN cc_start: 0.7365 (m-40) cc_final: 0.6965 (m110) REVERT: 7 162 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6699 (ttt90) REVERT: 7 247 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7574 (tmm160) REVERT: 7 268 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7910 (mt-10) REVERT: 7 396 ASP cc_start: 0.5880 (p0) cc_final: 0.5665 (m-30) REVERT: 7 484 THR cc_start: 0.7352 (m) cc_final: 0.7062 (m) REVERT: 7 498 MET cc_start: 0.5830 (ptt) cc_final: 0.5562 (ppp) REVERT: 7 515 LEU cc_start: 0.8336 (mt) cc_final: 0.8107 (mm) REVERT: 7 537 ILE cc_start: 0.7766 (mt) cc_final: 0.7500 (mm) REVERT: 7 556 THR cc_start: 0.8563 (t) cc_final: 0.8322 (m) REVERT: 7 598 PHE cc_start: 0.8244 (m-80) cc_final: 0.7932 (m-80) REVERT: 7 621 MET cc_start: 0.7767 (ttp) cc_final: 0.7533 (ttm) REVERT: 7 688 THR cc_start: 0.8425 (m) cc_final: 0.8115 (p) REVERT: 7 714 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6454 (tm-30) REVERT: B 227 TYR cc_start: 0.6252 (m-80) cc_final: 0.5676 (m-80) REVERT: B 269 LYS cc_start: 0.6520 (ttmm) cc_final: 0.5299 (mppt) REVERT: B 272 ASP cc_start: 0.5871 (t0) cc_final: 0.5649 (m-30) REVERT: B 823 MET cc_start: 0.7932 (mtt) cc_final: 0.7572 (mtt) REVERT: B 834 LEU cc_start: 0.6823 (mm) cc_final: 0.6067 (tp) REVERT: C 39 ARG cc_start: 0.6703 (ttm110) cc_final: 0.6262 (ttp-110) REVERT: C 48 TYR cc_start: 0.7356 (t80) cc_final: 0.7089 (t80) REVERT: C 188 LYS cc_start: 0.7797 (mtmt) cc_final: 0.7067 (mptt) REVERT: C 215 THR cc_start: 0.8340 (p) cc_final: 0.7959 (t) REVERT: C 234 GLU cc_start: 0.6483 (mt-10) cc_final: 0.5964 (mp0) REVERT: C 235 ASP cc_start: 0.6344 (p0) cc_final: 0.5978 (p0) REVERT: C 237 GLU cc_start: 0.6988 (mp0) cc_final: 0.6634 (mt-10) REVERT: C 318 LYS cc_start: 0.7556 (ptpt) cc_final: 0.7194 (pttm) REVERT: C 322 LEU cc_start: 0.8030 (mm) cc_final: 0.7816 (mm) REVERT: C 348 ARG cc_start: 0.6643 (mtm110) cc_final: 0.6242 (mtt90) REVERT: C 361 ASP cc_start: 0.7494 (m-30) cc_final: 0.7254 (m-30) REVERT: C 362 ILE cc_start: 0.7969 (mt) cc_final: 0.7644 (mm) REVERT: C 407 MET cc_start: 0.8218 (mtp) cc_final: 0.8015 (mtm) REVERT: C 477 LYS cc_start: 0.7346 (mttm) cc_final: 0.7072 (mttm) REVERT: C 505 THR cc_start: 0.8292 (t) cc_final: 0.7812 (m) REVERT: C 556 ILE cc_start: 0.7415 (pt) cc_final: 0.7096 (tp) REVERT: C 664 LYS cc_start: 0.7645 (mtpp) cc_final: 0.7271 (mtpt) REVERT: C 665 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6512 (mp0) REVERT: D 204 LYS cc_start: 0.7437 (pttp) cc_final: 0.7222 (pttm) REVERT: D 408 ASP cc_start: 0.7188 (m-30) cc_final: 0.6902 (m-30) REVERT: D 483 GLN cc_start: 0.6386 (tp40) cc_final: 0.6067 (mt0) REVERT: D 580 TYR cc_start: 0.7467 (t80) cc_final: 0.7256 (t80) REVERT: D 609 VAL cc_start: 0.7302 (m) cc_final: 0.7060 (t) REVERT: D 649 MET cc_start: 0.7580 (mmt) cc_final: 0.6866 (mmt) REVERT: D 686 LEU cc_start: 0.7412 (mt) cc_final: 0.7146 (mp) REVERT: E 5 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7000 (ttp-110) REVERT: E 33 ASN cc_start: 0.7307 (m-40) cc_final: 0.7000 (m110) REVERT: E 182 MET cc_start: 0.8289 (ttm) cc_final: 0.8045 (ttp) REVERT: E 209 ARG cc_start: 0.7129 (mmm-85) cc_final: 0.6905 (mmt-90) REVERT: E 249 LYS cc_start: 0.7826 (mmtp) cc_final: 0.7472 (mppt) REVERT: E 300 ILE cc_start: 0.8175 (mm) cc_final: 0.7885 (mm) REVERT: E 356 GLU cc_start: 0.5173 (mp0) cc_final: 0.4915 (mm-30) REVERT: E 369 ILE cc_start: 0.6890 (pt) cc_final: 0.6656 (mt) REVERT: E 404 MET cc_start: 0.6942 (ttm) cc_final: 0.6266 (tpt) REVERT: E 485 MET cc_start: 0.8380 (ttm) cc_final: 0.8101 (ttp) REVERT: E 497 MET cc_start: 0.8261 (mtt) cc_final: 0.8054 (mtm) REVERT: E 592 SER cc_start: 0.6593 (m) cc_final: 0.5691 (p) REVERT: E 597 GLU cc_start: 0.6101 (pm20) cc_final: 0.5882 (mm-30) REVERT: E 614 LEU cc_start: 0.7858 (mt) cc_final: 0.7651 (mt) REVERT: E 661 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6698 (mt-10) REVERT: F 147 ASP cc_start: 0.6027 (t0) cc_final: 0.5763 (t0) REVERT: F 348 VAL cc_start: 0.6827 (m) cc_final: 0.6555 (t) REVERT: F 362 GLN cc_start: 0.8225 (tt0) cc_final: 0.7869 (tt0) REVERT: F 608 LEU cc_start: 0.8214 (mt) cc_final: 0.7981 (mt) REVERT: F 764 ILE cc_start: 0.7034 (mp) cc_final: 0.6593 (pp) REVERT: G 15 ASN cc_start: 0.7027 (m-40) cc_final: 0.5910 (t0) REVERT: G 133 ASP cc_start: 0.6119 (p0) cc_final: 0.5857 (t70) REVERT: G 282 SER cc_start: 0.8223 (p) cc_final: 0.8002 (m) REVERT: G 291 GLN cc_start: 0.7971 (mt0) cc_final: 0.7606 (mt0) REVERT: G 317 GLU cc_start: 0.6698 (tt0) cc_final: 0.6432 (tt0) REVERT: G 402 MET cc_start: 0.3603 (mpp) cc_final: 0.3386 (tpt) REVERT: G 412 ASN cc_start: 0.7504 (t0) cc_final: 0.7057 (m-40) REVERT: G 449 LYS cc_start: 0.7185 (mtmm) cc_final: 0.6734 (mmmm) REVERT: G 459 MET cc_start: 0.7681 (ttp) cc_final: 0.7294 (ttm) REVERT: G 618 TYR cc_start: 0.7520 (t80) cc_final: 0.7198 (t80) REVERT: G 640 GLU cc_start: 0.7510 (pt0) cc_final: 0.6841 (pt0) REVERT: G 690 LEU cc_start: 0.8568 (mt) cc_final: 0.8350 (mt) REVERT: H 34 LYS cc_start: 0.3929 (tttt) cc_final: 0.3697 (tptp) REVERT: H 92 ASN cc_start: 0.5095 (t0) cc_final: 0.4760 (t0) REVERT: H 138 LYS cc_start: 0.3443 (mmmt) cc_final: 0.2405 (tptm) REVERT: H 288 GLU cc_start: 0.5147 (pm20) cc_final: 0.4772 (mm-30) REVERT: H 300 ILE cc_start: 0.5733 (mp) cc_final: 0.5420 (mp) REVERT: H 310 LEU cc_start: 0.5495 (tt) cc_final: 0.5174 (pp) REVERT: H 324 ASP cc_start: 0.6655 (p0) cc_final: 0.6381 (p0) REVERT: H 332 LEU cc_start: 0.6044 (mt) cc_final: 0.5723 (tp) REVERT: H 339 LYS cc_start: 0.6180 (mmpt) cc_final: 0.5688 (mttt) REVERT: H 358 ILE cc_start: 0.3342 (pt) cc_final: 0.3135 (mt) REVERT: H 398 PHE cc_start: 0.3084 (t80) cc_final: 0.2822 (t80) REVERT: H 402 GLU cc_start: 0.1981 (mp0) cc_final: 0.1461 (mt-10) REVERT: H 452 MET cc_start: 0.5993 (mmp) cc_final: 0.5595 (mmt) REVERT: H 465 LYS cc_start: 0.4018 (mppt) cc_final: 0.3655 (mmmt) REVERT: I 152 LYS cc_start: 0.4068 (mttt) cc_final: 0.3861 (tppt) REVERT: I 158 LEU cc_start: 0.2630 (tt) cc_final: 0.2375 (mt) REVERT: I 233 THR cc_start: 0.4841 (p) cc_final: 0.4345 (p) REVERT: I 325 LYS cc_start: 0.3803 (mppt) cc_final: 0.3492 (ttpp) REVERT: I 382 MET cc_start: 0.2503 (mmp) cc_final: 0.1094 (tpt) REVERT: I 524 MET cc_start: 0.8730 (mmp) cc_final: 0.8413 (mmm) REVERT: I 662 GLU cc_start: 0.6373 (tt0) cc_final: 0.6121 (tp30) REVERT: I 672 GLU cc_start: 0.5562 (pm20) cc_final: 0.5329 (pm20) REVERT: I 697 ILE cc_start: 0.2752 (mm) cc_final: 0.2421 (pt) outliers start: 5 outliers final: 6 residues processed: 1951 average time/residue: 1.5859 time to fit residues: 3954.6137 Evaluate side-chains 1035 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1029 time to evaluate : 5.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 671 ILE Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 717 optimal weight: 3.9990 chunk 644 optimal weight: 7.9990 chunk 357 optimal weight: 5.9990 chunk 220 optimal weight: 0.5980 chunk 434 optimal weight: 5.9990 chunk 344 optimal weight: 0.3980 chunk 666 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 405 optimal weight: 6.9990 chunk 495 optimal weight: 0.8980 chunk 771 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 454 ASN ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 856 GLN 3 52 ASN 3 259 GLN 3 269 GLN 3 307 ASN 3 340 GLN 3 374 HIS ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 493 GLN 3 587 ASN 4 327 ASN 4 380 ASN ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 726 ASN 5 195 ASN 5 334 GLN ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 539 ASN 5 560 HIS 5 585 ASN 5 587 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 700 ASN 7 87 GLN ** 7 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 108 GLN 7 297 GLN 7 657 ASN B 353 GLN B 433 ASN B 615 GLN B 658 ASN B 666 ASN C 29 GLN C 52 ASN C 324 ASN C 374 HIS C 487 HIS C 691 ASN C 722 ASN D 229 GLN D 253 GLN D 320 ASN D 327 ASN D 685 ASN D 726 ASN E 108 GLN E 235 ASN E 334 GLN E 454 GLN E 499 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 GLN F 125 GLN F 264 GLN F 347 ASN F 583 GLN F 633 ASN F 698 ASN G 19 ASN G 107 GLN G 123 ASN G 178 ASN G 518 ASN G 558 ASN H 439 HIS ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 ASN ** I 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 657 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 69476 Z= 0.282 Angle : 0.650 12.087 93996 Z= 0.339 Chirality : 0.046 0.272 10834 Planarity : 0.006 0.079 12062 Dihedral : 7.876 175.044 9640 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 3.48 % Allowed : 12.17 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.09), residues: 8483 helix: 0.62 (0.09), residues: 3524 sheet: -0.23 (0.12), residues: 1604 loop : -0.29 (0.10), residues: 3355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 436 HIS 0.011 0.001 HIS 6 653 PHE 0.021 0.002 PHE H 169 TYR 0.024 0.002 TYR D 580 ARG 0.008 0.001 ARG H 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1362 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1098 time to evaluate : 5.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.5716 (mt-10) REVERT: 2 232 ARG cc_start: 0.6549 (mmm-85) cc_final: 0.5936 (mtp180) REVERT: 2 258 LEU cc_start: 0.7006 (tt) cc_final: 0.6554 (mt) REVERT: 2 326 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6395 (pmt170) REVERT: 2 374 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5450 (ttm110) REVERT: 2 651 ASN cc_start: 0.8224 (m-40) cc_final: 0.7694 (m-40) REVERT: 2 667 VAL cc_start: 0.7165 (OUTLIER) cc_final: 0.6834 (p) REVERT: 2 684 ARG cc_start: 0.3859 (OUTLIER) cc_final: 0.3114 (ptp90) REVERT: 2 686 LEU cc_start: 0.4836 (pt) cc_final: 0.4431 (mt) REVERT: 2 783 MET cc_start: 0.6217 (ttp) cc_final: 0.6013 (ttt) REVERT: 2 798 ILE cc_start: 0.5161 (mt) cc_final: 0.4701 (pt) REVERT: 3 27 ARG cc_start: 0.7723 (tpt170) cc_final: 0.7068 (ttp80) REVERT: 3 52 ASN cc_start: 0.5312 (m-40) cc_final: 0.5057 (m110) REVERT: 3 97 ILE cc_start: 0.8050 (mm) cc_final: 0.7781 (mt) REVERT: 3 188 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7280 (ttpt) REVERT: 3 234 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6084 (tm-30) REVERT: 3 237 GLU cc_start: 0.7109 (mp0) cc_final: 0.6883 (mt-10) REVERT: 3 261 MET cc_start: 0.7971 (mtp) cc_final: 0.7481 (mtt) REVERT: 3 274 ILE cc_start: 0.8767 (pt) cc_final: 0.8237 (tp) REVERT: 3 353 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8624 (mm) REVERT: 3 365 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6718 (tp40) REVERT: 3 497 ILE cc_start: 0.7446 (pt) cc_final: 0.7167 (mt) REVERT: 3 504 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8130 (t) REVERT: 3 566 LEU cc_start: 0.8303 (mt) cc_final: 0.8068 (mp) REVERT: 3 688 ASN cc_start: 0.7473 (m110) cc_final: 0.7191 (m110) REVERT: 4 233 MET cc_start: 0.8642 (ttt) cc_final: 0.8417 (mtp) REVERT: 4 266 GLN cc_start: 0.7797 (tp40) cc_final: 0.7458 (tp-100) REVERT: 4 327 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7835 (m110) REVERT: 4 366 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6624 (mp10) REVERT: 4 375 ASP cc_start: 0.6705 (m-30) cc_final: 0.6416 (m-30) REVERT: 4 404 ASP cc_start: 0.6847 (m-30) cc_final: 0.6537 (m-30) REVERT: 4 477 ASP cc_start: 0.6961 (t0) cc_final: 0.6448 (t0) REVERT: 4 583 LYS cc_start: 0.7911 (mmpt) cc_final: 0.7507 (mtmm) REVERT: 4 715 LYS cc_start: 0.7004 (pttp) cc_final: 0.6377 (tppp) REVERT: 4 718 ARG cc_start: 0.6730 (tpp80) cc_final: 0.5997 (tpt170) REVERT: 4 726 ASN cc_start: 0.7371 (m-40) cc_final: 0.6987 (t0) REVERT: 4 756 GLU cc_start: 0.7657 (tt0) cc_final: 0.7427 (tp30) REVERT: 5 5 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6367 (mmm-85) REVERT: 5 139 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8360 (pp) REVERT: 5 184 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6305 (mtm-85) REVERT: 5 210 SER cc_start: 0.8100 (m) cc_final: 0.7688 (t) REVERT: 5 239 ASP cc_start: 0.7269 (m-30) cc_final: 0.6973 (m-30) REVERT: 5 279 ASP cc_start: 0.7257 (p0) cc_final: 0.7004 (p0) REVERT: 5 358 LEU cc_start: 0.5327 (mt) cc_final: 0.5078 (tm) REVERT: 5 556 VAL cc_start: 0.6480 (t) cc_final: 0.6206 (p) REVERT: 5 564 ARG cc_start: 0.6545 (ttt180) cc_final: 0.5830 (ttt180) REVERT: 5 574 ASN cc_start: 0.7476 (m-40) cc_final: 0.7242 (m-40) REVERT: 5 581 ASN cc_start: 0.5719 (t0) cc_final: 0.4688 (m-40) REVERT: 5 654 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: 5 671 ILE cc_start: 0.7073 (mm) cc_final: 0.6871 (mt) REVERT: 6 172 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6771 (mm-30) REVERT: 6 174 TYR cc_start: 0.7917 (t80) cc_final: 0.7404 (t80) REVERT: 6 299 GLU cc_start: 0.7059 (pm20) cc_final: 0.6247 (mt-10) REVERT: 6 328 THR cc_start: 0.6457 (p) cc_final: 0.6236 (p) REVERT: 6 347 ASN cc_start: 0.6695 (t0) cc_final: 0.5885 (m-40) REVERT: 6 367 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7637 (mt-10) REVERT: 6 518 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5494 (tm-30) REVERT: 6 675 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7336 (mpp-170) REVERT: 6 764 ILE cc_start: 0.7345 (mt) cc_final: 0.6748 (pp) REVERT: 6 794 ARG cc_start: 0.5390 (mtp-110) cc_final: 0.4601 (mtm110) REVERT: 7 64 MET cc_start: 0.8750 (mmt) cc_final: 0.8460 (mmt) REVERT: 7 69 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7692 (mtpt) REVERT: 7 76 ASN cc_start: 0.7772 (t0) cc_final: 0.7400 (m110) REVERT: 7 81 ASP cc_start: 0.7844 (m-30) cc_final: 0.7528 (t0) REVERT: 7 141 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7890 (t) REVERT: 7 159 ASN cc_start: 0.7330 (m-40) cc_final: 0.6877 (m110) REVERT: 7 162 ARG cc_start: 0.7159 (ttm-80) cc_final: 0.6736 (ttm170) REVERT: 7 188 GLU cc_start: 0.6037 (tt0) cc_final: 0.5493 (tt0) REVERT: 7 247 ARG cc_start: 0.7815 (tpp80) cc_final: 0.7423 (ttp80) REVERT: 7 276 ARG cc_start: 0.7780 (mmt-90) cc_final: 0.7194 (mpt180) REVERT: 7 449 LYS cc_start: 0.7214 (mtmt) cc_final: 0.6720 (tmtp) REVERT: 7 498 MET cc_start: 0.6088 (ptt) cc_final: 0.5636 (mtm) REVERT: 7 537 ILE cc_start: 0.7878 (mt) cc_final: 0.7513 (mm) REVERT: 7 598 PHE cc_start: 0.8357 (m-80) cc_final: 0.7964 (m-80) REVERT: 7 714 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6705 (tm-30) REVERT: B 247 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6004 (ttm170) REVERT: B 267 MET cc_start: 0.7041 (mmm) cc_final: 0.6823 (mmm) REVERT: B 269 LYS cc_start: 0.6484 (ttmm) cc_final: 0.5228 (mppt) REVERT: B 272 ASP cc_start: 0.6011 (t0) cc_final: 0.5671 (m-30) REVERT: B 293 ILE cc_start: 0.6882 (mt) cc_final: 0.6532 (tt) REVERT: B 358 GLU cc_start: 0.4854 (tp30) cc_final: 0.4512 (pp20) REVERT: B 413 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6553 (m-30) REVERT: B 496 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6808 (ttmm) REVERT: B 501 MET cc_start: 0.7668 (mmm) cc_final: 0.7161 (mmt) REVERT: B 506 TYR cc_start: 0.6436 (t80) cc_final: 0.6221 (t80) REVERT: B 626 GLN cc_start: 0.7685 (mt0) cc_final: 0.7478 (mm110) REVERT: B 694 ARG cc_start: 0.6719 (mtm110) cc_final: 0.6517 (mtm110) REVERT: B 705 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.5895 (mtp180) REVERT: B 829 VAL cc_start: 0.6665 (m) cc_final: 0.6423 (m) REVERT: B 834 LEU cc_start: 0.6995 (mm) cc_final: 0.6310 (tp) REVERT: C 36 THR cc_start: 0.7196 (p) cc_final: 0.6860 (m) REVERT: C 39 ARG cc_start: 0.7028 (ttm110) cc_final: 0.6520 (ttp-110) REVERT: C 48 TYR cc_start: 0.7489 (t80) cc_final: 0.7200 (t80) REVERT: C 188 LYS cc_start: 0.7923 (mtmt) cc_final: 0.7512 (mttp) REVERT: C 205 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7447 (OUTLIER) REVERT: C 222 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8011 (p) REVERT: C 234 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6045 (mp0) REVERT: C 235 ASP cc_start: 0.6865 (p0) cc_final: 0.6558 (p0) REVERT: C 237 GLU cc_start: 0.7068 (mp0) cc_final: 0.6670 (mt-10) REVERT: C 348 ARG cc_start: 0.6900 (mtm110) cc_final: 0.6346 (mtt90) REVERT: C 407 MET cc_start: 0.8249 (mtp) cc_final: 0.8001 (mtm) REVERT: C 464 LEU cc_start: 0.7898 (mt) cc_final: 0.7525 (mt) REVERT: C 477 LYS cc_start: 0.7163 (mttm) cc_final: 0.6547 (mttp) REVERT: C 505 THR cc_start: 0.8399 (t) cc_final: 0.7949 (m) REVERT: C 556 ILE cc_start: 0.7270 (pt) cc_final: 0.6879 (mm) REVERT: C 656 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7655 (tp) REVERT: C 664 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7261 (mtpt) REVERT: C 723 LYS cc_start: 0.7060 (pttt) cc_final: 0.6710 (tttt) REVERT: D 228 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7529 (ttpm) REVERT: D 235 GLU cc_start: 0.6234 (mt-10) cc_final: 0.5633 (tp30) REVERT: D 408 ASP cc_start: 0.7360 (m-30) cc_final: 0.7031 (m-30) REVERT: D 445 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6911 (mtt180) REVERT: D 483 GLN cc_start: 0.6657 (tp40) cc_final: 0.6060 (mt0) REVERT: D 534 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7168 (tp30) REVERT: D 686 LEU cc_start: 0.7328 (mt) cc_final: 0.7111 (mp) REVERT: D 715 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6152 (ptmm) REVERT: E 5 ARG cc_start: 0.7570 (ttp80) cc_final: 0.7026 (ttp-110) REVERT: E 33 ASN cc_start: 0.7384 (m-40) cc_final: 0.7091 (m110) REVERT: E 209 ARG cc_start: 0.7131 (mmm-85) cc_final: 0.6786 (mmt-90) REVERT: E 249 LYS cc_start: 0.7801 (mmtp) cc_final: 0.7540 (mppt) REVERT: E 280 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7665 (mtp85) REVERT: E 354 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6290 (mm-30) REVERT: E 404 MET cc_start: 0.7268 (ttm) cc_final: 0.6449 (tpt) REVERT: E 430 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6786 (tm-30) REVERT: E 458 MET cc_start: 0.5583 (mtp) cc_final: 0.5228 (mtm) REVERT: E 469 MET cc_start: 0.7988 (mmm) cc_final: 0.7408 (mmm) REVERT: E 564 ARG cc_start: 0.6777 (ttt180) cc_final: 0.5760 (ttm-80) REVERT: E 592 SER cc_start: 0.6599 (m) cc_final: 0.5917 (p) REVERT: E 597 GLU cc_start: 0.6241 (pm20) cc_final: 0.5819 (mm-30) REVERT: E 601 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7236 (mmp-170) REVERT: E 614 LEU cc_start: 0.7678 (mt) cc_final: 0.7419 (mt) REVERT: E 661 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6735 (mt-10) REVERT: F 168 MET cc_start: 0.6403 (mmm) cc_final: 0.6042 (mmt) REVERT: F 313 MET cc_start: 0.3962 (mpt) cc_final: 0.2417 (ptt) REVERT: F 352 ARG cc_start: 0.7000 (mtp85) cc_final: 0.6643 (mmm160) REVERT: F 362 GLN cc_start: 0.8408 (tt0) cc_final: 0.7971 (tt0) REVERT: F 521 LYS cc_start: 0.4748 (mmpt) cc_final: 0.4332 (mmtp) REVERT: F 583 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7339 (mp-120) REVERT: F 737 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7193 (mttt) REVERT: G 15 ASN cc_start: 0.7414 (m-40) cc_final: 0.6214 (t0) REVERT: G 187 ASP cc_start: 0.6749 (t0) cc_final: 0.6001 (m-30) REVERT: G 247 ARG cc_start: 0.8111 (ttt90) cc_final: 0.7660 (ttp80) REVERT: G 291 GLN cc_start: 0.7916 (mt0) cc_final: 0.7618 (mt0) REVERT: G 297 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: G 412 ASN cc_start: 0.7513 (t0) cc_final: 0.6933 (m-40) REVERT: G 427 ASP cc_start: 0.7764 (m-30) cc_final: 0.7484 (m-30) REVERT: G 537 ILE cc_start: 0.8041 (mt) cc_final: 0.7741 (mm) REVERT: G 556 THR cc_start: 0.8068 (t) cc_final: 0.7677 (m) REVERT: G 583 ASN cc_start: 0.7117 (p0) cc_final: 0.6849 (p0) REVERT: G 607 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: G 618 TYR cc_start: 0.7546 (t80) cc_final: 0.7141 (t80) REVERT: G 640 GLU cc_start: 0.7321 (pt0) cc_final: 0.6607 (tt0) REVERT: G 690 LEU cc_start: 0.8544 (mt) cc_final: 0.8290 (mt) REVERT: H 51 LYS cc_start: 0.3313 (tttt) cc_final: 0.3020 (tptt) REVERT: H 143 TYR cc_start: 0.3135 (t80) cc_final: 0.2806 (t80) REVERT: H 173 LEU cc_start: 0.2036 (mt) cc_final: 0.1754 (pp) REVERT: H 282 ARG cc_start: 0.5317 (ttm-80) cc_final: 0.5072 (ttm-80) REVERT: H 284 PHE cc_start: 0.5071 (m-80) cc_final: 0.4828 (m-80) REVERT: H 322 SER cc_start: 0.4432 (m) cc_final: 0.4117 (p) REVERT: H 332 LEU cc_start: 0.6280 (mt) cc_final: 0.5874 (tp) REVERT: H 342 ARG cc_start: 0.5389 (ttp-110) cc_final: 0.4736 (ttp80) REVERT: H 398 PHE cc_start: 0.3363 (t80) cc_final: 0.3122 (t80) REVERT: H 402 GLU cc_start: 0.2399 (mp0) cc_final: 0.2091 (mm-30) REVERT: H 426 TYR cc_start: 0.3074 (t80) cc_final: 0.1602 (p90) REVERT: H 452 MET cc_start: 0.6213 (mmp) cc_final: 0.5944 (mmt) REVERT: H 465 LYS cc_start: 0.4038 (mppt) cc_final: 0.3683 (mmmt) REVERT: I 120 MET cc_start: 0.2083 (pp-130) cc_final: 0.0591 (mpt) REVERT: I 125 ARG cc_start: 0.3424 (mmm-85) cc_final: 0.3053 (mmm160) REVERT: I 144 MET cc_start: 0.3871 (mmt) cc_final: 0.3626 (mmm) REVERT: I 152 LYS cc_start: 0.4143 (mttt) cc_final: 0.3780 (tppt) REVERT: I 158 LEU cc_start: 0.3051 (tt) cc_final: 0.2551 (mp) REVERT: I 325 LYS cc_start: 0.3766 (mppt) cc_final: 0.3332 (ttpp) REVERT: I 382 MET cc_start: 0.2467 (mmp) cc_final: 0.1604 (ptp) REVERT: I 662 GLU cc_start: 0.6496 (tt0) cc_final: 0.5857 (tp30) REVERT: I 672 GLU cc_start: 0.5572 (pm20) cc_final: 0.5326 (pm20) outliers start: 264 outliers final: 99 residues processed: 1273 average time/residue: 1.5611 time to fit residues: 2555.2470 Evaluate side-chains 1045 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 914 time to evaluate : 5.