Starting phenix.real_space_refine on Tue Nov 19 16:22:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p63_17459/11_2024/8p63_17459.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p63_17459/11_2024/8p63_17459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p63_17459/11_2024/8p63_17459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p63_17459/11_2024/8p63_17459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p63_17459/11_2024/8p63_17459.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p63_17459/11_2024/8p63_17459.cif" } resolution = 3.7 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= 0.000 sd= 0.001 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 7 6.06 5 P 25 5.49 5 Mg 3 5.21 5 S 239 5.16 5 C 33533 2.51 5 N 9125 2.21 5 O 10028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 52960 Number of models: 1 Model: "" Number of chains: 21 Chain: "2" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5235 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 636} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "3" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5063 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 619} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "4" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4702 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 568} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "5" Number of atoms: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5409 Classifications: {'peptide': 687} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 660} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "6" Number of atoms: 5032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5032 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 21, 'TRANS': 614} Chain breaks: 3 Chain: "7" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5223 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 30, 'TRANS': 632} Chain breaks: 2 Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "C" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain breaks: 2 Chain: "D" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2014 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 229} Chain: "E" Number of atoms: 4276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4276 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 14, 'TRANS': 534} Chain breaks: 4 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLU:plan': 9, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 121 Chain: "F" Number of atoms: 4339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4339 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 513} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 6628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 6628 Classifications: {'peptide': 825} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 32, 'TRANS': 792} Chain breaks: 8 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "H" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1663 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1591 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 9, 'TRANS': 180} Chain breaks: 1 Chain: "2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1330 SG CYS 2 344 25.090 63.793 155.980 1.00183.34 S ATOM 1509 SG CYS 2 367 27.186 67.100 158.326 1.00188.15 S ATOM 11539 SG CYS 4 349 40.885 81.509 191.620 1.00135.19 S ATOM 11560 SG CYS 4 352 39.727 83.304 193.735 1.00144.80 S ATOM 11749 SG CYS 4 376 38.029 80.069 194.545 1.00155.61 S ATOM 16192 SG CYS 5 186 47.128 40.478 152.327 1.00136.17 S ATOM 16342 SG CYS 5 211 44.857 42.455 152.629 1.00147.00 S ATOM 21683 SG CYS 6 311 31.219 79.202 171.793 1.00130.91 S ATOM 21705 SG CYS 6 314 27.617 80.062 171.775 1.00137.74 S ATOM 21862 SG CYS 6 333 29.507 80.507 175.070 1.00136.50 S ATOM 21896 SG CYS 6 338 28.958 77.012 173.762 1.00152.39 S ATOM 27072 SG CYS 7 265 60.390 58.825 199.661 1.00159.84 S ATOM 27263 SG CYS 7 289 59.472 57.646 197.205 1.00178.08 S ATOM 48611 SG CYS G2108 90.481 127.572 49.855 1.00120.80 S ATOM 48638 SG CYS G2111 91.361 131.261 50.566 1.00123.03 S ATOM 48787 SG CYS G2130 88.505 129.375 52.534 1.00113.57 S ATOM 48811 SG CYS G2133 88.276 130.565 48.928 1.00112.12 S ATOM 49074 SG CYS G2164 92.665 95.695 87.758 1.00 66.55 S ATOM 49097 SG CYS G2167 94.881 97.461 90.298 1.00 71.61 S ATOM 49198 SG CYS G2179 95.453 94.004 88.914 1.00 74.04 S Time building chain proxies: 27.64, per 1000 atoms: 0.52 Number of scatterers: 52960 At special positions: 0 Unit cell: (149.04, 171.72, 232.2, 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 