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 396 THR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 661 LEU Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 2 residue 863 ILE Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 537 ASP Chi-restraints excluded: chain 3 residue 656 LEU Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 327 ASN Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 366 GLN Chi-restraints excluded: chain 4 residue 490 VAL Chi-restraints excluded: chain 4 residue 592 SER Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 5 ARG Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 177 THR Chi-restraints excluded: chain 5 residue 184 ARG Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 592 SER Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 518 GLU Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 294 THR Chi-restraints excluded: chain 7 residue 329 ARG Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 601 ARG Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 583 GLN Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 737 LYS Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 607 ASP Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 440 TYR Chi-restraints excluded: chain I residue 119 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 239 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 428 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 642 optimal weight: 4.9990 chunk 525 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 773 optimal weight: 0.9980 chunk 835 optimal weight: 0.3980 chunk 688 optimal weight: 8.9990 chunk 766 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 620 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 561 HIS 2 666 ASN 3 307 ASN 3 324 ASN 3 340 GLN 3 398 HIS 3 564 HIS 3 587 ASN 4 327 ASN 4 613 GLN 5 72 ASN ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 334 GLN 5 499 GLN 5 500 GLN 5 587 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 297 GLN 7 384 HIS 7 683 GLN B 433 ASN ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN D 229 GLN D 253 GLN D 327 ASN D 685 ASN D 726 ASN E 108 GLN E 424 GLN E 454 GLN E 685 GLN F 347 ASN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 575 ASN G 623 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 69476 Z= 0.231 Angle : 0.585 11.183 93996 Z= 0.303 Chirality : 0.044 0.258 10834 Planarity : 0.005 0.065 12062 Dihedral : 7.588 176.200 9632 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Rotamer: Outliers : 3.70 % Allowed : 15.14 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.09), residues: 8483 helix: 0.93 (0.09), residues: 3533 sheet: -0.22 (0.12), residues: 1570 loop : -0.24 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 112 HIS 0.009 0.001 HIS 6 653 PHE 0.024 0.002 PHE I 210 TYR 0.024 0.002 TYR 6 136 ARG 0.007 0.001 ARG 4 772 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 960 time to evaluate : 6.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 232 ARG cc_start: 0.6573 (mmm-85) cc_final: 0.5953 (mtp180) REVERT: 2 326 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6097 (pmt170) REVERT: 2 358 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.4609 (tm-30) REVERT: 2 374 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5446 (ttm110) REVERT: 2 592 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7362 (mm-30) REVERT: 2 651 ASN cc_start: 0.8187 (m-40) cc_final: 0.7655 (m-40) REVERT: 2 684 ARG cc_start: 0.3935 (OUTLIER) cc_final: 0.3180 (ptp90) REVERT: 2 686 LEU cc_start: 0.4790 (pt) cc_final: 0.4384 (mt) REVERT: 2 687 VAL cc_start: 0.5864 (t) cc_final: 0.5660 (p) REVERT: 2 798 ILE cc_start: 0.5391 (mt) cc_final: 0.4936 (pt) REVERT: 3 27 ARG cc_start: 0.7899 (tpt170) cc_final: 0.7133 (ttp80) REVERT: 3 188 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7246 (ttpt) REVERT: 3 234 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6091 (tm-30) REVERT: 3 274 ILE cc_start: 0.8801 (pt) cc_final: 0.8311 (tp) REVERT: 3 353 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8661 (mm) REVERT: 3 357 LYS cc_start: 0.7283 (pmtt) cc_final: 0.6460 (ptpt) REVERT: 3 365 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6706 (tp40) REVERT: 3 497 ILE cc_start: 0.7450 (pt) cc_final: 0.7201 (mt) REVERT: 3 688 ASN cc_start: 0.7439 (m110) cc_final: 0.7131 (m110) REVERT: 4 232 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7421 (pt0) REVERT: 4 266 GLN cc_start: 0.7814 (tp40) cc_final: 0.7471 (tp-100) REVERT: 4 296 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7506 (mm) REVERT: 4 404 ASP cc_start: 0.6842 (m-30) cc_final: 0.6504 (m-30) REVERT: 4 477 ASP cc_start: 0.7191 (t0) cc_final: 0.6785 (t0) REVERT: 4 579 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7481 (mm-40) REVERT: 4 583 LYS cc_start: 0.7891 (mmpt) cc_final: 0.7485 (mtmm) REVERT: 4 686 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7065 (tp) REVERT: 4 715 LYS cc_start: 0.6976 (pttp) cc_final: 0.6336 (tppp) REVERT: 4 726 ASN cc_start: 0.7471 (m-40) cc_final: 0.7056 (t0) REVERT: 4 756 GLU cc_start: 0.7581 (tt0) cc_final: 0.7286 (tp30) REVERT: 5 72 ASN cc_start: 0.7789 (t0) cc_final: 0.7504 (t0) REVERT: 5 103 ILE cc_start: 0.7005 (mt) cc_final: 0.6802 (tp) REVERT: 5 139 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8350 (pp) REVERT: 5 279 ASP cc_start: 0.7242 (p0) cc_final: 0.7000 (p0) REVERT: 5 358 LEU cc_start: 0.5402 (mt) cc_final: 0.5114 (tm) REVERT: 5 404 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.5822 (mmp) REVERT: 5 469 MET cc_start: 0.7600 (mmm) cc_final: 0.7322 (mmm) REVERT: 5 556 VAL cc_start: 0.6634 (t) cc_final: 0.6348 (p) REVERT: 5 581 ASN cc_start: 0.5543 (t0) cc_final: 0.4761 (m-40) REVERT: 5 654 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: 5 689 MET cc_start: 0.7139 (mmm) cc_final: 0.6833 (mmm) REVERT: 6 105 ASP cc_start: 0.7344 (m-30) cc_final: 0.7094 (t0) REVERT: 6 172 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6736 (mm-30) REVERT: 6 174 TYR cc_start: 0.7952 (t80) cc_final: 0.7377 (t80) REVERT: 6 299 GLU cc_start: 0.7104 (pm20) cc_final: 0.6290 (mt-10) REVERT: 6 328 THR cc_start: 0.6477 (p) cc_final: 0.6259 (p) REVERT: 6 347 ASN cc_start: 0.6732 (t0) cc_final: 0.5953 (m-40) REVERT: 6 367 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7783 (mt-10) REVERT: 6 518 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5514 (tm-30) REVERT: 6 675 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7355 (mpp-170) REVERT: 6 696 ARG cc_start: 0.6902 (tpt90) cc_final: 0.6164 (tmt-80) REVERT: 6 724 ASP cc_start: 0.7065 (m-30) cc_final: 0.6675 (m-30) REVERT: 6 764 ILE cc_start: 0.7343 (mt) cc_final: 0.6742 (pp) REVERT: 6 783 ASP cc_start: 0.5767 (t0) cc_final: 0.5483 (t0) REVERT: 6 794 ARG cc_start: 0.5506 (mtp-110) cc_final: 0.4671 (mtm110) REVERT: 6 833 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6586 (mp10) REVERT: 7 64 MET cc_start: 0.8696 (mmt) cc_final: 0.8465 (mmt) REVERT: 7 69 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7696 (mtpt) REVERT: 7 76 ASN cc_start: 0.7790 (t0) cc_final: 0.7401 (m110) REVERT: 7 81 ASP cc_start: 0.7832 (m-30) cc_final: 0.7406 (t0) REVERT: 7 124 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7015 (p0) REVERT: 7 159 ASN cc_start: 0.7381 (m-40) cc_final: 0.6980 (m110) REVERT: 7 162 ARG cc_start: 0.7108 (ttm-80) cc_final: 0.6901 (ttt90) REVERT: 7 188 GLU cc_start: 0.6127 (tt0) cc_final: 0.5705 (tt0) REVERT: 7 244 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8517 (tp) REVERT: 7 247 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7432 (ttp80) REVERT: 7 449 LYS cc_start: 0.7134 (mtmt) cc_final: 0.6687 (tmtp) REVERT: 7 498 MET cc_start: 0.6083 (ptt) cc_final: 0.5790 (mtm) REVERT: 7 502 VAL cc_start: 0.4905 (OUTLIER) cc_final: 0.4393 (t) REVERT: 7 537 ILE cc_start: 0.7852 (mt) cc_final: 0.7574 (tt) REVERT: 7 598 PHE cc_start: 0.8289 (m-80) cc_final: 0.7940 (m-80) REVERT: 7 714 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6725 (tm-30) REVERT: B 198 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7275 (mp) REVERT: B 267 MET cc_start: 0.7110 (mmm) cc_final: 0.6821 (mmm) REVERT: B 269 LYS cc_start: 0.6405 (ttmm) cc_final: 0.5084 (mppt) REVERT: B 378 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5548 (tm-30) REVERT: B 496 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6815 (ttmm) REVERT: B 626 GLN cc_start: 0.7736 (mt0) cc_final: 0.7530 (mm110) REVERT: B 690 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5798 (mp0) REVERT: B 705 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.5855 (mtp180) REVERT: B 829 VAL cc_start: 0.6568 (m) cc_final: 0.6305 (m) REVERT: B 834 LEU cc_start: 0.6920 (mm) cc_final: 0.6261 (tp) REVERT: C 36 THR cc_start: 0.7313 (p) cc_final: 0.6979 (m) REVERT: C 39 ARG cc_start: 0.7219 (ttm110) cc_final: 0.6574 (ttp-110) REVERT: C 48 TYR cc_start: 0.7444 (t80) cc_final: 0.7209 (t80) REVERT: C 51 ASN cc_start: 0.6416 (m-40) cc_final: 0.6170 (m110) REVERT: C 188 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7573 (mttt) REVERT: C 205 LYS cc_start: 0.8086 (mmtm) cc_final: 0.7610 (mtpt) REVERT: C 222 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8064 (p) REVERT: C 234 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6076 (mp0) REVERT: C 235 ASP cc_start: 0.6955 (p0) cc_final: 0.6619 (p0) REVERT: C 237 GLU cc_start: 0.7120 (mp0) cc_final: 0.6637 (mt-10) REVERT: C 348 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6455 (mtt90) REVERT: C 477 LYS cc_start: 0.7152 (mttm) cc_final: 0.6645 (mttp) REVERT: C 505 THR cc_start: 0.8430 (t) cc_final: 0.7995 (m) REVERT: C 556 ILE cc_start: 0.7269 (pt) cc_final: 0.6883 (mm) REVERT: C 656 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7524 (tp) REVERT: C 664 LYS cc_start: 0.7653 (mtpp) cc_final: 0.7228 (mtpt) REVERT: C 681 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7582 (tmmm) REVERT: C 723 LYS cc_start: 0.7265 (pttt) cc_final: 0.6772 (tttp) REVERT: D 235 GLU cc_start: 0.6433 (mt-10) cc_final: 0.5765 (tp30) REVERT: D 302 LYS cc_start: 0.7517 (mmtp) cc_final: 0.7069 (mtpp) REVERT: D 408 ASP cc_start: 0.7425 (m-30) cc_final: 0.7071 (m-30) REVERT: D 445 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6941 (mtt180) REVERT: D 483 GLN cc_start: 0.6910 (tp40) cc_final: 0.6157 (mt0) REVERT: D 534 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7126 (tp30) REVERT: D 693 ASP cc_start: 0.6548 (t0) cc_final: 0.5812 (p0) REVERT: D 726 ASN cc_start: 0.6997 (m-40) cc_final: 0.6767 (m-40) REVERT: D 730 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5449 (mt-10) REVERT: D 779 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6943 (ptmt) REVERT: E 5 ARG cc_start: 0.7535 (ttp80) cc_final: 0.6990 (ttp-110) REVERT: E 29 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7747 (mtpt) REVERT: E 33 ASN cc_start: 0.7333 (m-40) cc_final: 0.7110 (m110) REVERT: E 209 ARG cc_start: 0.7219 (mmm-85) cc_final: 0.6849 (mmt-90) REVERT: E 249 LYS cc_start: 0.7701 (mmtp) cc_final: 0.7423 (mppt) REVERT: E 280 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7702 (mtp85) REVERT: E 337 VAL cc_start: 0.1846 (OUTLIER) cc_final: 0.1546 (t) REVERT: E 354 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6231 (mm-30) REVERT: E 404 MET cc_start: 0.7352 (ttm) cc_final: 0.6068 (mmp) REVERT: E 458 MET cc_start: 0.5857 (mtp) cc_final: 0.5530 (mtm) REVERT: E 469 MET cc_start: 0.7957 (mmm) cc_final: 0.7411 (mmm) REVERT: E 564 ARG cc_start: 0.6806 (ttt180) cc_final: 0.5900 (ttm-80) REVERT: E 592 SER cc_start: 0.6465 (m) cc_final: 0.6129 (p) REVERT: E 593 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6476 (mt-10) REVERT: E 597 GLU cc_start: 0.6235 (pm20) cc_final: 0.5788 (mm-30) REVERT: E 614 LEU cc_start: 0.7669 (mt) cc_final: 0.7439 (mt) REVERT: E 661 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6706 (mt-10) REVERT: F 168 MET cc_start: 0.6313 (mmm) cc_final: 0.6100 (mmt) REVERT: F 313 MET cc_start: 0.4057 (mpt) cc_final: 0.2477 (ptt) REVERT: F 319 ASP cc_start: 0.5843 (t0) cc_final: 0.5601 (t0) REVERT: F 352 ARG cc_start: 0.6989 (mtp85) cc_final: 0.6628 (mmm160) REVERT: F 362 GLN cc_start: 0.8414 (tt0) cc_final: 0.7949 (tt0) REVERT: F 737 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7256 (mttt) REVERT: G 15 ASN cc_start: 0.7408 (m-40) cc_final: 0.7201 (m110) REVERT: G 187 ASP cc_start: 0.6775 (t0) cc_final: 0.6187 (m-30) REVERT: G 247 ARG cc_start: 0.8113 (ttt90) cc_final: 0.7647 (ttp80) REVERT: G 291 GLN cc_start: 0.7899 (mt0) cc_final: 0.7627 (mt0) REVERT: G 297 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: G 402 MET cc_start: 0.5766 (tmm) cc_final: 0.4980 (mmm) REVERT: G 412 ASN cc_start: 0.7516 (t0) cc_final: 0.6948 (m-40) REVERT: G 427 ASP cc_start: 0.7730 (m-30) cc_final: 0.7484 (m-30) REVERT: G 502 VAL cc_start: 0.5562 (OUTLIER) cc_final: 0.5331 (t) REVERT: G 556 THR cc_start: 0.8062 (t) cc_final: 0.7669 (m) REVERT: G 575 ASN cc_start: 0.6834 (OUTLIER) cc_final: 0.6578 (p0) REVERT: G 583 ASN cc_start: 0.7043 (p0) cc_final: 0.6781 (p0) REVERT: G 607 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6847 (m-30) REVERT: G 618 TYR cc_start: 0.7554 (t80) cc_final: 0.7106 (t80) REVERT: G 690 LEU cc_start: 0.8529 (mt) cc_final: 0.8275 (mt) REVERT: H 31 ASN cc_start: 0.3806 (p0) cc_final: 0.3597 (m-40) REVERT: H 51 LYS cc_start: 0.3041 (tttt) cc_final: 0.2801 (ttpm) REVERT: H 141 LYS cc_start: 0.3493 (mmmt) cc_final: 0.3240 (ttmt) REVERT: H 173 LEU cc_start: 0.1881 (mt) cc_final: 0.1552 (pp) REVERT: H 282 ARG cc_start: 0.5326 (ttm-80) cc_final: 0.5079 (ttm-80) REVERT: H 284 PHE cc_start: 0.5155 (m-80) cc_final: 0.4860 (m-80) REVERT: H 319 MET cc_start: 0.4073 (OUTLIER) cc_final: 0.3646 (tpp) REVERT: H 322 SER cc_start: 0.4455 (m) cc_final: 0.4002 (p) REVERT: H 332 LEU cc_start: 0.6214 (mt) cc_final: 0.5816 (tp) REVERT: H 342 ARG cc_start: 0.5231 (ttp-110) cc_final: 0.4613 (ttp80) REVERT: H 398 PHE cc_start: 0.3427 (t80) cc_final: 0.3190 (t80) REVERT: H 402 GLU cc_start: 0.2621 (OUTLIER) cc_final: 0.2402 (mm-30) REVERT: H 426 TYR cc_start: 0.3014 (t80) cc_final: 0.1599 (p90) REVERT: H 452 MET cc_start: 0.6201 (mmp) cc_final: 0.5971 (mmt) REVERT: I 120 MET cc_start: 0.2124 (pp-130) cc_final: 0.0635 (mpt) REVERT: I 152 LYS cc_start: 0.4016 (mttt) cc_final: 0.3669 (ttpt) REVERT: I 155 PHE cc_start: 0.2878 (OUTLIER) cc_final: 0.2636 (m-80) REVERT: I 158 LEU cc_start: 0.3233 (tt) cc_final: 0.2693 (mp) REVERT: I 325 LYS cc_start: 0.3632 (mppt) cc_final: 0.3276 (ttpp) REVERT: I 382 MET cc_start: 0.2403 (mmp) cc_final: 0.1561 (ptp) REVERT: I 662 GLU cc_start: 0.6414 (tt0) cc_final: 0.6015 (tp30) REVERT: I 672 GLU cc_start: 0.5593 (pm20) cc_final: 0.5338 (pm20) REVERT: I 697 ILE cc_start: 0.2985 (mm) cc_final: 0.2743 (mm) outliers start: 281 outliers final: 115 residues processed: 1136 average time/residue: 1.5509 time to fit residues: 2274.6766 Evaluate side-chains 1038 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 880 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 358 GLU Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 592 GLU Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 661 LEU Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 537 ASP Chi-restraints excluded: chain 4 residue 232 GLU Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 686 LEU Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 102 SER Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 177 THR Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 404 MET Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 592 SER Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 501 GLN Chi-restraints excluded: chain 6 residue 518 GLU Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 124 ASN Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 297 GLN Chi-restraints excluded: chain 7 residue 329 ARG Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 506 MET Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 737 LYS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 575 ASN Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 607 ASP Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 402 GLU Chi-restraints excluded: chain I residue 155 PHE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 519 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 764 optimal weight: 10.0000 chunk 581 optimal weight: 0.0170 chunk 401 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 369 optimal weight: 0.9990 chunk 519 optimal weight: 7.9990 chunk 776 optimal weight: 2.9990 chunk 821 optimal weight: 7.9990 chunk 405 optimal weight: 1.9990 chunk 735 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 666 ASN 2 856 GLN 3 324 ASN 3 340 GLN 3 587 ASN 4 613 GLN ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 587 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN 7 297 GLN B 433 ASN ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN D 327 ASN D 413 HIS E 334 GLN E 359 GLN ** E 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 GLN F 347 ASN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 698 ASN ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 623 ASN ** I 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 69476 Z= 0.221 Angle : 0.569 11.086 93996 Z= 0.294 Chirality : 0.044 0.258 10834 Planarity : 0.005 0.058 12062 Dihedral : 7.446 173.776 9632 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.44 % Favored : 97.52 % Rotamer: Outliers : 4.12 % Allowed : 15.92 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.40 (0.09), residues: 8483 helix: 1.11 (0.09), residues: 3535 sheet: -0.26 (0.12), residues: 1582 loop : -0.23 (0.10), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 112 HIS 0.010 0.001 HIS 6 653 PHE 0.026 0.002 PHE C 345 TYR 0.021 0.002 TYR 6 136 ARG 0.008 0.000 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 938 time to evaluate : 6.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5716 (mt-10) REVERT: 2 232 ARG cc_start: 0.6582 (mmm-85) cc_final: 0.5959 (mtp180) REVERT: 2 326 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6260 (pmt170) REVERT: 2 358 GLU cc_start: 0.5712 (OUTLIER) cc_final: 0.4641 (tm-30) REVERT: 2 374 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5356 (ttm110) REVERT: 2 422 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6670 (pp20) REVERT: 2 651 ASN cc_start: 0.8151 (m-40) cc_final: 0.7619 (m-40) REVERT: 2 667 VAL cc_start: 0.7159 (OUTLIER) cc_final: 0.6799 (p) REVERT: 2 684 ARG cc_start: 0.3927 (OUTLIER) cc_final: 0.3061 (ptp90) REVERT: 2 686 LEU cc_start: 0.4805 (pt) cc_final: 0.4338 (mt) REVERT: 2 777 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.6510 (tppt) REVERT: 2 789 VAL cc_start: 0.8066 (p) cc_final: 0.7769 (t) REVERT: 2 798 ILE cc_start: 0.5287 (mt) cc_final: 0.4858 (pt) REVERT: 2 847 ASP cc_start: 0.6758 (t0) cc_final: 0.6491 (t0) REVERT: 3 27 ARG cc_start: 0.7916 (tpt170) cc_final: 0.7091 (ttp80) REVERT: 3 188 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7242 (ttpt) REVERT: 3 208 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7397 (mtp180) REVERT: 3 234 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6044 (tm-30) REVERT: 3 261 MET cc_start: 0.7924 (mtm) cc_final: 0.7543 (mtt) REVERT: 3 274 ILE cc_start: 0.8780 (pt) cc_final: 0.8209 (tt) REVERT: 3 318 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7207 (tmtt) REVERT: 3 353 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8613 (mm) REVERT: 3 357 LYS cc_start: 0.7194 (pmtt) cc_final: 0.6423 (ptpt) REVERT: 3 365 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6829 (OUTLIER) REVERT: 3 482 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6086 (t70) REVERT: 3 497 ILE cc_start: 0.7541 (pt) cc_final: 0.7302 (mt) REVERT: 3 688 ASN cc_start: 0.7422 (m110) cc_final: 0.7053 (m110) REVERT: 4 266 GLN cc_start: 0.7647 (tp40) cc_final: 0.7411 (tp-100) REVERT: 4 296 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7536 (mm) REVERT: 4 404 ASP cc_start: 0.6800 (m-30) cc_final: 0.6403 (m-30) REVERT: 4 579 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7442 (mm-40) REVERT: 4 583 LYS cc_start: 0.8008 (mmpt) cc_final: 0.7536 (mtmm) REVERT: 4 636 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7555 (mtpt) REVERT: 4 715 LYS cc_start: 0.7017 (pttp) cc_final: 0.6363 (tppp) REVERT: 4 726 ASN cc_start: 0.7576 (m-40) cc_final: 0.7155 (t0) REVERT: 4 756 GLU cc_start: 0.7602 (tt0) cc_final: 0.7316 (tp30) REVERT: 5 29 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7273 (mtmp) REVERT: 5 72 ASN cc_start: 0.7676 (t0) cc_final: 0.7386 (t0) REVERT: 5 139 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8349 (pp) REVERT: 5 184 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6290 (mtm-85) REVERT: 5 279 ASP cc_start: 0.7293 (p0) cc_final: 0.7038 (p0) REVERT: 5 358 LEU cc_start: 0.5395 (mt) cc_final: 0.5103 (tm) REVERT: 5 369 ILE cc_start: 0.7948 (pt) cc_final: 0.7372 (tt) REVERT: 5 388 ILE cc_start: 0.8239 (mt) cc_final: 0.7989 (mm) REVERT: 5 404 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.5760 (mmp) REVERT: 5 469 MET cc_start: 0.7562 (mmm) cc_final: 0.7267 (mmm) REVERT: 5 556 VAL cc_start: 0.6593 (t) cc_final: 0.6282 (p) REVERT: 5 581 ASN cc_start: 0.5672 (t0) cc_final: 0.4644 (m-40) REVERT: 5 654 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: 5 689 MET cc_start: 0.7076 (mmm) cc_final: 0.6787 (mmm) REVERT: 6 174 TYR cc_start: 0.7973 (t80) cc_final: 0.7392 (t80) REVERT: 6 299 GLU cc_start: 0.7118 (pm20) cc_final: 0.6291 (mt-10) REVERT: 6 328 THR cc_start: 0.6416 (p) cc_final: 0.6200 (p) REVERT: 6 347 ASN cc_start: 0.6737 (t0) cc_final: 0.5987 (m-40) REVERT: 6 367 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7802 (mt-10) REVERT: 6 518 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5521 (tm-30) REVERT: 6 561 GLU cc_start: 0.5964 (pt0) cc_final: 0.5677 (mt-10) REVERT: 6 614 ARG cc_start: 0.6527 (ttp-170) cc_final: 0.6176 (ttm110) REVERT: 6 653 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6544 (p-80) REVERT: 6 675 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7363 (mpp-170) REVERT: 6 696 ARG cc_start: 0.6871 (tpt90) cc_final: 0.6127 (tmt170) REVERT: 6 724 ASP cc_start: 0.7155 (m-30) cc_final: 0.6765 (m-30) REVERT: 6 750 GLN cc_start: 0.6162 (OUTLIER) cc_final: 0.5917 (pm20) REVERT: 6 764 ILE cc_start: 0.7362 (mt) cc_final: 0.6735 (pp) REVERT: 6 783 ASP cc_start: 0.5891 (t0) cc_final: 0.5596 (t0) REVERT: 6 794 ARG cc_start: 0.5761 (mtp-110) cc_final: 0.4756 (mtm110) REVERT: 6 833 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6613 (mp10) REVERT: 7 64 MET cc_start: 0.8639 (mmt) cc_final: 0.8432 (mmt) REVERT: 7 69 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7721 (mtpp) REVERT: 7 76 ASN cc_start: 0.7806 (t0) cc_final: 0.7392 (m110) REVERT: 7 81 ASP cc_start: 0.7834 (m-30) cc_final: 0.7415 (t0) REVERT: 7 124 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.6912 (p0) REVERT: 7 159 ASN cc_start: 0.7380 (m-40) cc_final: 0.7005 (m110) REVERT: 7 160 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6126 (pt0) REVERT: 7 162 ARG cc_start: 0.7134 (ttm-80) cc_final: 0.6894 (ttt90) REVERT: 7 188 GLU cc_start: 0.6233 (tt0) cc_final: 0.5844 (tt0) REVERT: 7 244 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8524 (tp) REVERT: 7 247 ARG cc_start: 0.7880 (tpp80) cc_final: 0.7400 (ttp80) REVERT: 7 449 LYS cc_start: 0.7167 (mtmt) cc_final: 0.6737 (tmtp) REVERT: 7 502 VAL cc_start: 0.4984 (OUTLIER) cc_final: 0.4568 (t) REVERT: 7 537 ILE cc_start: 0.7835 (mt) cc_final: 0.7568 (tt) REVERT: 7 598 PHE cc_start: 0.8292 (m-80) cc_final: 0.7984 (m-80) REVERT: 7 714 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6553 (tm-30) REVERT: B 194 TYR cc_start: 0.6541 (m-10) cc_final: 0.6301 (m-10) REVERT: B 198 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7360 (mp) REVERT: B 267 MET cc_start: 0.7134 (mmm) cc_final: 0.6824 (mmm) REVERT: B 269 LYS cc_start: 0.6343 (ttmm) cc_final: 0.5024 (mppt) REVERT: B 273 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6772 (mt) REVERT: B 378 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.5536 (tm-30) REVERT: B 496 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6785 (ttmm) REVERT: B 611 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7276 (ptpt) REVERT: B 626 GLN cc_start: 0.7744 (mt0) cc_final: 0.7509 (mm110) REVERT: B 705 ARG cc_start: 0.6285 (OUTLIER) cc_final: 0.5903 (mtp180) REVERT: B 788 ARG cc_start: 0.7213 (tpp-160) cc_final: 0.6914 (mmp80) REVERT: B 829 VAL cc_start: 0.6587 (m) cc_final: 0.6335 (m) REVERT: B 834 LEU cc_start: 0.6895 (mm) cc_final: 0.6275 (tp) REVERT: C 36 THR cc_start: 0.7212 (p) cc_final: 0.6872 (m) REVERT: C 51 ASN cc_start: 0.6280 (m-40) cc_final: 0.6029 (m110) REVERT: C 188 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7696 (mttp) REVERT: C 205 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7610 (mtpt) REVERT: C 222 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8108 (p) REVERT: C 234 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6109 (mp0) REVERT: C 235 ASP cc_start: 0.7019 (p0) cc_final: 0.6684 (p0) REVERT: C 237 GLU cc_start: 0.7093 (mp0) cc_final: 0.6674 (mt-10) REVERT: C 348 ARG cc_start: 0.6985 (mtm110) cc_final: 0.6455 (mtt90) REVERT: C 464 LEU cc_start: 0.7967 (mt) cc_final: 0.7614 (mt) REVERT: C 477 LYS cc_start: 0.7157 (mttm) cc_final: 0.6683 (mttm) REVERT: C 505 THR cc_start: 0.8480 (t) cc_final: 0.8058 (m) REVERT: C 556 ILE cc_start: 0.7194 (pt) cc_final: 0.6825 (mm) REVERT: C 656 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7510 (tp) REVERT: C 664 LYS cc_start: 0.7665 (mtpp) cc_final: 0.7233 (mtpt) REVERT: C 681 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7556 (tmmm) REVERT: C 723 LYS cc_start: 0.7173 (pttt) cc_final: 0.6721 (tttp) REVERT: D 235 GLU cc_start: 0.6389 (mt-10) cc_final: 0.5706 (tp30) REVERT: D 302 LYS cc_start: 0.7555 (mmtp) cc_final: 0.7088 (mtpp) REVERT: D 394 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8540 (tmtp) REVERT: D 408 ASP cc_start: 0.7490 (m-30) cc_final: 0.7171 (m-30) REVERT: D 445 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6966 (mtt180) REVERT: D 483 GLN cc_start: 0.6944 (tp40) cc_final: 0.6165 (mt0) REVERT: D 534 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7031 (tp30) REVERT: D 690 GLU cc_start: 0.6516 (tt0) cc_final: 0.6151 (tp30) REVERT: D 693 ASP cc_start: 0.6537 (t0) cc_final: 0.5845 (p0) REVERT: D 715 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.5969 (ptmm) REVERT: D 779 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6889 (ptmt) REVERT: D 830 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6513 (mtp180) REVERT: E 5 ARG cc_start: 0.7473 (ttp80) cc_final: 0.7002 (ttp-110) REVERT: E 33 ASN cc_start: 0.7354 (m-40) cc_final: 0.7111 (m110) REVERT: E 77 LYS cc_start: 0.8023 (mttm) cc_final: 0.7700 (mtpp) REVERT: E 144 ASN cc_start: 0.7155 (OUTLIER) cc_final: 0.6770 (t0) REVERT: E 146 ILE cc_start: 0.7549 (pt) cc_final: 0.7322 (pt) REVERT: E 209 ARG cc_start: 0.7082 (mmm-85) cc_final: 0.6732 (mmt180) REVERT: E 249 LYS cc_start: 0.7694 (mmtp) cc_final: 0.7195 (mppt) REVERT: E 280 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7708 (mtp85) REVERT: E 354 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6074 (mm-30) REVERT: E 368 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6397 (tt0) REVERT: E 404 MET cc_start: 0.7307 (ttm) cc_final: 0.6109 (mmp) REVERT: E 458 MET cc_start: 0.5919 (mtp) cc_final: 0.5496 (mtm) REVERT: E 469 MET cc_start: 0.7957 (mmm) cc_final: 0.7399 (mmm) REVERT: E 497 MET cc_start: 0.8414 (mtm) cc_final: 0.8138 (mtm) REVERT: E 557 LYS cc_start: 0.5668 (mmmt) cc_final: 0.5205 (tmtm) REVERT: E 564 ARG cc_start: 0.6803 (ttt180) cc_final: 0.5902 (ttm-80) REVERT: E 592 SER cc_start: 0.6541 (m) cc_final: 0.6179 (p) REVERT: E 593 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6370 (mt-10) REVERT: E 597 GLU cc_start: 0.6270 (pm20) cc_final: 0.5812 (mm-30) REVERT: E 661 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6699 (mt-10) REVERT: F 313 MET cc_start: 0.4290 (mpt) cc_final: 0.2731 (ptt) REVERT: F 352 ARG cc_start: 0.7017 (mtp85) cc_final: 0.6664 (mmm160) REVERT: F 362 GLN cc_start: 0.8390 (tt0) cc_final: 0.7909 (tt0) REVERT: F 421 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6538 (mm) REVERT: F 446 ARG cc_start: 0.7469 (ptt90) cc_final: 0.7224 (ptt90) REVERT: F 737 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7165 (mttt) REVERT: G 187 ASP cc_start: 0.6793 (t0) cc_final: 0.6283 (m-30) REVERT: G 247 ARG cc_start: 0.8086 (ttt90) cc_final: 0.7633 (ttp80) REVERT: G 291 GLN cc_start: 0.7914 (mt0) cc_final: 0.7669 (mt0) REVERT: G 297 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: G 412 ASN cc_start: 0.7593 (t0) cc_final: 0.7011 (m-40) REVERT: G 427 ASP cc_start: 0.7684 (m-30) cc_final: 0.7440 (m-30) REVERT: G 484 THR cc_start: 0.7316 (m) cc_final: 0.6721 (p) REVERT: G 502 VAL cc_start: 0.5787 (OUTLIER) cc_final: 0.5564 (t) REVERT: G 556 THR cc_start: 0.8084 (t) cc_final: 0.7689 (m) REVERT: G 583 ASN cc_start: 0.7054 (p0) cc_final: 0.6767 (p0) REVERT: G 607 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6939 (m-30) REVERT: G 612 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6928 (tp) REVERT: G 618 TYR cc_start: 0.7541 (t80) cc_final: 0.7116 (t80) REVERT: G 690 LEU cc_start: 0.8536 (mt) cc_final: 0.8262 (mt) REVERT: H 138 LYS cc_start: 0.3273 (mmmt) cc_final: 0.2150 (tptm) REVERT: H 164 ILE cc_start: 0.4914 (OUTLIER) cc_final: 0.4534 (mp) REVERT: H 173 LEU cc_start: 0.2186 (mt) cc_final: 0.1638 (pp) REVERT: H 284 PHE cc_start: 0.5241 (m-80) cc_final: 0.4875 (m-80) REVERT: H 319 MET cc_start: 0.4048 (OUTLIER) cc_final: 0.3619 (tpp) REVERT: H 332 LEU cc_start: 0.6238 (mt) cc_final: 0.5831 (tp) REVERT: I 120 MET cc_start: 0.2478 (OUTLIER) cc_final: 0.0678 (mpt) REVERT: I 152 LYS cc_start: 0.4007 (mttt) cc_final: 0.3673 (tppt) REVERT: I 155 PHE cc_start: 0.2832 (OUTLIER) cc_final: 0.2626 (m-80) REVERT: I 158 LEU cc_start: 0.3043 (tt) cc_final: 0.2251 (mm) REVERT: I 325 LYS cc_start: 0.3568 (mppt) cc_final: 0.3186 (ttpp) REVERT: I 341 ARG cc_start: 0.3917 (mtt90) cc_final: 0.3349 (mmm160) REVERT: I 382 MET cc_start: 0.2225 (mmp) cc_final: 0.1506 (ptp) REVERT: I 662 GLU cc_start: 0.6456 (tt0) cc_final: 0.6065 (tp30) REVERT: I 672 GLU cc_start: 0.5653 (pm20) cc_final: 0.5362 (pm20) outliers start: 313 outliers final: 132 residues processed: 1154 average time/residue: 1.5593 time to fit residues: 2327.8810 Evaluate side-chains 1052 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 863 time to evaluate : 5.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 358 GLU Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 396 THR Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 670 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 208 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 537 ASP Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 4 residue 490 VAL Chi-restraints excluded: chain 4 residue 636 LYS Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 102 SER Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 177 THR Chi-restraints excluded: chain 5 residue 184 ARG Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 404 MET Chi-restraints excluded: chain 5 residue 509 ILE Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 592 SER Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 501 GLN Chi-restraints excluded: chain 6 residue 518 GLU Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 6 residue 750 GLN Chi-restraints excluded: chain 6 residue 767 LYS Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 124 ASN Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 329 ARG Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain 7 residue 710 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 830 ARG Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 645 ASP Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 737 LYS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 607 ASP Chi-restraints excluded: chain G residue 612 LEU Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 155 PHE Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 696 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 684 optimal weight: 2.9990 chunk 466 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 611 optimal weight: 9.9990 chunk 339 optimal weight: 2.9990 chunk 701 optimal weight: 7.9990 chunk 567 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 419 optimal weight: 7.9990 chunk 737 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 666 ASN 3 324 ASN 3 340 GLN 3 587 ASN ** 3 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 613 GLN ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 587 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN C 492 GLN ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 253 GLN E 685 GLN F 347 ASN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 623 ASN H 367 ASN ** I 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 673 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 69476 Z= 0.225 Angle : 0.570 10.744 93996 Z= 0.294 Chirality : 0.044 0.241 10834 Planarity : 0.004 0.058 12062 Dihedral : 7.338 175.398 9630 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.52 % Favored : 97.45 % Rotamer: Outliers : 4.33 % Allowed : 16.93 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.09), residues: 8483 helix: 1.17 (0.09), residues: 3537 sheet: -0.29 (0.12), residues: 1578 loop : -0.22 (0.10), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 112 HIS 0.010 0.001 HIS 6 653 PHE 0.024 0.002 PHE I 702 TYR 0.021 0.002 TYR 6 136 ARG 0.008 0.000 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 923 time to evaluate : 6.