7 29.99 S 239 16.00 P 25 15.00 Mg 3 11.99 O 10028 8.00 N 9125 7.00 C 33533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.39 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 902 " pdb="ZN ZN 2 902 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 2 902 " - pdb=" SG CYS 2 367 " pdb=" ZN 41001 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 376 " pdb=" ZN 51702 " pdb="ZN ZN 51702 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 51702 " - pdb=" SG CYS 5 186 " pdb=" ZN 61102 " pdb="ZN ZN 61102 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61102 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61102 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61102 " - pdb=" SG CYS 6 333 " pdb=" ZN 7 901 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 265 " pdb=" ZN G4001 " pdb="ZN ZN G4001 " - pdb=" SG CYS G2133 " pdb="ZN ZN G4001 " - pdb=" SG CYS G2111 " pdb="ZN ZN G4001 " - pdb=" SG CYS G2108 " pdb="ZN ZN G4001 " - pdb=" SG CYS G2130 " pdb=" ZN G4002 " pdb="ZN ZN G4002 " - pdb=" SG CYS G2167 " pdb="ZN ZN G4002 " - pdb=" SG CYS G2164 " pdb="ZN ZN G4002 " - pdb=" SG CYS G2179 " Number of angles added : 12 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12604 Finding SS restraints... Secondary structure from input PDB file: 253 helices and 53 sheets defined 46.0% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain '2' and resid 182 through 187 Processing helix chain '2' and resid 193 through 199 removed outlier: 4.171A pdb=" N THR 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 200 through 216 removed outlier: 3.686A pdb=" N ARG 2 205 " --> pdb=" O PRO 2 201 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 238 removed outlier: 3.647A pdb=" N ALA 2 229 " --> pdb=" O SER 2 225 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 252 removed outlier: 3.621A pdb=" N SER 2 252 " --> pdb=" O HIS 2 248 " (cutoff:3.500A) Processing helix chain '2' and resid 253 through 263 removed outlier: 3.597A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 283 removed outlier: 3.952A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 289 removed outlier: 3.683A pdb=" N ARG 2 288 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 435 through 443 removed outlier: 3.731A pdb=" N ASN 2 439 " --> pdb=" O ASP 2 435 " (cutoff:3.500A) Processing helix chain '2' and resid 477 through 488 Processing helix chain '2' and resid 492 through 500 removed outlier: 3.620A 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 548 through 560 Processing helix chain '2' and resid 572 through 577 removed outlier: 3.556A pdb=" N THR 2 577 " --> pdb=" O ALA 2 573 " (cutoff:3.500A) Processing helix chain '2' and resid 596 through 600 Processing helix chain '2' and resid 613 through 618 Processing helix chain '2' and resid 620 through 625 Processing helix chain '2' and resid 652 through 656 removed outlier: 3.978A pdb=" N ARG 2 656 " --> pdb=" O ASN 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 666 Processing helix chain '2' and resid 670 through 675 Processing helix chain '2' and resid 688 through 706 Processing helix chain '2' and resid 739 through 754 removed outlier: 4.007A pdb=" N GLU 2 754 " --> pdb=" O LYS 2 750 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 773 Processing helix chain '2' and resid 782 through 795 removed outlier: 3.838A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) Processing helix chain '2' and resid 796 through 800 Processing helix chain '2' and resid 806 through 824 removed outlier: 4.221A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 847 removed outlier: 3.619A pdb=" N LEU 2 834 " --> pdb=" O SER 2 830 " (cutoff:3.500A) Processing helix chain '2' and resid 853 through 861 Processing helix chain '3' and resid 19 through 35 Processing helix chain '3' and resid 36 through 54 removed outlier: 4.058A pdb=" N ALA 3 54 " --> pdb=" O SER 3 50 " (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 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 121 through 137 Processing helix chain '3' and resid 145 through 149 removed outlier: 3.527A pdb=" N SER 3 148 " --> pdb=" O SER 3 145 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER 3 149 " --> pdb=" O ALA 3 146 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 145 through 149' 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 343 through 355 Processing helix chain '3' and resid 358 through 366 Processing helix chain '3' and resid 374 through 386 removed outlier: 3.656A pdb=" N MET 3 386 " --> pdb=" O LEU 3 382 " (cutoff:3.500A) Processing helix chain '3' and resid 415 through 426 Processing helix chain '3' and resid 438 through 443 removed outlier: 3.632A pdb=" N THR 3 443 " --> pdb=" O GLY 3 439 " (cutoff:3.500A) Processing helix chain '3' and resid 479 through 493 removed outlier: 3.606A pdb=" N ARG 3 483 " --> pdb=" O THR 3 479 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL 3 484 " --> pdb=" O ASP 3 480 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE 3 486 " --> pdb=" O ASP 3 482 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN 3 492 " --> pdb=" O GLU 3 488 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 533 removed outlier: 3.553A pdb=" N ILE 3 533 " --> pdb=" O PRO 3 529 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 541 Processing helix chain '3' and resid 554 through 570 Processing helix chain '3' and resid 652 through 667 removed outlier: 3.730A pdb=" N GLU 3 665 " --> pdb=" O GLN 3 661 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL 3 667 " --> pdb=" O ALA 3 663 " (cutoff:3.500A) Processing helix chain '3' and resid 672 through 688 Processing helix chain '3' and resid 698 through 716 removed outlier: 3.982A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG 3 716 " --> pdb=" O HIS 3 712 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 removed outlier: 3.577A pdb=" N ALA 3 726 " --> pdb=" O ASN 3 722 " (cutoff:3.500A) Processing helix chain '4' and resid 188 through 200 removed outlier: 4.002A pdb=" N THR 4 192 " --> pdb=" O GLN 4 188 " (cutoff:3.500A) Processing helix chain '4' and resid 203 through 211 Processing helix chain '4' and resid 224 through 237 removed outlier: 3.529A pdb=" N LYS 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) Processing helix chain '4' and resid 245 through 250 Processing helix chain '4' and resid 251 through 264 removed outlier: 4.217A pdb=" N ASP 4 256 " --> pdb=" O LYS 4 252 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU 4 257 " --> pdb=" O GLN 4 253 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 285 removed outlier: 3.552A pdb=" N VAL 4 268 " --> pdb=" O TYR 4 264 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL 4 281 " --> pdb=" O LYS 4 277 " (cutoff:3.500A) Processing helix chain '4' and resid 318 through 322 removed outlier: 3.541A pdb=" N ILE 4 322 " --> pdb=" O PRO 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 403 through 406 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 505 through 514 removed outlier: 3.560A pdb=" N ILE 4 509 " --> pdb=" O ASP 4 505 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG 4 510 " --> pdb=" O LEU 4 506 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU 4 511 " --> pdb=" O ALA 4 507 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 527 removed outlier: 3.873A pdb=" N ILE 4 526 " --> pdb=" O LEU 4 522 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 573 through 585 removed outlier: 3.770A pdb=" N ILE 4 577 " --> pdb=" O SER 4 573 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 619 through 624 Processing helix chain '4' and resid 639 through 649 removed outlier: 4.065A pdb=" N SER 4 643 " --> pdb=" O ASP 4 639 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 removed outlier: 3.946A pdb=" N ASN 4 691 " --> pdb=" O PRO 4 687 " (cutoff:3.500A) Processing helix chain '4' and resid 695 through 701 Processing helix chain '4' and resid 713 through 729 Processing helix chain '4' and resid 745 through 758 Processing helix chain '4' and resid 763 through 781 removed outlier: 3.772A pdb=" N LYS 4 767 " --> pdb=" O THR 4 763 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR 4 768 " --> pdb=" O GLU 4 764 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY 4 781 " --> pdb=" O MET 4 777 " (cutoff:3.500A) Processing helix chain '4' and resid 794 through 811 removed outlier: 3.540A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) Processing helix chain '4' and resid 812 through 814 No H-bonds generated for 'chain '4' and resid 812 through 814' Processing helix chain '4' and resid 818 through 835 removed outlier: 3.794A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) Processing helix chain '5' and resid 21 through 38 Processing helix chain '5' and resid 44 through 57 removed outlier: 3.512A pdb=" N VAL 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) Processing helix chain '5' and resid 65 through 72 Processing helix chain '5' and resid 72 through 82 removed outlier: 4.085A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 101 Proline residue: 5 88 - end of helix removed outlier: 3.740A pdb=" N THR 5 95 