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5722 (mt-10) REVERT: 2 232 ARG cc_start: 0.6596 (mmm-85) cc_final: 0.5959 (mtp180) REVERT: 2 326 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6318 (pmt170) REVERT: 2 358 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.4627 (tm-30) REVERT: 2 374 ARG cc_start: 0.6149 (OUTLIER) cc_final: 0.5351 (ttm110) REVERT: 2 422 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6618 (pp20) REVERT: 2 651 ASN cc_start: 0.8149 (m-40) cc_final: 0.7628 (m-40) REVERT: 2 667 VAL cc_start: 0.7004 (OUTLIER) cc_final: 0.6660 (p) REVERT: 2 684 ARG cc_start: 0.3924 (OUTLIER) cc_final: 0.3100 (ptp90) REVERT: 2 686 LEU cc_start: 0.4852 (pt) cc_final: 0.4238 (mt) REVERT: 2 789 VAL cc_start: 0.8115 (p) cc_final: 0.7825 (t) REVERT: 2 798 ILE cc_start: 0.5338 (mt) cc_final: 0.4886 (pt) REVERT: 2 847 ASP cc_start: 0.6900 (t0) cc_final: 0.6623 (t0) REVERT: 3 23 ASP cc_start: 0.7472 (m-30) cc_final: 0.7271 (m-30) REVERT: 3 188 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7253 (ttpt) REVERT: 3 208 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7341 (mtp180) REVERT: 3 234 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6020 (tm-30) REVERT: 3 274 ILE cc_start: 0.8709 (pt) cc_final: 0.8206 (tt) REVERT: 3 315 ILE cc_start: 0.5149 (OUTLIER) cc_final: 0.4787 (mm) REVERT: 3 318 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7219 (tmtt) REVERT: 3 353 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8602 (mm) REVERT: 3 357 LYS cc_start: 0.7146 (pmtt) cc_final: 0.6447 (ptpt) REVERT: 3 365 GLN cc_start: 0.7345 (mm-40) cc_final: 0.6882 (mm110) REVERT: 3 455 ARG cc_start: 0.5967 (mmm160) cc_final: 0.5647 (mtt180) REVERT: 3 482 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6139 (t70) REVERT: 4 266 GLN cc_start: 0.7645 (tp40) cc_final: 0.7381 (tp-100) REVERT: 4 296 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7621 (mm) REVERT: 4 302 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7260 (ptpt) REVERT: 4 404 ASP cc_start: 0.6801 (m-30) cc_final: 0.6408 (m-30) REVERT: 4 411 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8011 (p) REVERT: 4 534 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: 4 579 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7444 (mm-40) REVERT: 4 583 LYS cc_start: 0.8150 (mmpt) cc_final: 0.7597 (mtmm) REVERT: 4 636 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7558 (mtpt) REVERT: 4 715 LYS cc_start: 0.7043 (pttp) cc_final: 0.6460 (mmtp) REVERT: 4 726 ASN cc_start: 0.7605 (m-40) cc_final: 0.7194 (t0) REVERT: 4 756 GLU cc_start: 0.7548 (tt0) cc_final: 0.7251 (tp30) REVERT: 5 29 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7321 (mtmp) REVERT: 5 72 ASN cc_start: 0.7681 (t0) cc_final: 0.7412 (t0) REVERT: 5 139 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8332 (pp) REVERT: 5 358 LEU cc_start: 0.5425 (mt) cc_final: 0.5114 (tm) REVERT: 5 369 ILE cc_start: 0.7940 (pt) cc_final: 0.7417 (tt) REVERT: 5 388 ILE cc_start: 0.8238 (mt) cc_final: 0.8002 (mm) REVERT: 5 404 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.5751 (mmm) REVERT: 5 469 MET cc_start: 0.7623 (mmm) cc_final: 0.7289 (mmm) REVERT: 5 556 VAL cc_start: 0.6552 (t) cc_final: 0.6240 (p) REVERT: 5 581 ASN cc_start: 0.5435 (t0) cc_final: 0.4563 (m-40) REVERT: 5 654 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6972 (mt-10) REVERT: 5 675 ARG cc_start: 0.7294 (ttp80) cc_final: 0.7003 (ptt90) REVERT: 5 689 MET cc_start: 0.7107 (mmm) cc_final: 0.6754 (mmm) REVERT: 6 174 TYR cc_start: 0.7991 (t80) cc_final: 0.7381 (t80) REVERT: 6 299 GLU cc_start: 0.7111 (pm20) cc_final: 0.6341 (mt-10) REVERT: 6 347 ASN cc_start: 0.6735 (t0) cc_final: 0.5979 (m-40) REVERT: 6 561 GLU cc_start: 0.5966 (pt0) cc_final: 0.5674 (mt-10) REVERT: 6 614 ARG cc_start: 0.6599 (ttp-170) cc_final: 0.6183 (ttm110) REVERT: 6 675 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7387 (mpp-170) REVERT: 6 696 ARG cc_start: 0.6811 (tpt90) cc_final: 0.6401 (tpt90) REVERT: 6 724 ASP cc_start: 0.7167 (m-30) cc_final: 0.6774 (m-30) REVERT: 6 764 ILE cc_start: 0.7356 (mt) cc_final: 0.6744 (pp) REVERT: 6 783 ASP cc_start: 0.5752 (t0) cc_final: 0.5542 (t0) REVERT: 6 833 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6655 (mp10) REVERT: 7 8 ILE cc_start: 0.8513 (pt) cc_final: 0.8274 (tt) REVERT: 7 64 MET cc_start: 0.8614 (mmt) cc_final: 0.8411 (mmt) REVERT: 7 69 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7733 (mtpp) REVERT: 7 76 ASN cc_start: 0.7827 (t0) cc_final: 0.7408 (m110) REVERT: 7 81 ASP cc_start: 0.7806 (m-30) cc_final: 0.7411 (t0) REVERT: 7 124 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.6967 (p0) REVERT: 7 159 ASN cc_start: 0.7389 (m-40) cc_final: 0.7021 (m110) REVERT: 7 160 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6209 (pt0) REVERT: 7 162 ARG cc_start: 0.7182 (ttm-80) cc_final: 0.6907 (ttt90) REVERT: 7 188 GLU cc_start: 0.6349 (tt0) cc_final: 0.5930 (tt0) REVERT: 7 244 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8520 (tp) REVERT: 7 247 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7436 (ttp80) REVERT: 7 449 LYS cc_start: 0.7227 (mtmt) cc_final: 0.6797 (tmtp) REVERT: 7 502 VAL cc_start: 0.4992 (OUTLIER) cc_final: 0.4525 (t) REVERT: 7 537 ILE cc_start: 0.7765 (mt) cc_final: 0.7534 (tt) REVERT: 7 598 PHE cc_start: 0.8341 (m-80) cc_final: 0.8074 (m-80) REVERT: 7 714 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6452 (tm-30) REVERT: B 184 GLU cc_start: 0.4622 (mm-30) cc_final: 0.4097 (tm-30) REVERT: B 198 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7363 (mp) REVERT: B 247 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6673 (mtm180) REVERT: B 267 MET cc_start: 0.7221 (mmm) cc_final: 0.6871 (mmm) REVERT: B 269 LYS cc_start: 0.6360 (ttmm) cc_final: 0.5009 (mppt) REVERT: B 378 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5542 (tm-30) REVERT: B 496 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6750 (ttmm) REVERT: B 536 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7507 (p0) REVERT: B 705 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5915 (mtp180) REVERT: B 788 ARG cc_start: 0.7258 (tpp-160) cc_final: 0.6979 (mmp80) REVERT: B 793 LEU cc_start: 0.6990 (pp) cc_final: 0.6567 (mp) REVERT: B 829 VAL cc_start: 0.6607 (m) cc_final: 0.6397 (m) REVERT: B 834 LEU cc_start: 0.6840 (mm) cc_final: 0.6245 (tp) REVERT: C 36 THR cc_start: 0.7181 (p) cc_final: 0.6833 (m) REVERT: C 51 ASN cc_start: 0.6065 (m-40) cc_final: 0.5844 (m110) REVERT: C 188 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7679 (mttp) REVERT: C 205 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7610 (mtpt) REVERT: C 222 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8147 (p) REVERT: C 234 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6131 (mp0) REVERT: C 235 ASP cc_start: 0.7068 (p0) cc_final: 0.6712 (p0) REVERT: C 237 GLU cc_start: 0.7048 (mp0) cc_final: 0.6645 (mt-10) REVERT: C 348 ARG cc_start: 0.6961 (mtm110) cc_final: 0.6401 (mtt90) REVERT: C 456 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.5520 (ppt-90) REVERT: C 464 LEU cc_start: 0.7974 (mt) cc_final: 0.7626 (mt) REVERT: C 477 LYS cc_start: 0.7119 (mttm) cc_final: 0.6636 (mttm) REVERT: C 505 THR cc_start: 0.8479 (t) cc_final: 0.8057 (m) REVERT: C 556 ILE cc_start: 0.7217 (pt) cc_final: 0.6832 (mm) REVERT: C 656 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7501 (tp) REVERT: C 664 LYS cc_start: 0.7703 (mtpp) cc_final: 0.7273 (mtpt) REVERT: C 681 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7552 (tmmm) REVERT: C 723 LYS cc_start: 0.7187 (pttt) cc_final: 0.6702 (ttmm) REVERT: D 235 GLU cc_start: 0.6416 (mt-10) cc_final: 0.5721 (tp30) REVERT: D 302 LYS cc_start: 0.7591 (mmtp) cc_final: 0.7084 (mtpp) REVERT: D 327 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7868 (m110) REVERT: D 394 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8573 (tmtp) REVERT: D 408 ASP cc_start: 0.7564 (m-30) cc_final: 0.7247 (m-30) REVERT: D 445 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7009 (mtt180) REVERT: D 483 GLN cc_start: 0.6972 (tp40) cc_final: 0.6140 (mt0) REVERT: D 534 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7037 (tp30) REVERT: D 690 GLU cc_start: 0.6617 (tt0) cc_final: 0.6065 (tp30) REVERT: D 693 ASP cc_start: 0.6528 (t0) cc_final: 0.5884 (p0) REVERT: D 715 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6101 (ptmm) REVERT: D 730 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5478 (mt-10) REVERT: D 779 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6867 (ptmt) REVERT: D 830 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6514 (mtp180) REVERT: D 847 MET cc_start: 0.5784 (OUTLIER) cc_final: 0.5128 (mmm) REVERT: E 5 ARG cc_start: 0.7491 (ttp80) cc_final: 0.7014 (ttp-110) REVERT: E 29 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7689 (mtpt) REVERT: E 33 ASN cc_start: 0.7340 (m-40) cc_final: 0.7111 (m110) REVERT: E 77 LYS cc_start: 0.8032 (mttm) cc_final: 0.7672 (mtpp) REVERT: E 209 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6881 (mmt180) REVERT: E 249 LYS cc_start: 0.7693 (mmtp) cc_final: 0.7403 (mppt) REVERT: E 354 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6110 (mm-30) REVERT: E 368 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6397 (tt0) REVERT: E 404 MET cc_start: 0.7289 (ttm) cc_final: 0.6899 (tpt) REVERT: E 458 MET cc_start: 0.6016 (mtp) cc_final: 0.5622 (mtm) REVERT: E 469 MET cc_start: 0.7980 (mmm) cc_final: 0.7422 (mmm) REVERT: E 497 MET cc_start: 0.8410 (mtm) cc_final: 0.8078 (mtm) REVERT: E 557 LYS cc_start: 0.5635 (mmmt) cc_final: 0.5185 (tmtm) REVERT: E 564 ARG cc_start: 0.6806 (ttt180) cc_final: 0.5917 (ttm-80) REVERT: E 592 SER cc_start: 0.6563 (m) cc_final: 0.6175 (p) REVERT: E 597 GLU cc_start: 0.6267 (pm20) cc_final: 0.5809 (mm-30) REVERT: E 661 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6608 (mt-10) REVERT: F 190 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.6182 (ttt180) REVERT: F 313 MET cc_start: 0.4350 (mpt) cc_final: 0.3051 (ptm) REVERT: F 362 GLN cc_start: 0.8400 (tt0) cc_final: 0.7920 (tt0) REVERT: F 421 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6567 (mm) REVERT: F 446 ARG cc_start: 0.7460 (ptt90) cc_final: 0.6474 (ptp-110) REVERT: F 654 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6122 (tp30) REVERT: F 737 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7192 (mttt) REVERT: G 130 LYS cc_start: 0.7212 (pttp) cc_final: 0.6946 (ptpt) REVERT: G 187 ASP cc_start: 0.6854 (t0) cc_final: 0.6400 (m-30) REVERT: G 247 ARG cc_start: 0.8039 (ttt90) cc_final: 0.7552 (ttp80) REVERT: G 291 GLN cc_start: 0.7902 (mt0) cc_final: 0.7638 (mm110) REVERT: G 297 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: G 412 ASN cc_start: 0.7555 (t0) cc_final: 0.7017 (m-40) REVERT: G 427 ASP cc_start: 0.7630 (m-30) cc_final: 0.7394 (m-30) REVERT: G 502 VAL cc_start: 0.5855 (OUTLIER) cc_final: 0.5619 (t) REVERT: G 556 THR cc_start: 0.8109 (t) cc_final: 0.7708 (m) REVERT: G 583 ASN cc_start: 0.7077 (p0) cc_final: 0.6828 (p0) REVERT: G 607 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: G 612 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.6968 (tp) REVERT: G 618 TYR cc_start: 0.7464 (t80) cc_final: 0.7126 (t80) REVERT: G 654 GLU cc_start: 0.6119 (mp0) cc_final: 0.5726 (tm-30) REVERT: G 690 LEU cc_start: 0.8530 (mt) cc_final: 0.8249 (mt) REVERT: H 35 LEU cc_start: 0.5370 (tt) cc_final: 0.5011 (tp) REVERT: H 284 PHE cc_start: 0.5253 (m-80) cc_final: 0.4793 (m-80) REVERT: H 319 MET cc_start: 0.4079 (OUTLIER) cc_final: 0.3710 (tpp) REVERT: H 331 GLU cc_start: 0.5435 (mt-10) cc_final: 0.5061 (mt-10) REVERT: H 332 LEU cc_start: 0.6207 (mt) cc_final: 0.5830 (tp) REVERT: I 120 MET cc_start: 0.2524 (OUTLIER) cc_final: 0.0727 (mpt) REVERT: I 152 LYS cc_start: 0.4027 (mttt) cc_final: 0.3673 (ttpt) REVERT: I 155 PHE cc_start: 0.2736 (OUTLIER) cc_final: 0.2520 (m-80) REVERT: I 158 LEU cc_start: 0.2647 (tt) cc_final: 0.1943 (mm) REVERT: I 325 LYS cc_start: 0.3424 (mppt) cc_final: 0.3032 (ttpp) REVERT: I 341 ARG cc_start: 0.3643 (mtt90) cc_final: 0.3083 (mmm160) REVERT: I 365 ILE cc_start: 0.3037 (tt) cc_final: 0.2800 (mp) REVERT: I 382 MET cc_start: 0.2258 (mmp) cc_final: 0.1600 (ptp) REVERT: I 662 GLU cc_start: 0.6537 (tt0) cc_final: 0.6080 (tp30) outliers start: 329 outliers final: 150 residues processed: 1157 average time/residue: 1.5061 time to fit residues: 2262.2592 Evaluate side-chains 1098 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 888 time to evaluate : 5.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 358 GLU Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 670 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 208 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 537 ASP Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 356 MET Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 490 VAL Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 636 LYS Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 102 SER Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 177 THR Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 404 MET Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 592 SER Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 501 GLN Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 6 residue 767 LYS Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 124 ASN Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 329 ARG Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain 7 residue 710 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 456 ARG Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 830 ARG Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 737 LYS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 531 GLU Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 607 ASP Chi-restraints excluded: chain G residue 612 LEU Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 271 ARG Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 298 THR Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 155 PHE Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 665 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 276 optimal weight: 0.0980 chunk 739 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 482 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 822 optimal weight: 1.9990 chunk 682 optimal weight: 4.9990 chunk 380 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 431 optimal weight: 7.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 666 ASN 3 324 ASN 3 487 HIS 3 503 HIS 3 587 ASN 3 682 ASN 4 613 GLN ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 587 GLN 6 366 ASN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 GLN B 666 ASN B 768 HIS C 210 HIS ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 253 GLN D 327 ASN D 685 ASN E 685 GLN F 347 ASN ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 367 ASN ** I 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 69476 Z= 0.244 Angle : 0.583 10.517 93996 Z= 0.300 Chirality : 0.044 0.251 10834 Planarity : 0.005 0.072 12062 Dihedral : 7.284 177.139 9630 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.52 % Favored : 97.45 % Rotamer: Outliers : 4.58 % Allowed : 17.33 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.43 (0.09), residues: 8483 helix: 1.18 (0.09), residues: 3537 sheet: -0.36 (0.12), residues: 1628 loop : -0.21 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 112 HIS 0.010 0.001 HIS 6 653 PHE 0.025 0.002 PHE I 210 TYR 0.021 0.002 TYR 6 136 ARG 0.009 0.001 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 930 time to evaluate : 6.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5765 (mt-10) REVERT: 2 232 ARG cc_start: 0.6568 (mmm-85) cc_final: 0.5937 (mtp180) REVERT: 2 269 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6631 (ttmt) REVERT: 2 326 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6362 (pmt170) REVERT: 2 358 GLU cc_start: 0.5629 (OUTLIER) cc_final: 0.4609 (tm-30) REVERT: 2 374 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5340 (ttm110) REVERT: 2 422 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6624 (pp20) REVERT: 2 626 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7546 (mm110) REVERT: 2 651 ASN cc_start: 0.8118 (m-40) cc_final: 0.7765 (m-40) REVERT: 2 684 ARG cc_start: 0.4020 (OUTLIER) cc_final: 0.3221 (ptp90) REVERT: 2 686 LEU cc_start: 0.4936 (pt) cc_final: 0.4370 (mt) REVERT: 2 787 SER cc_start: 0.6787 (p) cc_final: 0.6577 (t) REVERT: 2 789 VAL cc_start: 0.8155 (p) cc_final: 0.7865 (t) REVERT: 2 798 ILE cc_start: 0.5329 (mt) cc_final: 0.4903 (pt) REVERT: 2 847 ASP cc_start: 0.6903 (t0) cc_final: 0.6629 (t0) REVERT: 3 40 ASP cc_start: 0.6729 (p0) cc_final: 0.6392 (m-30) REVERT: 3 117 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: 3 188 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7182 (ttpt) REVERT: 3 208 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7330 (mtp180) REVERT: 3 234 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6151 (tm-30) REVERT: 3 261 MET cc_start: 0.7908 (mtm) cc_final: 0.7529 (mtt) REVERT: 3 274 ILE cc_start: 0.8736 (pt) cc_final: 0.8248 (tt) REVERT: 3 318 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7223 (tmtt) REVERT: 3 353 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8600 (mm) REVERT: 3 357 LYS cc_start: 0.7189 (pmtt) cc_final: 0.6489 (ptpt) REVERT: 3 362 ILE cc_start: 0.8096 (mt) cc_final: 0.7776 (mt) REVERT: 3 365 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6797 (mm110) REVERT: 3 455 ARG cc_start: 0.5984 (mmm160) cc_final: 0.5683 (mtt180) REVERT: 3 482 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6117 (t70) REVERT: 3 486 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7988 (mt) REVERT: 3 587 ASN cc_start: 0.6518 (m-40) cc_final: 0.4743 (t0) REVERT: 4 266 GLN cc_start: 0.7601 (tp40) cc_final: 0.7362 (tp-100) REVERT: 4 296 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7649 (mm) REVERT: 4 404 ASP cc_start: 0.6823 (m-30) cc_final: 0.6470 (m-30) REVERT: 4 411 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8004 (p) REVERT: 4 510 ARG cc_start: 0.7687 (mmm-85) cc_final: 0.7062 (mmm160) REVERT: 4 534 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: 4 579 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7449 (mm-40) REVERT: 4 583 LYS cc_start: 0.8255 (mmpt) cc_final: 0.7646 (mtmm) REVERT: 4 636 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7585 (mtpt) REVERT: 4 713 ASP cc_start: 0.6669 (t0) cc_final: 0.6467 (t70) REVERT: 4 715 LYS cc_start: 0.7036 (pttp) cc_final: 0.6670 (mmtp) REVERT: 4 726 ASN cc_start: 0.7676 (m-40) cc_final: 0.7270 (t0) REVERT: 4 729 LEU cc_start: 0.7867 (mt) cc_final: 0.7598 (mt) REVERT: 4 756 GLU cc_start: 0.7551 (tt0) cc_final: 0.7252 (tp30) REVERT: 5 29 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7584 (mttp) REVERT: 5 72 ASN cc_start: 0.7731 (t0) cc_final: 0.7465 (t0) REVERT: 5 139 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8359 (pp) REVERT: 5 358 LEU cc_start: 0.5567 (mt) cc_final: 0.5227 (tm) REVERT: 5 369 ILE cc_start: 0.7646 (pt) cc_final: 0.7435 (tt) REVERT: 5 388 ILE cc_start: 0.8235 (mt) cc_final: 0.7995 (mm) REVERT: 5 404 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.5749 (mmm) REVERT: 5 556 VAL cc_start: 0.6581 (t) cc_final: 0.6302 (p) REVERT: 5 581 ASN cc_start: 0.5471 (t0) cc_final: 0.4628 (m-40) REVERT: 5 654 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6903 (mt-10) REVERT: 5 675 ARG cc_start: 0.7230 (ttp80) cc_final: 0.6941 (ptt90) REVERT: 5 689 MET cc_start: 0.7075 (mmm) cc_final: 0.6718 (mmm) REVERT: 6 174 TYR cc_start: 0.8029 (t80) cc_final: 0.7426 (t80) REVERT: 6 299 GLU cc_start: 0.7083 (pm20) cc_final: 0.6320 (mt-10) REVERT: 6 347 ASN cc_start: 0.6720 (t0) cc_final: 0.5988 (m-40) REVERT: 6 518 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5625 (tm-30) REVERT: 6 561 GLU cc_start: 0.6000 (pt0) cc_final: 0.5684 (mt-10) REVERT: 6 614 ARG cc_start: 0.6533 (ttp-170) cc_final: 0.6275 (ttm110) REVERT: 6 675 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7429 (mpp-170) REVERT: 6 696 ARG cc_start: 0.6853 (tpt90) cc_final: 0.6423 (tpt90) REVERT: 6 724 ASP cc_start: 0.7174 (m-30) cc_final: 0.6783 (m-30) REVERT: 6 764 ILE cc_start: 0.7296 (mt) cc_final: 0.6684 (pp) REVERT: 6 833 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6641 (mp10) REVERT: 7 8 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8359 (tt) REVERT: 7 64 MET cc_start: 0.8608 (mmt) cc_final: 0.8394 (mmt) REVERT: 7 69 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7712 (mtpp) REVERT: 7 76 ASN cc_start: 0.7852 (t0) cc_final: 0.7342 (m110) REVERT: 7 81 ASP cc_start: 0.7799 (m-30) cc_final: 0.7443 (t0) REVERT: 7 124 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.6976 (p0) REVERT: 7 159 ASN cc_start: 0.7378 (m-40) cc_final: 0.7009 (m110) REVERT: 7 160 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6164 (pt0) REVERT: 7 162 ARG cc_start: 0.7201 (ttm-80) cc_final: 0.6914 (ttt90) REVERT: 7 188 GLU cc_start: 0.6171 (tt0) cc_final: 0.5839 (tt0) REVERT: 7 244 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8516 (tp) REVERT: 7 247 ARG cc_start: 0.7792 (tpp80) cc_final: 0.7413 (ttp80) REVERT: 7 449 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6833 (tmtp) REVERT: 7 502 VAL cc_start: 0.4903 (OUTLIER) cc_final: 0.4427 (t) REVERT: 7 537 ILE cc_start: 0.7776 (mt) cc_final: 0.7520 (tt) REVERT: 7 590 LEU cc_start: 0.7835 (tp) cc_final: 0.7589 (tm) REVERT: 7 598 PHE cc_start: 0.8424 (m-80) cc_final: 0.8163 (m-80) REVERT: 7 660 VAL cc_start: 0.8191 (t) cc_final: 0.7904 (t) REVERT: B 184 GLU cc_start: 0.4836 (mm-30) cc_final: 0.4331 (tm-30) REVERT: B 247 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6778 (mtm180) REVERT: B 267 MET cc_start: 0.7224 (mmm) cc_final: 0.6878 (mmm) REVERT: B 269 LYS cc_start: 0.6398 (ttmm) cc_final: 0.5046 (mppt) REVERT: B 378 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.5429 (tm-30) REVERT: B 496 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6707 (ttmm) REVERT: B 536 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7446 (p0) REVERT: B 705 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.5921 (mtp180) REVERT: B 788 ARG cc_start: 0.7264 (tpp-160) cc_final: 0.7044 (mmp80) REVERT: B 793 LEU cc_start: 0.7015 (pp) cc_final: 0.6720 (mp) REVERT: B 829 VAL cc_start: 0.6640 (m) cc_final: 0.6429 (m) REVERT: B 834 LEU cc_start: 0.6869 (mm) cc_final: 0.6279 (tp) REVERT: C 36 THR cc_start: 0.7303 (p) cc_final: 0.6882 (m) REVERT: C 51 ASN cc_start: 0.6212 (m-40) cc_final: 0.5977 (m110) REVERT: C 188 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7723 (mttp) REVERT: C 205 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7621 (mtpt) REVERT: C 222 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8252 (p) REVERT: C 234 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6161 (mp0) REVERT: C 235 ASP cc_start: 0.7103 (p0) cc_final: 0.6758 (p0) REVERT: C 237 GLU cc_start: 0.7019 (mp0) cc_final: 0.6607 (mt-10) REVERT: C 348 ARG cc_start: 0.7020 (mtm110) cc_final: 0.6432 (mtt90) REVERT: C 456 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.5544 (ppt-90) REVERT: C 477 LYS cc_start: 0.7122 (mttm) cc_final: 0.6622 (mttm) REVERT: C 505 THR cc_start: 0.8522 (t) cc_final: 0.8079 (m) REVERT: C 556 ILE cc_start: 0.7233 (pt) cc_final: 0.6836 (mm) REVERT: C 656 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7485 (tp) REVERT: C 664 LYS cc_start: 0.7623 (mtpp) cc_final: 0.7192 (mtpt) REVERT: C 681 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7549 (tmmm) REVERT: C 723 LYS cc_start: 0.7220 (pttt) cc_final: 0.6728 (ttmm) REVERT: D 235 GLU cc_start: 0.6359 (mt-10) cc_final: 0.5794 (tp30) REVERT: D 302 LYS cc_start: 0.7689 (mmtp) cc_final: 0.7108 (mtpp) REVERT: D 394 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8599 (tmtp) REVERT: D 408 ASP cc_start: 0.7574 (m-30) cc_final: 0.7287 (m-30) REVERT: D 434 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7267 (tp30) REVERT: D 445 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7020 (mtt180) REVERT: D 483 GLN cc_start: 0.6811 (tp40) cc_final: 0.5957 (mt0) REVERT: D 534 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7029 (tp30) REVERT: D 690 GLU cc_start: 0.6545 (tt0) cc_final: 0.6074 (tp30) REVERT: D 693 ASP cc_start: 0.6513 (t0) cc_final: 0.5885 (p0) REVERT: D 779 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6908 (ptmt) REVERT: D 819 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7333 (mm) REVERT: D 830 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6547 (mtp180) REVERT: D 847 MET cc_start: 0.5775 (OUTLIER) cc_final: 0.5125 (mmm) REVERT: E 5 ARG cc_start: 0.7480 (ttp80) cc_final: 0.6993 (ttp-110) REVERT: E 33 ASN cc_start: 0.7343 (m-40) cc_final: 0.7117 (m110) REVERT: E 77 LYS cc_start: 0.8022 (mttm) cc_final: 0.7685 (mtpp) REVERT: E 209 ARG cc_start: 0.7203 (mmm-85) cc_final: 0.6858 (mmt180) REVERT: E 249 LYS cc_start: 0.7701 (mmtp) cc_final: 0.7384 (mppt) REVERT: E 280 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7714 (mtp85) REVERT: E 354 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6160 (mm-30) REVERT: E 368 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6435 (tt0) REVERT: E 404 MET cc_start: 0.7435 (ttm) cc_final: 0.7000 (tpt) REVERT: E 458 MET cc_start: 0.5990 (mtp) cc_final: 0.5595 (mtm) REVERT: E 469 MET cc_start: 0.7967 (mmm) cc_final: 0.7546 (mmm) REVERT: E 497 MET cc_start: 0.8385 (mtm) cc_final: 0.8079 (mtm) REVERT: E 513 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7874 (pp) REVERT: E 557 LYS cc_start: 0.5596 (mmmt) cc_final: 0.5161 (tmtm) REVERT: E 564 ARG cc_start: 0.6826 (ttt180) cc_final: 0.5961 (ttm-80) REVERT: E 592 SER cc_start: 0.6548 (m) cc_final: 0.6160 (p) REVERT: E 597 GLU cc_start: 0.6328 (pm20) cc_final: 0.5821 (mm-30) REVERT: E 661 GLU cc_start: 0.6579 (mt-10) cc_final: 0.6265 (mt-10) REVERT: F 352 ARG cc_start: 0.7156 (mtp85) cc_final: 0.6784 (mmm160) REVERT: F 362 GLN cc_start: 0.8444 (tt0) cc_final: 0.7967 (tt0) REVERT: F 421 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6611 (mm) REVERT: F 446 ARG cc_start: 0.7490 (ptt90) cc_final: 0.6532 (ptp-110) REVERT: F 737 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7238 (mttt) REVERT: G 130 LYS cc_start: 0.7221 (pttp) cc_final: 0.6913 (ptpt) REVERT: G 190 GLU cc_start: 0.6521 (mt-10) cc_final: 0.6308 (mt-10) REVERT: G 247 ARG cc_start: 0.8044 (ttt90) cc_final: 0.7546 (ttp80) REVERT: G 291 GLN cc_start: 0.7891 (mt0) cc_final: 0.7620 (mm110) REVERT: G 297 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: G 386 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7319 (mppt) REVERT: G 396 ASP cc_start: 0.5095 (p0) cc_final: 0.4494 (t0) REVERT: G 402 MET cc_start: 0.5341 (mmm) cc_final: 0.4325 (mmm) REVERT: G 412 ASN cc_start: 0.7570 (t0) cc_final: 0.7035 (m-40) REVERT: G 427 ASP cc_start: 0.7687 (m-30) cc_final: 0.7472 (m-30) REVERT: G 502 VAL cc_start: 0.5853 (OUTLIER) cc_final: 0.5613 (t) REVERT: G 529 MET cc_start: 0.7111 (mtm) cc_final: 0.6797 (OUTLIER) REVERT: G 556 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7688 (m) REVERT: G 583 ASN cc_start: 0.7122 (p0) cc_final: 0.6836 (p0) REVERT: G 607 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: G 612 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.6964 (tp) REVERT: G 618 TYR cc_start: 0.7542 (t80) cc_final: 0.7253 (t80) REVERT: G 690 LEU cc_start: 0.8520 (mt) cc_final: 0.8230 (mt) REVERT: H 35 LEU cc_start: 0.5461 (tt) cc_final: 0.5161 (mp) REVERT: H 79 TYR cc_start: 0.6112 (m-80) cc_final: 0.5841 (m-10) REVERT: H 138 LYS cc_start: 0.3535 (mmmt) cc_final: 0.2445 (mmmm) REVERT: H 284 PHE cc_start: 0.5413 (m-80) cc_final: 0.4838 (m-80) REVERT: H 319 MET cc_start: 0.4089 (OUTLIER) cc_final: 0.3714 (tpp) REVERT: H 331 GLU cc_start: 0.5482 (mt-10) cc_final: 0.5098 (mt-10) REVERT: H 332 LEU cc_start: 0.6192 (mt) cc_final: 0.5786 (tp) REVERT: H 389 TYR cc_start: 0.0822 (m-80) cc_final: 0.0482 (m-80) REVERT: I 120 MET cc_start: 0.2597 (OUTLIER) cc_final: 0.0798 (mpt) REVERT: I 128 PHE cc_start: 0.2754 (m-10) cc_final: 0.2536 (m-10) REVERT: I 152 LYS cc_start: 0.4037 (mttt) cc_final: 0.3653 (tppt) REVERT: I 158 LEU cc_start: 0.2712 (tt) cc_final: 0.2005 (mm) REVERT: I 325 LYS cc_start: 0.3587 (mppt) cc_final: 0.3045 (ttpp) REVERT: I 341 ARG cc_start: 0.3486 (mtt90) cc_final: 0.2797 (mmm160) REVERT: I 365 ILE cc_start: 0.2561 (tt) cc_final: 0.2274 (mp) REVERT: I 382 MET cc_start: 0.2212 (mmp) cc_final: 0.1620 (ptp) REVERT: I 662 GLU cc_start: 0.6556 (tt0) cc_final: 0.6131 (tp30) outliers start: 348 outliers final: 175 residues processed: 1173 average time/residue: 1.5367 time to fit residues: 2334.8877 Evaluate side-chains 1125 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 889 time to evaluate : 5.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 358 GLU Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 626 GLN Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 670 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 117 GLU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 208 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 3 residue 537 ASP Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 356 MET Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 490 VAL Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 636 LYS Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 177 THR Chi-restraints excluded: chain 5 residue 184 ARG Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 404 MET Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 622 LEU Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 443 LEU Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 501 GLN Chi-restraints excluded: chain 6 residue 518 GLU Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 6 residue 767 LYS Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 124 ASN Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 329 ARG Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain 7 residue 651 VAL Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain 7 residue 710 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 456 ARG Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 830 ARG Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 737 LYS Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 607 ASP Chi-restraints excluded: chain G residue 612 LEU Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 271 ARG Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 298 THR Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 665 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 792 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 468 optimal weight: 6.9990 chunk 600 optimal weight: 4.9990 chunk 465 optimal weight: 1.9990 chunk 692 optimal weight: 7.9990 chunk 459 optimal weight: 1.9990 chunk 819 optimal weight: 6.9990 chunk 512 optimal weight: 2.9990 chunk 499 optimal weight: 3.9990 chunk 378 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 666 ASN 3 254 GLN 3 503 HIS 4 613 GLN ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 579 ASN 5 587 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 9 GLN 7 112 HIS 7 297 GLN 7 316 GLN C 340 GLN ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 253 GLN D 259 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 ASN E 560 HIS E 571 HIS E 685 GLN F 269 ASN F 347 ASN ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 367 ASN ** I 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 673 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 69476 Z= 0.327 Angle : 0.652 11.024 93996 Z= 0.335 Chirality : 0.047 0.289 10834 Planarity : 0.005 0.061 12062 Dihedral : 7.427 178.498 9630 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.22 % Rotamer: Outliers : 4.74 % Allowed : 18.01 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.21 (0.09), residues: 8483 helix: 1.00 (0.09), residues: 3542 sheet: -0.45 (0.12), residues: 1624 loop : -0.34 (0.10), residues: 3317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 112 HIS 0.009 0.001 HIS 6 653 PHE 0.026 0.002 PHE I 702 TYR 0.027 0.002 TYR 6 136 ARG 0.023 0.001 ARG B 489 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 938 time to evaluate : 6.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.5719 (mt-10) REVERT: 2 232 ARG cc_start: 0.6660 (mmm-85) cc_final: 0.5992 (mtp180) REVERT: 2 269 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6601 (ttmt) REVERT: 2 326 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6602 (pmt170) REVERT: 2 374 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5320 (ttm110) REVERT: 2 422 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6829 (pp20) REVERT: 2 684 ARG cc_start: 0.4096 (OUTLIER) cc_final: 0.3217 (ptp90) REVERT: 2 789 VAL cc_start: 0.8227 (p) cc_final: 0.7944 (t) REVERT: 2 798 ILE cc_start: 0.5420 (mt) cc_final: 0.4938 (pt) REVERT: 2 847 ASP cc_start: 0.6772 (t0) cc_final: 0.6520 (t0) REVERT: 3 40 ASP cc_start: 0.6644 (p0) cc_final: 0.6384 (m-30) REVERT: 3 117 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: 3 188 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7100 (ttpt) REVERT: 3 208 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7307 (mtp180) REVERT: 3 234 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6573 (tm-30) REVERT: 3 274 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8271 (tt) REVERT: 3 315 ILE cc_start: 0.5523 (OUTLIER) cc_final: 0.5111 (mm) REVERT: 3 318 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7242 (tmtt) REVERT: 3 353 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8570 (mm) REVERT: 3 362 ILE cc_start: 0.8133 (mt) cc_final: 0.7806 (mt) REVERT: 3 365 GLN cc_start: 0.7319 (mm-40) cc_final: 0.6857 (mm110) REVERT: 3 455 ARG cc_start: 0.5989 (mmm160) cc_final: 0.5719 (mtt180) REVERT: 3 482 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6220 (t70) REVERT: 3 587 ASN cc_start: 0.6399 (m-40) cc_final: 0.4672 (t0) REVERT: 4 235 GLU cc_start: 0.7245 (mt-10) cc_final: 0.7040 (mt-10) REVERT: 4 266 GLN cc_start: 0.7594 (tp40) cc_final: 0.7349 (tp-100) REVERT: 4 296 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7726 (mm) REVERT: 4 404 ASP cc_start: 0.6856 (m-30) cc_final: 0.6478 (m-30) REVERT: 4 411 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.7993 (p) REVERT: 4 510 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7084 (mmm160) REVERT: 4 534 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: 4 579 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7480 (mm-40) REVERT: 4 583 LYS cc_start: 0.8190 (mmpt) cc_final: 0.7598 (mtmm) REVERT: 4 594 LYS cc_start: 0.6190 (ttpp) cc_final: 0.5771 (tptp) REVERT: 4 636 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7556 (mtpt) REVERT: 4 690 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6648 (tt0) REVERT: 4 715 LYS cc_start: 0.7045 (pttp) cc_final: 0.6637 (mmtp) REVERT: 4 726 ASN cc_start: 0.7688 (m-40) cc_final: 0.7318 (t0) REVERT: 4 729 LEU cc_start: 0.8068 (mt) cc_final: 0.7742 (mt) REVERT: 4 756 GLU cc_start: 0.7579 (tt0) cc_final: 0.7270 (tp30) REVERT: 5 5 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6705 (tmm-80) REVERT: 5 72 ASN cc_start: 0.7744 (t0) cc_final: 0.7468 (t0) REVERT: 5 139 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8466 (pp) REVERT: 5 145 GLN cc_start: 0.7151 (mt0) cc_final: 0.6859 (mm-40) REVERT: 5 358 LEU cc_start: 0.5701 (mt) cc_final: 0.5317 (tm) REVERT: 5 369 ILE cc_start: 0.7644 (pt) cc_final: 0.7427 (tt) REVERT: 5 388 ILE cc_start: 0.8239 (mt) cc_final: 0.7989 (mm) REVERT: 5 404 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.5853 (mmm) REVERT: 5 458 MET cc_start: 0.6288 (pmm) cc_final: 0.4549 (ptp) REVERT: 5 581 ASN cc_start: 0.5654 (t0) cc_final: 0.4825 (m-40) REVERT: 5 625 ASN cc_start: 0.6192 (m110) cc_final: 0.5295 (t0) REVERT: 5 654 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: 5 689 MET cc_start: 0.7022 (mmm) cc_final: 0.6688 (mmm) REVERT: 6 174 TYR cc_start: 0.8022 (t80) cc_final: 0.7409 (t80) REVERT: 6 299 GLU cc_start: 0.7081 (pm20) cc_final: 0.6416 (mt-10) REVERT: 6 313 MET cc_start: 0.5494 (OUTLIER) cc_final: 0.4584 (pmm) REVERT: 6 347 ASN cc_start: 0.6679 (t0) cc_final: 0.5992 (m-40) REVERT: 6 614 ARG cc_start: 0.6706 (ttp-170) cc_final: 0.6452 (ttm110) REVERT: 6 643 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7688 (mmpt) REVERT: 6 653 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6675 (p-80) REVERT: 6 696 ARG cc_start: 0.6852 (tpt90) cc_final: 0.6449 (tpt90) REVERT: 6 706 MET cc_start: 0.7772 (mtp) cc_final: 0.7568 (ttp) REVERT: 6 724 ASP cc_start: 0.7312 (m-30) cc_final: 0.6946 (m-30) REVERT: 6 764 ILE cc_start: 0.7353 (mt) cc_final: 0.6706 (pp) REVERT: 6 783 ASP cc_start: 0.6253 (t0) cc_final: 0.5746 (t0) REVERT: 6 794 ARG cc_start: 0.5522 (mtp-110) cc_final: 0.4784 (mtt90) REVERT: 6 833 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: 7 8 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8383 (tt) REVERT: 7 69 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7736 (mtpp) REVERT: 7 76 ASN cc_start: 0.7847 (t0) cc_final: 0.7399 (m110) REVERT: 7 81 ASP cc_start: 0.7724 (m-30) cc_final: 0.7416 (t0) REVERT: 7 92 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6939 (mttt) REVERT: 7 124 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7192 (p0) REVERT: 7 159 ASN cc_start: 0.7283 (m-40) cc_final: 0.6841 (m110) REVERT: 7 160 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6247 (pt0) REVERT: 7 162 ARG cc_start: 0.7358 (ttm-80) cc_final: 0.7037 (ttt90) REVERT: 7 188 GLU cc_start: 0.6428 (tt0) cc_final: 0.6115 (tt0) REVERT: 7 207 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7645 (pt) REVERT: 7 233 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6901 (p0) REVERT: 7 244 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8573 (tp) REVERT: 7 247 ARG cc_start: 0.7839 (tpp80) cc_final: 0.7446 (ttp80) REVERT: 7 449 LYS cc_start: 0.7382 (mtmt) cc_final: 0.6898 (tmtp) REVERT: 7 499 LYS cc_start: 0.7026 (tptm) cc_final: 0.6507 (ttmt) REVERT: 7 502 VAL cc_start: 0.4933 (OUTLIER) cc_final: 0.4446 (t) REVERT: 7 537 ILE cc_start: 0.7860 (mt) cc_final: 0.7525 (mm) REVERT: B 184 GLU cc_start: 0.4793 (mm-30) cc_final: 0.4373 (tm-30) REVERT: B 198 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7571 (mp) REVERT: B 247 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6809 (mtm180) REVERT: B 267 MET cc_start: 0.7258 (mmm) cc_final: 0.6887 (mmm) REVERT: B 269 LYS cc_start: 0.6502 (ttmm) cc_final: 0.5100 (mppt) REVERT: B 496 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6701 (ttmm) REVERT: B 536 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7453 (p0) REVERT: B 705 ARG cc_start: 0.6344 (OUTLIER) cc_final: 0.5909 (mtp180) REVERT: B 834 LEU cc_start: 0.6756 (mm) cc_final: 0.6185 (tp) REVERT: C 36 THR cc_start: 0.7364 (p) cc_final: 0.6906 (m) REVERT: C 188 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7697 (mttp) REVERT: C 205 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7630 (mtpt) REVERT: C 222 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8448 (p) REVERT: C 234 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6117 (mp0) REVERT: C 235 ASP cc_start: 0.7237 (p0) cc_final: 0.6880 (p0) REVERT: C 237 GLU cc_start: 0.6975 (mp0) cc_final: 0.6578 (mt-10) REVERT: C 348 ARG cc_start: 0.7042 (mtm110) cc_final: 0.6441 (mtt90) REVERT: C 456 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.5518 (ppt-90) REVERT: C 477 LYS cc_start: 0.7144 (mttm) cc_final: 0.6664 (mttp) REVERT: C 505 THR cc_start: 0.8491 (t) cc_final: 0.8021 (m) REVERT: C 556 ILE cc_start: 0.7316 (pt) cc_final: 0.6882 (mm) REVERT: C 557 ARG cc_start: 0.6277 (ttt-90) cc_final: 0.5864 (tpt-90) REVERT: C 572 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6464 (tt) REVERT: C 656 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7559 (tp) REVERT: C 664 LYS cc_start: 0.7606 (mtpp) cc_final: 0.7170 (mtpt) REVERT: C 681 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7576 (tmmm) REVERT: C 723 LYS cc_start: 0.7326 (pttt) cc_final: 0.6756 (ttmm) REVERT: D 235 GLU cc_start: 0.6393 (mt-10) cc_final: 0.5818 (tp30) REVERT: D 394 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8647 (tmtp) REVERT: D 408 ASP cc_start: 0.7464 (m-30) cc_final: 0.7176 (m-30) REVERT: D 445 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7118 (mtt180) REVERT: D 483 GLN cc_start: 0.6755 (tp40) cc_final: 0.5928 (mt0) REVERT: D 534 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7032 (tp30) REVERT: D 688 VAL cc_start: 0.7706 (t) cc_final: 0.7497 (p) REVERT: D 690 GLU cc_start: 0.6623 (tt0) cc_final: 