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 151 Processing helix chain '5' and resid 152 through 156 removed outlier: 3.607A pdb=" N VAL 5 156 " --> pdb=" O SER 5 153 " (cutoff:3.500A) Processing helix chain '5' and resid 261 through 265 removed outlier: 3.524A pdb=" N VAL 5 265 " --> pdb=" O PRO 5 262 " (cutoff:3.500A) 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 Processing helix chain '5' and resid 365 through 372 Processing helix chain '5' and resid 382 through 394 Processing helix chain '5' and resid 422 through 433 Processing helix chain '5' and resid 481 through 485 Processing helix chain '5' and resid 486 through 491 removed outlier: 3.594A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) Processing helix chain '5' and resid 492 through 499 removed outlier: 4.142A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) Processing helix chain '5' and resid 535 through 539 removed outlier: 3.523A pdb=" N ASP 5 538 " --> pdb=" O SER 5 535 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN 5 539 " --> pdb=" O PRO 5 536 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 535 through 539' Processing helix chain '5' and resid 543 through 550 removed outlier: 3.778A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE 5 550 " --> pdb=" O ILE 5 546 " (cutoff:3.500A) Processing helix chain '5' and resid 562 through 576 Processing helix chain '5' and resid 576 through 590 removed outlier: 3.620A pdb=" N ALA 5 580 " --> pdb=" O HIS 5 576 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN 5 581 " --> pdb=" O THR 5 577 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ALA 5 582 " --> pdb=" O GLY 5 578 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET 5 583 " --> pdb=" O ASN 5 579 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASN 5 585 " --> pdb=" O ASN 5 581 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 615 through 641 Processing helix chain '5' and resid 649 through 667 removed outlier: 3.667A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 690 removed outlier: 3.910A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) Processing helix chain '5' and resid 708 through 722 removed outlier: 3.542A pdb=" N GLU 5 717 " --> pdb=" O ARG 5 713 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS 5 719 " --> pdb=" O GLU 5 715 " (cutoff:3.500A) Processing helix chain '5' and resid 730 through 740 Processing helix chain '5' and resid 742 through 758 removed outlier: 4.209A pdb=" N LEU 5 746 " --> pdb=" O ARG 5 742 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA 5 747 " --> pdb=" O PHE 5 743 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU 5 748 " --> pdb=" O SER 5 744 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP 5 749 " --> pdb=" O GLN 5 745 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS 5 750 " --> pdb=" O LEU 5 746 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 121 Processing helix chain '6' and resid 134 through 147 Processing helix chain '6' and resid 155 through 160 removed outlier: 3.669A pdb=" N MET 6 160 " --> pdb=" O GLN 6 156 " (cutoff:3.500A) Processing helix chain '6' and resid 162 through 165 Processing helix chain '6' and resid 166 through 173 removed outlier: 3.945A pdb=" N GLN 6 173 " --> pdb=" O ALA 6 169 " (cutoff:3.500A) Processing helix chain '6' and resid 173 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 194 through 198 Processing helix chain '6' and resid 275 through 279 Processing helix chain '6' and resid 280 through 284 Processing helix chain '6' and resid 501 through 507 removed outlier: 3.718A pdb=" N SER 6 507 " --> pdb=" O VAL 6 503 " (cutoff:3.500A) Processing helix chain '6' and resid 509 through 522 removed outlier: 3.656A pdb=" N LEU 6 516 " --> pdb=" O GLU 6 512 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 532 removed outlier: 4.057A pdb=" N ARG 6 531 " --> pdb=" O ASP 6 527 " (cutoff:3.500A) Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 581 through 592 removed outlier: 3.885A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 626 through 631 Processing helix chain '6' and resid 645 through 659 removed outlier: 4.633A pdb=" N HIS 6 653 " --> pdb=" O GLN 6 649 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU 6 654 " --> pdb=" O VAL 6 650 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU 6 657 " --> pdb=" O HIS 6 653 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 709 removed outlier: 3.583A pdb=" N PHE 6 709 " --> pdb=" O ILE 6 705 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 736 removed outlier: 3.582A pdb=" N ASP 6 724 " --> pdb=" O