0.6173 (tp30) REVERT: D 693 ASP cc_start: 0.6549 (t0) cc_final: 0.5887 (p0) REVERT: D 779 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6947 (ptmt) REVERT: D 819 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7336 (mm) REVERT: D 830 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6592 (mtp180) REVERT: D 847 MET cc_start: 0.5578 (OUTLIER) cc_final: 0.4899 (mmm) REVERT: E 5 ARG cc_start: 0.7529 (ttp80) cc_final: 0.7039 (ttp-110) REVERT: E 77 LYS cc_start: 0.8060 (mttm) cc_final: 0.7748 (mtpp) REVERT: E 209 ARG cc_start: 0.7085 (mmm-85) cc_final: 0.6694 (mmt180) REVERT: E 221 MET cc_start: 0.3616 (OUTLIER) cc_final: 0.3185 (pmm) REVERT: E 249 LYS cc_start: 0.7775 (mmtp) cc_final: 0.7371 (mppt) REVERT: E 280 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7712 (mtp85) REVERT: E 354 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6066 (mm-30) REVERT: E 368 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6494 (tt0) REVERT: E 404 MET cc_start: 0.7452 (ttm) cc_final: 0.6999 (tpt) REVERT: E 458 MET cc_start: 0.6056 (mtp) cc_final: 0.5828 (mtm) REVERT: E 497 MET cc_start: 0.8405 (mtm) cc_final: 0.8104 (mtm) REVERT: E 513 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7921 (pt) REVERT: E 564 ARG cc_start: 0.6831 (ttt180) cc_final: 0.5995 (ttm-80) REVERT: E 592 SER cc_start: 0.6839 (m) cc_final: 0.6372 (p) REVERT: E 597 GLU cc_start: 0.6356 (pm20) cc_final: 0.5829 (mm-30) REVERT: E 625 ASN cc_start: 0.6506 (t0) cc_final: 0.6239 (m110) REVERT: E 661 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6225 (mt-10) REVERT: F 346 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5906 (tt) REVERT: F 352 ARG cc_start: 0.7200 (mtp85) cc_final: 0.6849 (mmm160) REVERT: F 362 GLN cc_start: 0.8472 (tt0) cc_final: 0.8019 (tt0) REVERT: F 403 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8803 (p) REVERT: F 421 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6757 (mm) REVERT: F 446 ARG cc_start: 0.7369 (ptt90) cc_final: 0.6504 (ptp-110) REVERT: F 654 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6155 (tp30) REVERT: F 737 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7424 (mttt) REVERT: G 130 LYS cc_start: 0.7258 (pttp) cc_final: 0.6943 (ptpt) REVERT: G 190 GLU cc_start: 0.6541 (mt-10) cc_final: 0.6301 (mt-10) REVERT: G 247 ARG cc_start: 0.8088 (ttt90) cc_final: 0.7597 (ttp80) REVERT: G 276 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6945 (mtm-85) REVERT: G 291 GLN cc_start: 0.7862 (mt0) cc_final: 0.7624 (mm110) REVERT: G 297 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: G 396 ASP cc_start: 0.4959 (p0) cc_final: 0.4352 (t0) REVERT: G 402 MET cc_start: 0.5669 (mmm) cc_final: 0.5440 (tmm) REVERT: G 412 ASN cc_start: 0.7603 (t0) cc_final: 0.7079 (m-40) REVERT: G 441 ASP cc_start: 0.7389 (p0) cc_final: 0.7167 (p0) REVERT: G 475 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7627 (ttmt) REVERT: G 502 VAL cc_start: 0.5854 (OUTLIER) cc_final: 0.5606 (t) REVERT: G 529 MET cc_start: 0.7119 (mtm) cc_final: 0.6778 (mtt) REVERT: G 556 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7801 (m) REVERT: G 583 ASN cc_start: 0.7423 (p0) cc_final: 0.7171 (p0) REVERT: G 607 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: G 612 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.6984 (tp) REVERT: G 690 LEU cc_start: 0.8531 (mt) cc_final: 0.8242 (mt) REVERT: H 152 LYS cc_start: 0.4708 (pttp) cc_final: 0.4342 (pptt) REVERT: H 284 PHE cc_start: 0.5551 (m-80) cc_final: 0.4911 (m-80) REVERT: H 319 MET cc_start: 0.4060 (OUTLIER) cc_final: 0.3614 (tpp) REVERT: H 331 GLU cc_start: 0.5578 (mt-10) cc_final: 0.5230 (mt-10) REVERT: H 332 LEU cc_start: 0.6238 (mt) cc_final: 0.5884 (tp) REVERT: H 371 GLU cc_start: 0.3482 (OUTLIER) cc_final: 0.3102 (pm20) REVERT: H 389 TYR cc_start: 0.1112 (m-80) cc_final: 0.0831 (m-80) REVERT: I 120 MET cc_start: 0.2593 (OUTLIER) cc_final: 0.0807 (mpt) REVERT: I 152 LYS cc_start: 0.3926 (mttt) cc_final: 0.3523 (ttpt) REVERT: I 155 PHE cc_start: 0.2776 (OUTLIER) cc_final: 0.2528 (m-80) REVERT: I 158 LEU cc_start: 0.2639 (tt) cc_final: 0.1941 (mm) REVERT: I 325 LYS cc_start: 0.3672 (mppt) cc_final: 0.3272 (mtmt) REVERT: I 382 MET cc_start: 0.2173 (mmp) cc_final: 0.1624 (ptp) REVERT: I 519 VAL cc_start: 0.7402 (m) cc_final: 0.6846 (t) REVERT: I 662 GLU cc_start: 0.6583 (tt0) cc_final: 0.6237 (tp30) outliers start: 360 outliers final: 175 residues processed: 1187 average time/residue: 1.5309 time to fit residues: 2351.7333 Evaluate side-chains 1124 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 877 time to evaluate : 6.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 670 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 117 GLU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 208 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 274 ILE Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 3 residue 537 ASP Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 490 VAL Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 636 LYS Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 690 GLU Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 5 ARG Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 177 THR Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 242 ILE Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 404 MET Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 509 ILE Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 622 LEU Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 501 GLN Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 643 LYS Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 92 LYS Chi-restraints excluded: chain 7 residue 124 ASN Chi-restraints excluded: chain 7 residue 151 GLU Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 294 THR Chi-restraints excluded: chain 7 residue 317 GLU Chi-restraints excluded: chain 7 residue 329 ARG Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 448 MET Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain 7 residue 651 VAL Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain 7 residue 710 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 456 ARG Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 830 ARG Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 273 ASN Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 737 LYS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 276 ARG Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 475 LYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 607 ASP Chi-restraints excluded: chain G residue 612 LEU Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 271 ARG Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 298 THR Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 371 GLU Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 155 PHE Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 665 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 506 optimal weight: 3.9990 chunk 327 optimal weight: 0.0670 chunk 489 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 520 optimal weight: 0.6980 chunk 558 optimal weight: 0.0070 chunk 405 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 643 optimal weight: 0.7980 overall best weight: 1.1138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 353 GLN 2 651 ASN 2 666 ASN 3 324 ASN 3 503 HIS 4 613 GLN ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 587 GLN ** 5 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 156 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 673 ASN 7 297 GLN 7 683 GLN C 51 ASN C 293 ASN C 324 ASN C 340 GLN ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 253 GLN D 327 ASN D 685 ASN E 560 HIS E 685 GLN F 269 ASN F 347 ASN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 367 ASN ** I 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 69476 Z= 0.199 Angle : 0.568 11.284 93996 Z= 0.292 Chirality : 0.043 0.264 10834 Planarity : 0.004 0.056 12062 Dihedral : 7.217 178.909 9630 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Rotamer: Outliers : 3.82 % Allowed : 19.45 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.39 (0.09), residues: 8483 helix: 1.20 (0.09), residues: 3537 sheet: -0.44 (0.12), residues: 1616 loop : -0.26 (0.10), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 112 HIS 0.011 0.001 HIS F 653 PHE 0.029 0.001 PHE I 210 TYR 0.020 0.001 TYR 6 136 ARG 0.010 0.000 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 935 time to evaluate : 6.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 232 ARG cc_start: 0.6536 (mmm-85) cc_final: 0.5889 (mtp180) REVERT: 2 269 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6536 (ttmt) REVERT: 2 326 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6321 (pmt170) REVERT: 2 374 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.5319 (ttm110) REVERT: 2 422 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6675 (pp20) REVERT: 2 457 LYS cc_start: 0.5961 (mmmt) cc_final: 0.5713 (tttp) REVERT: 2 667 VAL cc_start: 0.7045 (OUTLIER) cc_final: 0.6717 (p) REVERT: 2 684 ARG cc_start: 0.4040 (OUTLIER) cc_final: 0.3250 (ptp90) REVERT: 2 689 GLU cc_start: 0.5252 (OUTLIER) cc_final: 0.4788 (mt-10) REVERT: 2 789 VAL cc_start: 0.8200 (p) cc_final: 0.7949 (t) REVERT: 2 798 ILE cc_start: 0.5514 (mt) cc_final: 0.5061 (pt) REVERT: 2 847 ASP cc_start: 0.6917 (t0) cc_final: 0.6656 (t0) REVERT: 3 40 ASP cc_start: 0.6683 (p0) cc_final: 0.6382 (m-30) REVERT: 3 188 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7177 (ttpt) REVERT: 3 234 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6156 (tm-30) REVERT: 3 261 MET cc_start: 0.7932 (mtm) cc_final: 0.7529 (mtt) REVERT: 3 274 ILE cc_start: 0.8784 (pt) cc_final: 0.8317 (tt) REVERT: 3 315 ILE cc_start: 0.5263 (OUTLIER) cc_final: 0.4891 (mm) REVERT: 3 318 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7200 (tmtt) REVERT: 3 353 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8620 (mm) REVERT: 3 357 LYS cc_start: 0.7397 (pmtt) cc_final: 0.6597 (ptpt) REVERT: 3 362 ILE cc_start: 0.8103 (mt) cc_final: 0.7789 (mt) REVERT: 3 365 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6881 (mm110) REVERT: 3 455 ARG cc_start: 0.6016 (mmm160) cc_final: 0.5756 (mtt180) REVERT: 3 478 MET cc_start: 0.7582 (mtm) cc_final: 0.7377 (mtm) REVERT: 3 482 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6377 (t70) REVERT: 3 504 THR cc_start: 0.8355 (p) cc_final: 0.8027 (t) REVERT: 3 587 ASN cc_start: 0.6221 (m-40) cc_final: 0.4523 (t0) REVERT: 4 266 GLN cc_start: 0.7456 (tp40) cc_final: 0.7194 (tp-100) REVERT: 4 296 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7642 (mm) REVERT: 4 366 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: 4 404 ASP cc_start: 0.6872 (m-30) cc_final: 0.6504 (m-30) REVERT: 4 411 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8046 (p) REVERT: 4 471 ASP cc_start: 0.7984 (m-30) cc_final: 0.7527 (p0) REVERT: 4 510 ARG cc_start: 0.7635 (mmm-85) cc_final: 0.6981 (mmm160) REVERT: 4 534 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: 4 579 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7402 (mm-40) REVERT: 4 583 LYS cc_start: 0.8222 (mmpt) cc_final: 0.7606 (mtmm) REVERT: 4 612 LYS cc_start: 0.7731 (mmpt) cc_final: 0.7088 (mmtp) REVERT: 4 636 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7600 (mtpt) REVERT: 4 715 LYS cc_start: 0.6902 (pttp) cc_final: 0.6320 (mmtp) REVERT: 4 726 ASN cc_start: 0.7689 (m-40) cc_final: 0.7351 (t0) REVERT: 4 729 LEU cc_start: 0.7985 (mt) cc_final: 0.7703 (mt) REVERT: 4 756 GLU cc_start: 0.7504 (tt0) cc_final: 0.7192 (tp30) REVERT: 5 5 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6021 (tmm-80) REVERT: 5 72 ASN cc_start: 0.7703 (t0) cc_final: 0.7424 (t0) REVERT: 5 358 LEU cc_start: 0.5563 (mt) cc_final: 0.5239 (tm) REVERT: 5 369 ILE cc_start: 0.7630 (pt) cc_final: 0.7425 (tt) REVERT: 5 404 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.5735 (mmp) REVERT: 5 458 MET cc_start: 0.6328 (pmm) cc_final: 0.4535 (ptp) REVERT: 5 469 MET cc_start: 0.7729 (mmm) cc_final: 0.7429 (mmm) REVERT: 5 581 ASN cc_start: 0.5472 (t0) cc_final: 0.4650 (m-40) REVERT: 5 599 MET cc_start: 0.7296 (tpt) cc_final: 0.6893 (mtp) REVERT: 5 625 ASN cc_start: 0.6200 (m110) cc_final: 0.5356 (t0) REVERT: 5 654 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: 5 675 ARG cc_start: 0.7162 (ttp80) cc_final: 0.6886 (ptt90) REVERT: 5 689 MET cc_start: 0.7049 (mmm) cc_final: 0.6699 (mmm) REVERT: 6 133 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.4687 (pm20) REVERT: 6 174 TYR cc_start: 0.8040 (t80) cc_final: 0.7488 (t80) REVERT: 6 299 GLU cc_start: 0.7100 (pm20) cc_final: 0.6377 (mt-10) REVERT: 6 347 ASN cc_start: 0.6667 (t0) cc_final: 0.5960 (m-40) REVERT: 6 614 ARG cc_start: 0.6645 (ttp-170) cc_final: 0.6413 (ttm110) REVERT: 6 675 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7377 (mpp-170) REVERT: 6 724 ASP cc_start: 0.7154 (m-30) cc_final: 0.6804 (m-30) REVERT: 6 753 ARG cc_start: 0.6908 (mtm110) cc_final: 0.6661 (ttm-80) REVERT: 6 764 ILE cc_start: 0.7252 (mt) cc_final: 0.6625 (pp) REVERT: 6 783 ASP cc_start: 0.6140 (t0) cc_final: 0.5709 (t0) REVERT: 6 794 ARG cc_start: 0.5454 (mtp-110) cc_final: 0.5109 (mtp-110) REVERT: 6 833 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6623 (mp10) REVERT: 7 8 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8356 (tt) REVERT: 7 69 LYS cc_start: 0.8002 (mtmm) cc_final: 0.7708 (mtpt) REVERT: 7 76 ASN cc_start: 0.7804 (t0) cc_final: 0.7306 (m110) REVERT: 7 81 ASP cc_start: 0.7780 (m-30) cc_final: 0.7457 (t0) REVERT: 7 92 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6890 (mtpt) REVERT: 7 124 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.6850 (p0) REVERT: 7 159 ASN cc_start: 0.7252 (m-40) cc_final: 0.6814 (m110) REVERT: 7 160 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6214 (pt0) REVERT: 7 162 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.7039 (ttm170) REVERT: 7 188 GLU cc_start: 0.6227 (tt0) cc_final: 0.5912 (tt0) REVERT: 7 207 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7472 (pt) REVERT: 7 244 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8456 (tp) REVERT: 7 247 ARG cc_start: 0.7826 (tpp80) cc_final: 0.7451 (ttp80) REVERT: 7 449 LYS cc_start: 0.7306 (mtmt) cc_final: 0.6845 (tmtp) REVERT: 7 499 LYS cc_start: 0.6942 (tptm) cc_final: 0.6335 (ttmt) REVERT: 7 502 VAL cc_start: 0.4917 (OUTLIER) cc_final: 0.4451 (t) REVERT: 7 537 ILE cc_start: 0.7762 (mt) cc_final: 0.7521 (tt) REVERT: B 184 GLU cc_start: 0.4717 (mm-30) cc_final: 0.4199 (tm-30) REVERT: B 198 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7543 (mp) REVERT: B 237 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.6001 (mtt) REVERT: B 247 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6838 (mtm180) REVERT: B 269 LYS cc_start: 0.6463 (ttmm) cc_final: 0.5081 (mppt) REVERT: B 378 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.5450 (tm-30) REVERT: B 496 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6620 (ttmm) REVERT: B 536 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7125 (p0) REVERT: B 705 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.5870 (mtp180) REVERT: B 761 GLU cc_start: 0.7132 (mp0) cc_final: 0.6335 (tm-30) REVERT: B 834 LEU cc_start: 0.6942 (mm) cc_final: 0.6334 (tp) REVERT: C 36 THR cc_start: 0.7447 (p) cc_final: 0.6946 (m) REVERT: C 188 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7701 (mttp) REVERT: C 205 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7616 (mtpt) REVERT: C 222 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8316 (p) REVERT: C 234 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6162 (mp0) REVERT: C 235 ASP cc_start: 0.7184 (p0) cc_final: 0.6815 (p0) REVERT: C 237 GLU cc_start: 0.6980 (mp0) cc_final: 0.6585 (mt-10) REVERT: C 348 ARG cc_start: 0.7008 (mtm110) cc_final: 0.6429 (mtt90) REVERT: C 355 LYS cc_start: 0.6601 (mmmt) cc_final: 0.6005 (ptpt) REVERT: C 456 ARG cc_start: 0.5976 (OUTLIER) cc_final: 0.5279 (ppt-90) REVERT: C 477 LYS cc_start: 0.7082 (mttm) cc_final: 0.6639 (mttp) REVERT: C 505 THR cc_start: 0.8518 (t) cc_final: 0.8104 (m) REVERT: C 519 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.6945 (t) REVERT: C 556 ILE cc_start: 0.7187 (pt) cc_final: 0.6814 (mm) REVERT: C 557 ARG cc_start: 0.6063 (ttt-90) cc_final: 0.5736 (tpt-90) REVERT: C 656 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7527 (tp) REVERT: C 664 LYS cc_start: 0.7556 (mtpp) cc_final: 0.7138 (mtpt) REVERT: C 667 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8160 (t) REVERT: C 681 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7509 (tmmm) REVERT: C 723 LYS cc_start: 0.7289 (pttt) cc_final: 0.6701 (ttmm) REVERT: D 235 GLU cc_start: 0.6419 (mt-10) cc_final: 0.5829 (tp30) REVERT: D 302 LYS cc_start: 0.7649 (mmtp) cc_final: 0.7122 (mtpp) REVERT: D 394 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8548 (tmtp) REVERT: D 408 ASP cc_start: 0.7491 (m-30) cc_final: 0.7223 (m-30) REVERT: D 445 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6984 (mtt90) REVERT: D 483 GLN cc_start: 0.6711 (tp40) cc_final: 0.5901 (mt0) REVERT: D 534 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7022 (tp30) REVERT: D 690 GLU cc_start: 0.6834 (tt0) cc_final: 0.6322 (tp30) REVERT: D 693 ASP cc_start: 0.6546 (t0) cc_final: 0.5912 (p0) REVERT: D 779 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6926 (ptmt) REVERT: D 819 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7377 (mm) REVERT: D 830 ARG cc_start: 0.6898 (mpt-90) cc_final: 0.6530 (mtp180) REVERT: D 847 MET cc_start: 0.5539 (OUTLIER) cc_final: 0.4853 (mmm) REVERT: E 5 ARG cc_start: 0.7497 (ttp80) cc_final: 0.6990 (ttp-110) REVERT: E 77 LYS cc_start: 0.8035 (mttm) cc_final: 0.7725 (mtpp) REVERT: E 209 ARG cc_start: 0.7170 (mmm-85) cc_final: 0.6955 (mpt90) REVERT: E 249 LYS cc_start: 0.7710 (mmtp) cc_final: 0.7324 (mppt) REVERT: E 354 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6224 (mm-30) REVERT: E 368 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6432 (tt0) REVERT: E 404 MET cc_start: 0.7416 (ttm) cc_final: 0.7010 (tpt) REVERT: E 458 MET cc_start: 0.6179 (mtp) cc_final: 0.5732 (mtm) REVERT: E 497 MET cc_start: 0.8378 (mtm) cc_final: 0.8076 (mtm) REVERT: E 513 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8012 (pt) REVERT: E 592 SER cc_start: 0.6542 (m) cc_final: 0.6185 (p) REVERT: E 597 GLU cc_start: 0.6374 (pm20) cc_final: 0.5939 (mm-30) REVERT: E 625 ASN cc_start: 0.6376 (t0) cc_final: 0.6126 (m110) REVERT: E 661 GLU cc_start: 0.6531 (mt-10) cc_final: 0.6197 (mt-10) REVERT: F 346 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.5881 (tt) REVERT: F 352 ARG cc_start: 0.7228 (mtp85) cc_final: 0.6835 (mmm160) REVERT: F 362 GLN cc_start: 0.8395 (tt0) cc_final: 0.7956 (tt0) REVERT: F 420 THR cc_start: 0.7611 (p) cc_final: 0.7405 (t) REVERT: F 446 ARG cc_start: 0.7406 (ptt90) cc_final: 0.6497 (ptp-110) REVERT: F 696 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.7223 (tpt170) REVERT: G 130 LYS cc_start: 0.7045 (pttp) cc_final: 0.6791 (ptpt) REVERT: G 190 GLU cc_start: 0.6518 (mt-10) cc_final: 0.6296 (mt-10) REVERT: G 247 ARG cc_start: 0.8084 (ttt90) cc_final: 0.7604 (ttp80) REVERT: G 291 GLN cc_start: 0.7826 (mt0) cc_final: 0.7585 (mm110) REVERT: G 297 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: G 386 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7270 (mppt) REVERT: G 396 ASP cc_start: 0.4997 (p0) cc_final: 0.4404 (t0) REVERT: G 412 ASN cc_start: 0.7576 (t0) cc_final: 0.7054 (m-40) REVERT: G 475 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7459 (ttmt) REVERT: G 498 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5778 (mtt) REVERT: G 502 VAL cc_start: 0.5914 (OUTLIER) cc_final: 0.5644 (t) REVERT: G 529 MET cc_start: 0.7049 (mtm) cc_final: 0.6708 (mtt) REVERT: G 556 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7738 (m) REVERT: G 573 ARG cc_start: 0.6812 (mtp-110) cc_final: 0.6466 (ttt180) REVERT: G 583 ASN cc_start: 0.7200 (p0) cc_final: 0.6957 (p0) REVERT: G 612 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6928 (tp) REVERT: G 690 LEU cc_start: 0.8518 (mt) cc_final: 0.8243 (mt) REVERT: H 79 TYR cc_start: 0.6060 (m-80) cc_final: 0.5835 (m-10) REVERT: H 96 ILE cc_start: 0.3596 (OUTLIER) cc_final: 0.3366 (mt) REVERT: H 137 ILE cc_start: 0.4265 (mm) cc_final: 0.3802 (pp) REVERT: H 152 LYS cc_start: 0.4591 (pttp) cc_final: 0.4374 (pptt) REVERT: H 284 PHE cc_start: 0.5538 (m-80) cc_final: 0.4878 (m-80) REVERT: H 319 MET cc_start: 0.4068 (OUTLIER) cc_final: 0.3744 (tpp) REVERT: H 331 GLU cc_start: 0.5594 (mt-10) cc_final: 0.5215 (mt-10) REVERT: H 332 LEU cc_start: 0.6216 (mt) cc_final: 0.5866 (tp) REVERT: H 342 ARG cc_start: 0.5311 (ttp-110) cc_final: 0.4272 (ttp80) REVERT: H 389 TYR cc_start: 0.0995 (m-80) cc_final: 0.0768 (m-80) REVERT: I 120 MET cc_start: 0.2950 (OUTLIER) cc_final: 0.1302 (mpt) REVERT: I 152 LYS cc_start: 0.3915 (mttt) cc_final: 0.3569 (tppt) REVERT: I 155 PHE cc_start: 0.2847 (OUTLIER) cc_final: 0.2589 (m-80) REVERT: I 158 LEU cc_start: 0.2593 (tt) cc_final: 0.1891 (mm) REVERT: I 325 LYS cc_start: 0.3569 (mppt) cc_final: 0.3213 (mtmt) REVERT: I 344 PHE cc_start: 0.4301 (m-80) cc_final: 0.4006 (m-10) REVERT: I 382 MET cc_start: 0.2292 (mmp) cc_final: 0.1735 (ptp) REVERT: I 662 GLU cc_start: 0.6551 (tt0) cc_final: 0.6201 (tp30) REVERT: I 687 ASP cc_start: 0.5502 (OUTLIER) cc_final: 0.5297 (t0) outliers start: 290 outliers final: 133 residues processed: 1126 average time/residue: 1.5902 time to fit residues: 2326.3905 Evaluate side-chains 1080 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 881 time to evaluate : 5.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 670 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 689 GLU Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 3 residue 537 ASP Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 232 GLU Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 366 GLN Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 490 VAL Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 553 THR Chi-restraints excluded: chain 4 residue 636 LYS Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 5 ARG Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 177 THR Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 404 MET Chi-restraints excluded: chain 5 residue 484 LYS Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 646 ILE Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 133 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 501 GLN Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 92 LYS Chi-restraints excluded: chain 7 residue 124 ASN Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 317 GLU Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain 7 residue 651 VAL Chi-restraints excluded: chain 7 residue 656 VAL Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 456 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 475 LYS Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 612 LEU Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 271 ARG Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 298 THR Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 155 PHE Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 665 ARG Chi-restraints excluded: chain I residue 687 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 745 optimal weight: 3.9990 chunk 784 optimal weight: 2.9990 chunk 716 optimal weight: 7.9990 chunk 763 optimal weight: 3.9990 chunk 459 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 599 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 689 optimal weight: 10.0000 chunk 722 optimal weight: 1.9990 chunk 760 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 353 GLN 2 651 ASN 2 666 ASN 3 324 ASN 3 503 HIS 4 613 GLN ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 587 GLN 6 156 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 90 ASN 7 297 GLN C 340 GLN C 688 ASN D 229 GLN D 253 GLN D 576 GLN D 685 ASN E 560 HIS E 685 GLN F 269 ASN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 69476 Z= 0.326 Angle : 0.657 14.997 93996 Z= 0.336 Chirality : 0.047 0.336 10834 Planarity : 0.005 0.064 12062 Dihedral : 7.413 178.080 9630 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 3.87 % Allowed : 19.79 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.20 (0.09), residues: 8483 helix: 1.03 (0.09), residues: 3536 sheet: -0.50 (0.12), residues: 1624 loop : -0.37 (0.10), residues: 3323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 112 HIS 0.016 0.001 HIS F 653 PHE 0.027 0.002 PHE I 702 TYR 0.026 0.002 TYR 6 136 ARG 0.010 0.001 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 882 time to evaluate : 6.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 232 ARG cc_start: 0.6551 (mmm-85) cc_final: 0.5883 (mtp180) REVERT: 2 269 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6535 (ttmt) REVERT: 2 326 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.6538 (pmt170) REVERT: 2 374 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5321 (ttm110) REVERT: 2 422 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6823 (pp20) REVERT: 2 684 ARG cc_start: 0.4094 (OUTLIER) cc_final: 0.3235 (ptp90) REVERT: 2 789 VAL cc_start: 0.8240 (p) cc_final: 0.7974 (t) REVERT: 2 798 ILE cc_start: 0.5438 (mt) cc_final: 0.5004 (pt) REVERT: 2 847 ASP cc_start: 0.6913 (t0) cc_final: 0.6640 (t0) REVERT: 3 40 ASP cc_start: 0.6648 (p0) cc_final: 0.6387 (m-30) REVERT: 3 117 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: 3 188 LYS cc_start: 0.8082 (mtmm) cc_final: 0.7129 (ttpt) REVERT: 3 234 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: 3 274 ILE cc_start: 0.8511 (pt) cc_final: 0.8290 (tt) REVERT: 3 315 ILE cc_start: 0.5476 (OUTLIER) cc_final: 0.5051 (mm) REVERT: 3 318 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7224 (tmtt) REVERT: 3 353 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8587 (mm) REVERT: 3 357 LYS cc_start: 0.7474 (pmtt) cc_final: 0.6652 (ptpt) REVERT: 3 362 ILE cc_start: 0.8124 (mt) cc_final: 0.7776 (mt) REVERT: 3 365 GLN cc_start: 0.7390 (mm-40) cc_final: 0.6944 (mm110) REVERT: 3 455 ARG cc_start: 0.6003 (mmm160) cc_final: 0.5760 (mtt180) REVERT: 3 482 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6426 (t70) REVERT: 3 587 ASN cc_start: 0.6232 (m-40) cc_final: 0.4536 (t0) REVERT: 4 266 GLN cc_start: 0.7628 (tp40) cc_final: 0.7360 (tp-100) REVERT: 4 296 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7741 (mm) REVERT: 4 404 ASP cc_start: 0.6944 (m-30) cc_final: 0.6573 (m-30) REVERT: 4 411 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8014 (p) REVERT: 4 534 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: 4 579 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7452 (mm-40) REVERT: 4 583 LYS cc_start: 0.8165 (mmpt) cc_final: 0.7582 (mtmm) REVERT: 4 594 LYS cc_start: 0.6148 (ttpp) cc_final: 0.5768 (tptp) REVERT: 4 636 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7612 (mtpt) REVERT: 4 715 LYS cc_start: 0.7050 (pttp) cc_final: 0.6482 (mmtp) REVERT: 4 726 ASN cc_start: 0.7712 (m-40) cc_final: 0.7364 (t0) REVERT: 4 729 LEU cc_start: 0.8045 (mt) cc_final: 0.7737 (mt) REVERT: 4 756 GLU cc_start: 0.7513 (tt0) cc_final: 0.7207 (tp30) REVERT: 5 5 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6707 (tmm-80) REVERT: 5 29 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7656 (mttp) REVERT: 5 72 ASN cc_start: 0.7677 (t0) cc_final: 0.7425 (t0) REVERT: 5 145 GLN cc_start: 0.7152 (mt0) cc_final: 0.6845 (mm-40) REVERT: 5 358 LEU cc_start: 0.5726 (mt) cc_final: 0.5340 (tm) REVERT: 5 369 ILE cc_start: 0.7638 (pt) cc_final: 0.7427 (tt) REVERT: 5 388 ILE cc_start: 0.8234 (mt) cc_final: 0.8005 (mm) REVERT: 5 404 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.5818 (mmm) REVERT: 5 458 MET cc_start: 0.6334 (pmm) cc_final: 0.4452 (ptp) REVERT: 5 469 MET cc_start: 0.7947 (mmm) cc_final: 0.7598 (mmm) REVERT: 5 581 ASN cc_start: 0.5431 (t0) cc_final: 0.4788 (m-40) REVERT: 5 625 ASN cc_start: 0.6175 (m110) cc_final: 0.5331 (t0) REVERT: 5 654 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6957 (mt-10) REVERT: 5 675 ARG cc_start: 0.7181 (ttp80) cc_final: 0.6952 (ptt90) REVERT: 5 689 MET cc_start: 0.7113 (mmm) cc_final: 0.6745 (mmm) REVERT: 6 133 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.4851 (pm20) REVERT: 6 174 TYR cc_start: 0.8057 (t80) cc_final: 0.7473 (t80) REVERT: 6 299 GLU cc_start: 0.7079 (pm20) cc_final: 0.6419 (mt-10) REVERT: 6 347 ASN cc_start: 0.6619 (t0) cc_final: 0.5967 (m-40) REVERT: 6 614 ARG cc_start: 0.6718 (ttp-170) cc_final: 0.6425 (ttm110) REVERT: 6 643 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7680 (mmpt) REVERT: 6 675 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7450 (mpp-170) REVERT: 6 724 ASP cc_start: 0.7348 (m-30) cc_final: 0.6991 (m-30) REVERT: 6 764 ILE cc_start: 0.7407 (mt) cc_final: 0.6717 (pp) REVERT: 6 783 ASP cc_start: 0.6239 (t0) cc_final: 0.5832 (t0) REVERT: 6 833 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6548 (mp10) REVERT: 7 8 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8382 (tt) REVERT: 7 69 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7724 (mtpt) REVERT: 7 76 ASN cc_start: 0.7852 (t0) cc_final: 0.7409 (m110) REVERT: 7 81 ASP cc_start: 0.7702 (m-30) cc_final: 0.7417 (t0) REVERT: 7 92 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6925 (mttt) REVERT: 7 124 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7225 (p0) REVERT: 7 159 ASN cc_start: 0.7371 (m-40) cc_final: 0.6981 (m110) REVERT: 7 160 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6233 (pt0) REVERT: 7 162 ARG cc_start: 0.7375 (ttm-80) cc_final: 0.7031 (ttm-80) REVERT: 7 188 GLU cc_start: 0.6398 (tt0) cc_final: 0.6115 (tt0) REVERT: 7 233 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6889 (p0) REVERT: 7 244 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8532 (tp) REVERT: 7 247 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7450 (ttp80) REVERT: 7 449 LYS cc_start: 0.7363 (mtmt) cc_final: 0.6871 (tmtp) REVERT: 7 499 LYS cc_start: 0.6973 (tptm) cc_final: 0.6516 (ttmt) REVERT: 7 502 VAL cc_start: 0.4926 (OUTLIER) cc_final: 0.4413 (t) REVERT: 7 537 ILE cc_start: 0.7837 (mt) cc_final: 0.7520 (tt) REVERT: 7 660 VAL cc_start: 0.8163 (t) cc_final: 0.7876 (t) REVERT: B 184 GLU cc_start: 0.4779 (mm-30) cc_final: 0.4384 (tm-30) REVERT: B 198 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7585 (mp) REVERT: B 247 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6750 (mtm180) REVERT: B 269 LYS cc_start: 0.6549 (ttmm) cc_final: 0.5074 (mppt) REVERT: B 496 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6684 (ttmm) REVERT: B 536 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7386 (p0) REVERT: B 617 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7325 (mtt90) REVERT: B 705 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5767 (mtp180) REVERT: B 834 LEU cc_start: 0.6850 (mm) cc_final: 0.6327 (tp) REVERT: C 36 THR cc_start: 0.7533 (p) cc_final: 0.7046 (m) REVERT: C 43 ARG cc_start: 0.6860 (tpt90) cc_final: 0.6273 (ttm170) REVERT: C 51 ASN cc_start: 0.6424 (m-40) cc_final: 0.6198 (m110) REVERT: C 188 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7699 (mttp) REVERT: C 205 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7626 (mtpt) REVERT: C 222 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8382 (p) REVERT: C 234 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6114 (mp0) REVERT: C 235 ASP cc_start: 0.7243 (p0) cc_final: 0.6882 (p0) REVERT: C 237 GLU cc_start: 0.7012 (mp0) cc_final: 0.6596 (mt-10) REVERT: C 348 ARG cc_start: 0.7024 (mtm110) cc_final: 0.6428 (mtt90) REVERT: C 456 ARG cc_start: 0.6002 (OUTLIER) cc_final: 0.5471 (ppt-90) REVERT: C 477 LYS cc_start: 0.7132 (mttm) cc_final: 0.6661 (mttp) REVERT: C 505 THR cc_start: 0.8498 (t) cc_final: 0.8036 (m) REVERT: C 556 ILE cc_start: 0.7338 (pt) cc_final: 0.6883 (mm) REVERT: C 656 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7545 (tp) REVERT: C 664 LYS cc_start: 0.7620 (mtpp) cc_final: 0.7193 (mtpt) REVERT: C 681 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7560 (tmmm) REVERT: C 723 LYS cc_start: 0.7360 (pttt) cc_final: 0.6764 (ttmm) REVERT: D 212 ARG cc_start: 0.6071 (OUTLIER) cc_final: 0.5284 (mtm-85) REVERT: D 235 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6165 (tp30) REVERT: D 302 LYS cc_start: 0.7733 (mmtp) cc_final: 0.7118 (mtpp) REVERT: D 327 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.8026 (t0) REVERT: D 394 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8647 (tmtp) REVERT: D 408 ASP cc_start: 0.7576 (m-30) cc_final: 0.7284 (m-30) REVERT: D 445 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7079 (mtt90) REVERT: D 483 GLN cc_start: 0.6755 (tp40) cc_final: 0.5922 (mt0) REVERT: D 534 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: D 690 GLU cc_start: 0.6758 (tt0) cc_final: 0.6265 (tp30) REVERT: D 693 ASP cc_start: 0.6570 (t0) cc_final: 0.5932 (p0) REVERT: D 772 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7028 (ttp80) REVERT: D 779 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6910 (ptmt) REVERT: D 819 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7405 (mm) REVERT: D 830 ARG cc_start: 0.6993 (mpt-90) cc_final: 0.6581 (mtp180) REVERT: D 847 MET cc_start: 0.5566 (OUTLIER) cc_final: 0.5348 (mmm) REVERT: E 77 LYS cc_start: 0.8045 (mttm) cc_final: 0.7747 (mtpp) REVERT: E 209 ARG cc_start: 0.7122 (mmm-85) cc_final: 0.6751 (mpt90) REVERT: E 221 MET cc_start: 0.3858 (OUTLIER) cc_final: 0.3383 (pmm) REVERT: E 249 LYS cc_start: 0.7784 (mmtp) cc_final: 0.7379 (mppt) REVERT: E 354 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6141 (mm-30) REVERT: E 368 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6476 (tt0) REVERT: E 404 MET cc_start: 0.7438 (ttm) cc_final: 0.6996 (tpt) REVERT: E 458 MET cc_start: 0.6290 (mtp) cc_final: 0.6003 (mtm) REVERT: E 513 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7893 (pt) REVERT: E 597 GLU cc_start: 0.6409 (pm20) cc_final: 0.6053 (mm-30) REVERT: E 625 ASN cc_start: 0.6540 (t0) cc_final: 0.6224 (m110) REVERT: E 661 GLU cc_start: 0.6524 (mt-10) cc_final: 0.6194 (mt-10) REVERT: F 346 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6103 (tt) REVERT: F 352 ARG cc_start: 0.7219 (mtp85) cc_final: 0.6824 (mmm160) REVERT: F 362 GLN cc_start: 0.8428 (tt0) cc_final: 0.7982 (tt0) REVERT: F 446 ARG cc_start: 0.7410 (ptt90) cc_final: 0.6517 (ptp-110) REVERT: F 696 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.7199 (tpt170) REVERT: F 826 GLU cc_start: 0.6211 (tp30) cc_final: 0.5660 (mp0) REVERT: G 130 LYS cc_start: 0.7205 (pttp) cc_final: 0.6970 (ptpt) REVERT: G 190 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6271 (mt-10) REVERT: G 247 ARG cc_start: 0.8092 (ttt90) cc_final: 0.7601 (ttp80) REVERT: G 276 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6974 (mtm-85) REVERT: G 297 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: G 396 ASP cc_start: 0.4929 (p0) cc_final: 0.4383 (t0) REVERT: G 402 MET cc_start: 0.5704 (mmm) cc_final: 0.5472 (tmm) REVERT: G 412 ASN cc_start: 0.7604 (t0) cc_final: 0.7092 (m-40) REVERT: G 475 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7639 (ttmt) REVERT: G 502 VAL cc_start: 0.6058 (OUTLIER) cc_final: 0.5737 (t) REVERT: G 529 MET cc_start: 0.7088 (mtm) cc_final: 0.6736 (mtt) REVERT: G 556 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7787 (m) REVERT: G 573 ARG cc_start: 0.6761 (mtp-110) cc_final: 0.6409 (ttt180) REVERT: G 583 ASN cc_start: 0.7426 (p0) cc_final: 0.7194 (p0) REVERT: G 612 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.6980 (tp) REVERT: G 690 LEU cc_start: 0.8553 (mt) cc_final: 0.8285 (mt) REVERT: H 35 LEU cc_start: 0.4676 (tt) cc_final: 0.4220 (mp) REVERT: H 96 ILE cc_start: 0.3640 (OUTLIER) cc_final: 0.3403 (mt) REVERT: H 152 LYS cc_start: 0.4441 (pttp) cc_final: 0.4239 (pptt) REVERT: H 284 PHE cc_start: 0.5751 (m-80) cc_final: 0.4809 (m-80) REVERT: H 331 GLU cc_start: 0.5463 (mt-10) cc_final: 0.5118 (mt-10) REVERT: H 332 LEU cc_start: 0.6147 (mt) cc_final: 0.5804 (tp) REVERT: H 379 LYS cc_start: 0.4191 (mmmm) cc_final: 0.3697 (tptp) REVERT: H 389 TYR cc_start: 0.1277 (m-80) cc_final: 0.1027 (m-80) REVERT: H 443 PHE cc_start: 0.3071 (m-80) cc_final: 0.2850 (m-80) REVERT: I 120 MET cc_start: 0.2789 (OUTLIER) cc_final: 0.1319 (mpt) REVERT: I 152 LYS cc_start: 0.3961 (mttt) cc_final: 0.3682 (tppt) REVERT: I 155 PHE cc_start: 0.2516 (OUTLIER) cc_final: 0.2293 (m-80) REVERT: I 158 LEU cc_start: 0.2649 (tt) cc_final: 0.1933 (mm) REVERT: I 325 LYS cc_start: 0.3419 (mppt) cc_final: 0.3013 (mtmt) REVERT: I 382 MET cc_start: 0.2312 (mmp) cc_final: 0.1744 (ptp) REVERT: I 662 GLU cc_start: 0.6569 (tt0) cc_final: 0.6210 (tp30) REVERT: I 687 ASP cc_start: 0.5614 (OUTLIER) cc_final: 0.5390 (t0) REVERT: I 698 GLU cc_start: 0.4735 (tt0) cc_final: 0.3736 (pp20) outliers start: 294 outliers final: 166 residues processed: 1083 average time/residue: 1.5917 time to fit residues: 2226.0375 Evaluate side-chains 1094 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 864 time to evaluate : 6.