ASN 6 720 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR 6 725 " --> pdb=" O GLU 6 721 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU 6 726 " --> pdb=" O LYS 6 722 " (cutoff:3.500A) Processing helix chain '6' and resid 747 through 759 Processing helix chain '6' and resid 766 through 786 removed outlier: 3.657A pdb=" N ASP 6 784 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 814 removed outlier: 3.850A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 840 removed outlier: 3.679A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL 6 838 " --> pdb=" O SER 6 834 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 28 removed outlier: 3.948A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 removed outlier: 3.728A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 93 Processing helix chain '7' and resid 102 through 109 Processing helix chain '7' and resid 110 through 124 Processing helix chain '7' and resid 133 through 136 removed outlier: 3.539A pdb=" N ASP 7 136 " --> pdb=" O ASP 7 133 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 133 through 136' Processing helix chain '7' and resid 137 through 151 Processing helix chain '7' and resid 152 through 154 No H-bonds generated for 'chain '7' and resid 152 through 154' Processing helix chain '7' and resid 193 through 198 removed outlier: 3.790A pdb=" N THR 7 197 " --> pdb=" O PRO 7 193 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 215 removed outlier: 3.913A pdb=" N TYR 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) Processing helix chain '7' and resid 231 through 235 removed outlier: 3.662A pdb=" N LEU 7 235 " --> pdb=" O GLY 7 232 " (cutoff:3.500A) 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 359 through 363 removed outlier: 4.101A pdb=" N GLY 7 362 " --> pdb=" O PRO 7 359 " (cutoff:3.500A) Processing helix chain '7' and resid 388 through 392 removed outlier: 3.762A pdb=" N PHE 7 391 " --> pdb=" O PHE 7 388 " (cutoff:3.500A) Processing helix chain '7' and resid 394 through 407 Processing helix chain '7' and resid 410 through 419 removed outlier: 4.674A pdb=" N ALA 7 419 " --> pdb=" O ALA 7 415 " (cutoff:3.500A) Processing helix chain '7' and resid 425 through 438 removed outlier: 3.568A pdb=" N LYS 7 429 " --> pdb=" O ASN 7 425 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL 7 437 " --> pdb=" O LEU 7 433 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY 7 438 " --> pdb=" O LEU 7 434 " (cutoff:3.500A) Processing helix chain '7' and resid 444 through 448 removed outlier: 3.635A pdb=" N MET 7 448 " --> pdb=" O GLY 7 445 " (cutoff:3.500A) Processing helix chain '7' and resid 465 through 477 Processing helix chain '7' and resid 530 through 541 Processing helix chain '7' and resid 542 through 544 No H-bonds generated for 'chain '7' and resid 542 through 544' Processing helix chain '7' and resid 578 through 582 Processing helix chain '7' and resid 587 through 594 removed outlier: 3.638A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 623 removed outlier: 4.330A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 649 removed outlier: 3.838A pdb=" N ALA 7 643 " --> pdb=" O ARG 7 639 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG 7 649 " --> pdb=" O ALA 7 645 " (cutoff:3.500A) Processing helix chain '7' and resid 656 through 672 Processing helix chain '7' and resid 673 through 677 Processing helix chain '7' and resid 685 through 702 removed outlier: 3.896A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 726 removed outlier: 3.671A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.973A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 96 through 101 removed outlier: 4.302A pdb=" N ILE C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 Processing helix chain 'C' and resid 119 through 140 removed outlier: 4.095A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 167 removed outlier: 4.417A pdb=" N SER C 163 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 169 No H-bonds generated for 'chain 'C' and resid 168 through 169' Processing helix chain 'C' and resid 170 through 171 No H-bonds generated for 'chain 'C' and resid 170 through 171' Processing helix chain 'C' and resid 172 through 192 removed outlier: 4.380A pdb=" N ILE C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.751A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 112 removed outlier: 3.724A pdb=" N MET D 84 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 154 removed outlier: 3.940A pdb=" N LEU D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.515A pdb=" N