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 269 LYS Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 670 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 117 GLU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 482 ASP Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 3 residue 537 ASP Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 232 GLU Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 490 VAL Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 553 THR Chi-restraints excluded: chain 4 residue 636 LYS Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 686 LEU Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 5 ARG Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 177 THR Chi-restraints excluded: chain 5 residue 242 ILE Chi-restraints excluded: chain 5 residue 275 THR Chi-restraints excluded: chain 5 residue 323 ILE Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 404 MET Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 484 LYS Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 646 ILE Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 133 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 501 GLN Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 643 LYS Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 92 LYS Chi-restraints excluded: chain 7 residue 124 ASN Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 233 ASP Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 317 GLU Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 553 ILE Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain 7 residue 651 VAL Chi-restraints excluded: chain 7 residue 656 VAL Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 456 ARG Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 651 GLN Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 645 ASP Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 276 ARG Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 475 LYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 612 LEU Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 271 ARG Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 298 THR Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 155 PHE Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 665 ARG Chi-restraints excluded: chain I residue 687 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 501 optimal weight: 0.9990 chunk 807 optimal weight: 6.9990 chunk 492 optimal weight: 0.9990 chunk 382 optimal weight: 0.7980 chunk 561 optimal weight: 0.7980 chunk 846 optimal weight: 7.9990 chunk 779 optimal weight: 0.6980 chunk 674 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 520 optimal weight: 6.9990 chunk 413 optimal weight: 0.0000 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 666 ASN 3 324 ASN 3 503 HIS 4 613 GLN 5 273 ASN 5 587 GLN 6 156 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN 7 297 GLN 7 623 ASN C 532 ASN D 229 GLN D 253 GLN D 576 GLN ** D 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 ASN E 560 HIS E 685 GLN F 269 ASN F 347 ASN F 364 ASN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 321 GLN I 372 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 69476 Z= 0.167 Angle : 0.563 14.643 93996 Z= 0.288 Chirality : 0.043 0.324 10834 Planarity : 0.004 0.056 12062 Dihedral : 7.156 178.734 9630 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.48 % Rotamer: Outliers : 2.79 % Allowed : 21.07 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.45 (0.09), residues: 8483 helix: 1.28 (0.09), residues: 3534 sheet: -0.45 (0.13), residues: 1630 loop : -0.25 (0.10), residues: 3319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 112 HIS 0.015 0.001 HIS F 653 PHE 0.037 0.001 PHE I 344 TYR 0.021 0.001 TYR B 769 ARG 0.012 0.000 ARG 4 772 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 920 time to evaluate : 6.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 232 ARG cc_start: 0.6524 (mmm-85) cc_final: 0.5867 (mtp180) REVERT: 2 326 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6228 (pmt170) REVERT: 2 374 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.5311 (ttm110) REVERT: 2 422 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6662 (pp20) REVERT: 2 457 LYS cc_start: 0.5924 (mmmt) cc_final: 0.5697 (ttmm) REVERT: 2 667 VAL cc_start: 0.7012 (OUTLIER) cc_final: 0.6686 (p) REVERT: 2 684 ARG cc_start: 0.4037 (OUTLIER) cc_final: 0.3245 (ptp90) REVERT: 2 783 MET cc_start: 0.6461 (ttt) cc_final: 0.6257 (ttp) REVERT: 2 789 VAL cc_start: 0.8174 (p) cc_final: 0.7922 (t) REVERT: 2 798 ILE cc_start: 0.5573 (mt) cc_final: 0.5123 (pt) REVERT: 2 847 ASP cc_start: 0.6894 (t0) cc_final: 0.6654 (t0) REVERT: 3 40 ASP cc_start: 0.6680 (p0) cc_final: 0.6404 (m-30) REVERT: 3 188 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7171 (ttpt) REVERT: 3 234 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6173 (tm-30) REVERT: 3 261 MET cc_start: 0.7859 (mtm) cc_final: 0.7460 (mtt) REVERT: 3 274 ILE cc_start: 0.8775 (pt) cc_final: 0.8334 (tt) REVERT: 3 315 ILE cc_start: 0.5234 (OUTLIER) cc_final: 0.4858 (mm) REVERT: 3 318 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7153 (tmtt) REVERT: 3 357 LYS cc_start: 0.7226 (pmtt) cc_final: 0.6545 (ptpt) REVERT: 3 362 ILE cc_start: 0.8076 (mt) cc_final: 0.7808 (mt) REVERT: 3 365 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6531 (mt0) REVERT: 3 455 ARG cc_start: 0.6018 (mmm160) cc_final: 0.5767 (mtt180) REVERT: 3 504 THR cc_start: 0.8303 (p) cc_final: 0.8021 (t) REVERT: 3 587 ASN cc_start: 0.6177 (m-40) cc_final: 0.4481 (t0) REVERT: 3 688 ASN cc_start: 0.7337 (m-40) cc_final: 0.6968 (m110) REVERT: 3 719 LYS cc_start: 0.7580 (mttm) cc_final: 0.7219 (mmtt) REVERT: 4 266 GLN cc_start: 0.7439 (tp40) cc_final: 0.7171 (tp-100) REVERT: 4 296 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7622 (mm) REVERT: 4 404 ASP cc_start: 0.6854 (m-30) cc_final: 0.6487 (m-30) REVERT: 4 411 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8168 (p) REVERT: 4 534 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: 4 579 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7404 (mm-40) REVERT: 4 583 LYS cc_start: 0.8193 (mmpt) cc_final: 0.7661 (mtpt) REVERT: 4 610 ASP cc_start: 0.6698 (m-30) cc_final: 0.6487 (m-30) REVERT: 4 612 LYS cc_start: 0.7700 (mmpt) cc_final: 0.7154 (mmtp) REVERT: 4 715 LYS cc_start: 0.7066 (pttp) cc_final: 0.6507 (mmtp) REVERT: 4 726 ASN cc_start: 0.7694 (m-40) cc_final: 0.7353 (t0) REVERT: 4 729 LEU cc_start: 0.7966 (mt) cc_final: 0.7709 (mt) REVERT: 4 756 GLU cc_start: 0.7468 (tt0) cc_final: 0.7170 (tp30) REVERT: 5 5 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6017 (tmm-80) REVERT: 5 29 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7592 (mttp) REVERT: 5 72 ASN cc_start: 0.7578 (t0) cc_final: 0.7291 (t0) REVERT: 5 275 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8610 (m) REVERT: 5 358 LEU cc_start: 0.5550 (mt) cc_final: 0.5242 (tm) REVERT: 5 369 ILE cc_start: 0.7606 (pt) cc_final: 0.7397 (tt) REVERT: 5 404 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.5570 (mmm) REVERT: 5 458 MET cc_start: 0.6385 (pmm) cc_final: 0.4667 (ptp) REVERT: 5 469 MET cc_start: 0.7788 (mmm) cc_final: 0.7527 (mmm) REVERT: 5 581 ASN cc_start: 0.5464 (t0) cc_final: 0.4642 (m-40) REVERT: 5 594 ILE cc_start: 0.7326 (mt) cc_final: 0.6999 (mm) REVERT: 5 599 MET cc_start: 0.7245 (tpt) cc_final: 0.6972 (mtp) REVERT: 5 625 ASN cc_start: 0.6191 (m110) cc_final: 0.5366 (t0) REVERT: 5 654 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6958 (mt-10) REVERT: 5 689 MET cc_start: 0.7023 (mmm) cc_final: 0.6700 (mmm) REVERT: 6 133 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.4795 (pm20) REVERT: 6 174 TYR cc_start: 0.8037 (t80) cc_final: 0.7485 (t80) REVERT: 6 299 GLU cc_start: 0.7055 (pm20) cc_final: 0.6348 (mt-10) REVERT: 6 347 ASN cc_start: 0.6587 (t0) cc_final: 0.5945 (m-40) REVERT: 6 614 ARG cc_start: 0.6499 (ttp-170) cc_final: 0.6260 (ttm110) REVERT: 6 724 ASP cc_start: 0.7073 (m-30) cc_final: 0.6727 (m-30) REVERT: 6 753 ARG cc_start: 0.6947 (mtm110) cc_final: 0.6705 (ttm-80) REVERT: 6 764 ILE cc_start: 0.7246 (mt) cc_final: 0.6623 (pp) REVERT: 6 783 ASP cc_start: 0.6074 (t0) cc_final: 0.5723 (t0) REVERT: 6 794 ARG cc_start: 0.5447 (mtp-110) cc_final: 0.4992 (mtp-110) REVERT: 6 833 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6641 (mp10) REVERT: 7 8 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8349 (tt) REVERT: 7 69 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7703 (mtpt) REVERT: 7 76 ASN cc_start: 0.7820 (t0) cc_final: 0.7328 (m110) REVERT: 7 81 ASP cc_start: 0.7768 (m-30) cc_final: 0.7456 (t0) REVERT: 7 92 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6821 (mttt) REVERT: 7 124 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.6745 (p0) REVERT: 7 159 ASN cc_start: 0.7289 (m-40) cc_final: 0.6925 (m110) REVERT: 7 160 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6327 (pt0) REVERT: 7 162 ARG cc_start: 0.7247 (ttm-80) cc_final: 0.7001 (ttm170) REVERT: 7 188 GLU cc_start: 0.6168 (tt0) cc_final: 0.5882 (tt0) REVERT: 7 207 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7462 (pt) REVERT: 7 244 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8404 (tp) REVERT: 7 247 ARG cc_start: 0.7838 (tpp80) cc_final: 0.7506 (ttp80) REVERT: 7 499 LYS cc_start: 0.7018 (tptm) cc_final: 0.6322 (ttmt) REVERT: 7 502 VAL cc_start: 0.4806 (OUTLIER) cc_final: 0.4331 (t) REVERT: 7 537 ILE cc_start: 0.7757 (mt) cc_final: 0.7550 (tt) REVERT: B 184 GLU cc_start: 0.4617 (mm-30) cc_final: 0.4204 (tm-30) REVERT: B 198 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7542 (mp) REVERT: B 247 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6748 (mtm180) REVERT: B 267 MET cc_start: 0.7188 (mmm) cc_final: 0.6906 (mmm) REVERT: B 269 LYS cc_start: 0.6395 (ttmm) cc_final: 0.4975 (mppt) REVERT: B 378 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5482 (tm-30) REVERT: B 496 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6608 (ttmm) REVERT: B 536 ASP cc_start: 0.7752 (p0) cc_final: 0.7099 (p0) REVERT: B 761 GLU cc_start: 0.7064 (mp0) cc_final: 0.6288 (tm-30) REVERT: B 834 LEU cc_start: 0.6810 (mm) cc_final: 0.6330 (tp) REVERT: C 36 THR cc_start: 0.7436 (p) cc_final: 0.6887 (m) REVERT: C 51 ASN cc_start: 0.6432 (m-40) cc_final: 0.6213 (m110) REVERT: C 188 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7620 (mttp) REVERT: C 205 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7607 (mtpt) REVERT: C 222 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8331 (p) REVERT: C 234 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6120 (mp0) REVERT: C 235 ASP cc_start: 0.7177 (p0) cc_final: 0.6806 (p0) REVERT: C 237 GLU cc_start: 0.7022 (mp0) cc_final: 0.6618 (mt-10) REVERT: C 348 ARG cc_start: 0.7007 (mtm110) cc_final: 0.6423 (mtt90) REVERT: C 464 LEU cc_start: 0.8020 (mt) cc_final: 0.7680 (mt) REVERT: C 477 LYS cc_start: 0.7069 (mttm) cc_final: 0.6619 (mtmm) REVERT: C 490 MET cc_start: 0.8620 (mtm) cc_final: 0.8396 (mtm) REVERT: C 505 THR cc_start: 0.8509 (t) cc_final: 0.8095 (m) REVERT: C 556 ILE cc_start: 0.7167 (pt) cc_final: 0.6780 (mm) REVERT: C 557 ARG cc_start: 0.6060 (ttt-90) cc_final: 0.5728 (tpt-90) REVERT: C 656 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7467 (tp) REVERT: C 664 LYS cc_start: 0.7562 (mtpp) cc_final: 0.7145 (mtpt) REVERT: C 667 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8167 (t) REVERT: C 681 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7493 (tmmm) REVERT: C 723 LYS cc_start: 0.7266 (pttt) cc_final: 0.6689 (ttmm) REVERT: D 235 GLU cc_start: 0.6475 (mt-10) cc_final: 0.5826 (tp30) REVERT: D 302 LYS cc_start: 0.7620 (mmtp) cc_final: 0.7108 (mtpp) REVERT: D 408 ASP cc_start: 0.7501 (m-30) cc_final: 0.7215 (m-30) REVERT: D 434 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7126 (mp0) REVERT: D 445 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6958 (mtt180) REVERT: D 483 GLN cc_start: 0.6696 (tp40) cc_final: 0.5908 (mt0) REVERT: D 534 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7021 (tp30) REVERT: D 644 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8395 (m) REVERT: D 690 GLU cc_start: 0.6886 (tt0) cc_final: 0.6343 (tp30) REVERT: D 693 ASP cc_start: 0.6534 (t0) cc_final: 0.5891 (p0) REVERT: D 772 ARG cc_start: 0.7463 (ttp80) cc_final: 0.7065 (ttp80) REVERT: D 779 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.7020 (tttp) REVERT: D 819 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7446 (mm) REVERT: D 830 ARG cc_start: 0.6913 (mpt-90) cc_final: 0.6592 (mtp180) REVERT: D 847 MET cc_start: 0.5443 (OUTLIER) cc_final: 0.4797 (mmm) REVERT: E 5 ARG cc_start: 0.7462 (ttp80) cc_final: 0.6946 (ttp-110) REVERT: E 77 LYS cc_start: 0.8010 (mttm) cc_final: 0.7717 (mtpp) REVERT: E 249 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7349 (mppt) REVERT: E 354 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6214 (mt-10) REVERT: E 368 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6326 (tt0) REVERT: E 404 MET cc_start: 0.7395 (ttm) cc_final: 0.7009 (tpt) REVERT: E 458 MET cc_start: 0.6271 (mtp) cc_final: 0.5831 (mtm) REVERT: E 469 MET cc_start: 0.7986 (mmm) cc_final: 0.7498 (mmm) REVERT: E 513 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7846 (pp) REVERT: E 592 SER cc_start: 0.6459 (m) cc_final: 0.6052 (p) REVERT: E 597 GLU cc_start: 0.6415 (pm20) cc_final: 0.5956 (mm-30) REVERT: E 599 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7157 (tpp) REVERT: E 625 ASN cc_start: 0.6459 (t0) cc_final: 0.6179 (m110) REVERT: E 656 ILE cc_start: 0.7635 (mt) cc_final: 0.7405 (mm) REVERT: E 661 GLU cc_start: 0.6545 (mt-10) cc_final: 0.6171 (mt-10) REVERT: F 338 CYS cc_start: 0.2544 (OUTLIER) cc_final: 0.1159 (m) REVERT: F 346 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6043 (tt) REVERT: F 352 ARG cc_start: 0.7265 (mtp85) cc_final: 0.6838 (mmm160) REVERT: F 362 GLN cc_start: 0.8407 (tt0) cc_final: 0.7972 (tt0) REVERT: F 446 ARG cc_start: 0.7355 (ptt90) cc_final: 0.6445 (ptp-110) REVERT: F 645 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.6429 (p0) REVERT: F 696 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7183 (tpt170) REVERT: F 817 ASP cc_start: 0.6145 (p0) cc_final: 0.5675 (p0) REVERT: G 130 LYS cc_start: 0.7021 (pttp) cc_final: 0.6805 (ptpt) REVERT: G 190 GLU cc_start: 0.6444 (mt-10) cc_final: 0.6196 (mt-10) REVERT: G 247 ARG cc_start: 0.8043 (ttt90) cc_final: 0.7557 (ttp80) REVERT: G 297 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: G 386 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7414 (mppt) REVERT: G 396 ASP cc_start: 0.4826 (p0) cc_final: 0.4363 (t0) REVERT: G 412 ASN cc_start: 0.7605 (t0) cc_final: 0.7087 (m-40) REVERT: G 475 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7455 (ttmt) REVERT: G 498 MET cc_start: 0.5659 (mpp) cc_final: 0.5407 (mtt) REVERT: G 502 VAL cc_start: 0.6052 (OUTLIER) cc_final: 0.5620 (t) REVERT: G 529 MET cc_start: 0.7077 (mtm) cc_final: 0.6752 (OUTLIER) REVERT: G 538 HIS cc_start: 0.7673 (t-90) cc_final: 0.7370 (t-90) REVERT: G 541 MET cc_start: 0.8114 (mtt) cc_final: 0.7333 (mtm) REVERT: G 556 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7640 (m) REVERT: G 573 ARG cc_start: 0.6730 (mtp-110) cc_final: 0.6384 (ttt180) REVERT: G 583 ASN cc_start: 0.7091 (p0) cc_final: 0.6860 (p0) REVERT: G 612 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6897 (tp) REVERT: G 621 MET cc_start: 0.7162 (ttp) cc_final: 0.6913 (ttp) REVERT: G 690 LEU cc_start: 0.8427 (mt) cc_final: 0.8157 (mt) REVERT: H 19 MET cc_start: 0.3144 (mpt) cc_final: 0.2921 (mpt) REVERT: H 96 ILE cc_start: 0.3509 (OUTLIER) cc_final: 0.3255 (mt) REVERT: H 137 ILE cc_start: 0.4359 (mm) cc_final: 0.3913 (pp) REVERT: H 284 PHE cc_start: 0.5734 (m-80) cc_final: 0.4771 (m-80) REVERT: H 331 GLU cc_start: 0.5568 (mt-10) cc_final: 0.5206 (mt-10) REVERT: H 332 LEU cc_start: 0.6164 (mt) cc_final: 0.5878 (tp) REVERT: H 379 LYS cc_start: 0.4345 (mmmm) cc_final: 0.3854 (tptp) REVERT: H 389 TYR cc_start: 0.1099 (m-80) cc_final: 0.0882 (m-80) REVERT: I 120 MET cc_start: 0.2985 (pp-130) cc_final: 0.1364 (mpt) REVERT: I 152 LYS cc_start: 0.4228 (mttt) cc_final: 0.4006 (tppt) REVERT: I 158 LEU cc_start: 0.2814 (tt) cc_final: 0.2096 (mm) REVERT: I 325 LYS cc_start: 0.3367 (mppt) cc_final: 0.3033 (mtmt) REVERT: I 344 PHE cc_start: 0.4387 (m-10) cc_final: 0.4177 (m-10) REVERT: I 382 MET cc_start: 0.2016 (mmp) cc_final: 0.0934 (tpp) REVERT: I 662 GLU cc_start: 0.6519 (tt0) cc_final: 0.6081 (tp30) REVERT: I 698 GLU cc_start: 0.4692 (tt0) cc_final: 0.3688 (pp20) outliers start: 212 outliers final: 113 residues processed: 1063 average time/residue: 1.5467 time to fit residues: 2127.8814 Evaluate side-chains 1040 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 875 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 3 residue 537 ASP Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 232 GLU Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 490 VAL Chi-restraints excluded: chain 4 residue 534 GLU Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 693 ASP Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 5 ARG Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 177 THR Chi-restraints excluded: chain 5 residue 275 THR Chi-restraints excluded: chain 5 residue 323 ILE Chi-restraints excluded: chain 5 residue 342 ILE Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 404 MET Chi-restraints excluded: chain 5 residue 484 LYS Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 646 ILE Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 133 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 92 LYS Chi-restraints excluded: chain 7 residue 124 ASN Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 317 GLU Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain 7 residue 656 VAL Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 645 ASP Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 475 LYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 612 LEU Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 271 ARG Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 298 THR Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 665 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 535 optimal weight: 10.0000 chunk 718 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 621 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 675 optimal weight: 0.7980 chunk 282 optimal weight: 1.9990 chunk 693 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 433 ASN 2 666 ASN 3 324 ASN 3 503 HIS 4 380 ASN 4 613 GLN 5 587 GLN 6 156 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 297 GLN D 229 GLN D 253 GLN D 576 GLN ** D 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 ASN E 560 HIS ** E 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 GLN F 269 ASN F 347 ASN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 384 HIS ** I 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.182844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3838 r_free = 0.3838 target = 0.171787 restraints weight = 70784.838| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 0.31 r_work: 0.3795 rms_B_bonded: 0.59 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 1.08 restraints_weight: 0.2500 r_work: 0.3609 rms_B_bonded: 3.87 restraints_weight: 0.1250 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 69476 Z= 0.194 Angle : 0.615 61.591 93996 Z= 0.309 Chirality : 0.044 1.117 10834 Planarity : 0.004 0.057 12062 Dihedral : 7.154 178.697 9630 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.47 % Rotamer: Outliers : 2.49 % Allowed : 21.50 % Favored : 76.01 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.46 (0.09), residues: 8483 helix: 1.29 (0.09), residues: 3534 sheet: -0.44 (0.13), residues: 1630 loop : -0.25 (0.10), residues: 3319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 112 HIS 0.013 0.001 HIS 6 653 PHE 0.029 0.001 PHE I 344 TYR 0.019 0.001 TYR H 143 ARG 0.013 0.000 ARG B 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31630.13 seconds wall clock time: 544 minutes 30.88 seconds (32670.88 seconds total)