GLU D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 175 removed outlier: 3.747A pdb=" N LEU D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 198 Processing helix chain 'D' and resid 199 through 202 Processing helix chain 'D' and resid 203 through 207 Processing helix chain 'D' and resid 282 through 288 Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 35 through 52 removed outlier: 3.598A pdb=" N GLN E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 91 through 97 Processing helix chain 'E' and resid 130 through 136 removed outlier: 3.777A pdb=" N ILE E 134 " --> pdb=" O ASN E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.623A pdb=" N ALA E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.843A pdb=" N ILE E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 284 through 302 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 333 through 341 Processing helix chain 'E' and resid 341 through 349 Processing helix chain 'E' and resid 352 through 367 removed outlier: 3.821A pdb=" N LYS E 356 " --> pdb=" O ASN E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 400 removed outlier: 5.314A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASP E 397 " --> pdb=" O ASP E 393 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ARG E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR E 399 " --> pdb=" O ASN E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 434 Processing helix chain 'E' and resid 463 through 483 Processing helix chain 'E' and resid 489 through 517 removed outlier: 3.732A pdb=" N ARG E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA E 512 " --> pdb=" O ASN E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 540 removed outlier: 3.566A pdb=" N ARG E 540 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 558 Processing helix chain 'E' and resid 604 through 616 Processing helix chain 'E' and resid 636 through 647 removed outlier: 3.535A pdb=" N PHE E 640 " --> pdb=" O ASP E 636 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 27 removed outlier: 3.543A pdb=" N LEU F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.707A pdb=" N VAL F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 48 Processing helix chain 'F' and resid 56 through 71 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 195 through 200 Processing helix chain 'F' and resid 211 through 231 removed outlier: 4.230A pdb=" N VAL F 215 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE F 218 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU F 219 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 351 through 358 removed outlier: 3.703A pdb=" N THR F 358 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 391 removed outlier: 4.480A pdb=" N LYS F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE F 385 " --> pdb=" O LYS F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 425 removed outlier: 3.602A pdb=" N MET F 414 " --> pdb=" O ASP F 410 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 423 " --> pdb=" O LYS F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 469 removed outlier: 3.764A pdb=" N PHE F 462 " --> pdb=" O PHE F 458 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA F 464 " --> pdb=" O ASN F 460 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU F 465 " --> pdb=" O ASN F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 509 through 513 Processing helix chain 'F' and resid 515 through 520 Processing helix chain 'F' and resid 546 through 553 removed outlier: 3.531A pdb=" N HIS F 553 " --> pdb=" O ARG F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 595 through 610 removed outlier: 4.225A pdb=" N THR F 599 " --> pdb=" O LYS F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 631 removed outlier: 3.987A pdb=" N LEU F 630 " --> pdb=" O LEU F 626 " (cutoff:3.500A) Processing helix chain 'G' and resid 1403 through 1412 removed outlier: 3.811A pdb=" N GLU G1412 " --> pdb=" O LEU G1408 " (cutoff:3.500A) Processing helix chain 'G' and resid 1432 through 1441 Processing helix chain 'G' and resid 1455 through 1461 Processing helix chain 'G' and resid 1524 through 1539 Processing helix chain 'G' and resid 1539 through 1547 Processing helix chain 'G' and resid 1568 through 1570 No H-bonds generated for 'chain 'G' and resid 1568 through 1570' Processing helix chain 'G' and resid 1571 through 1584 removed outlier: 3.867A pdb=" N GLN G1575 " --> pdb=" O ARG G1571 " (cutoff:3.500A) Processing helix chain 'G' and resid 1596 through 1604 removed outlier: 3.547A pdb=" N ILE G1604 " --> pdb=" O LEU G1600 " (cutoff:3.500A) Processing helix chain 'G' and resid 1605 through 1610 removed outlier: 3.549A pdb=" N ASN G1608 " --> pdb=" O ARG G1605 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET G1610 " --> pdb=" O LEU G1607 " (cutoff:3.500A) Processing helix chain 'G' and resid 1626 through 1657 removed outlier: 4.377A pdb=" N THR G1630 " --> pdb=" O ASN G1626 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY G1643 " --> pdb=" O VAL G1639 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER G1644 " --> pdb=" O LEU G1640 " (cutoff:3.500A) Processing helix chain 'G' and resid 1659 through 1663 Processing helix chain 'G' and resid 1667 through 1683 removed outlier: 4.295A pdb=" N ILE G1671 " --> pdb=" O SER G1667 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G1672 " --> pdb=" O MET G1668 " (cutoff:3.500A) Processing helix chain 'G' and resid 1700 through 1704 removed outlier: 3.756A pdb=" N ASN G1703 " --> pdb=" O GLY G1700 " (cutoff:3.500A) Processing helix chain 'G' and resid 1706 through 1715 removed outlier: 3.832A pdb=" N ASN G1714 " --> pdb=" O SER G1710 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP G1715 " --> pdb=" O TRP G1711 " (cutoff:3.500A) Processing helix chain 'G' and resid 1738 through 1747 removed outlier: 3.506A pdb=" N SER G1747 " --> pdb=" O THR G1743 " (cutoff:3.500A) Processing helix chain 'G' and resid 1784 through 1804 Processing helix chain 'G' and resid 1806 through 1822 removed outlier: 4.425A pdb=" N ALA G1817 " --> pdb=" O VAL G1813 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER G1818 " --> pdb=" O ASN G1814 " (cutoff:3.500A) Processing helix chain 'G' and resid 1829 through 1854 removed outlier: 3.522A pdb=" N ARG G1833 " --> pdb=" O ASP G1829 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU G1854 " --> pdb=" O GLU G1850 " (cutoff:3.500A) Processing helix chain 'G' and resid 1874 through 1877 Processing helix chain 'G' and resid 1878 through 1892 Processing helix chain 'G' and resid 1893 through 1896 removed outlier: 3.538A pdb=" N SER G1896 " --> pdb=" O PRO G1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1893 through 1896' Processing helix chain 'G' and resid 1941 through 1945 Processing helix chain 'G' and resid 1949 through 1975 Processing helix chain 'G' and resid 2003 through 2006 removed outlier: 3.512A pdb=" N LEU G2006 " --> pdb=" O PHE G2003 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2003 through 2006' Processing helix chain 'G' and resid 2007 through 2026 Processing helix chain 'G' and resid 2049 through 2063 removed outlier: 3.725A pdb=" N GLU G2053 " --> pdb=" O ASN G2049 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET G2062 " --> pdb=" O LEU G2058 " (cutoff:3.500A) Processing helix chain 'G' and resid 2068 through 2083 removed outlier: 3.660A pdb=" N ILE G2082 " --> pdb=" O GLU G2078 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE G2083 " --> pdb=" O LEU G2079 " (cutoff:3.500A) Processing helix chain 'G' and resid 2089 through 2093 Processing helix chain 'G' and resid 2138 through 2159 Processing helix chain 'G' and resid 2190 through 2208 removed outlier: 3.931A pdb=" N ILE G2194 " --> pdb=" O PRO G2190 " (cutoff:3.500A) Processing helix chain 'G' and resid 2210 through 2219 Processing helix chain 'H' and resid 3 through 24 removed outlier: 3.708A pdb=" N ASN H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS H 8 " --> pdb=" O ASP H 4 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 61 Processing helix chain 'H' and resid 64 through 103 removed outlier: 3.599A pdb=" N LEU H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN H 103 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 142 removed outlier: 3.709A pdb=" N LYS H 142 " --> pdb=" O ILE H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 203 Processing helix chain 'I' and resid 12 through 22 Processing helix chain 'I' and resid 56 through 62 removed outlier: 4.356A pdb=" N LEU I 60 " --> pdb=" O ASP I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 82 removed outlier: 3.832A pdb=" N GLN I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 108 removed outlier: 3.810A pdb=" N ARG I 100 " --> pdb=" O LYS I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 129 Processing helix chain 'I' and resid 137 through 160 removed outlier: 3.529A pdb=" N LEU I 141 " --> pdb=" O PRO I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 199 removed outlier: 3.501A pdb=" N LEU I 181 " --> pdb=" O GLU I 177 " (cutoff:3.500A) Proline residue: I 183 - end of helix removed outlier: 3.722A pdb=" N GLU I 187 " --> pdb=" O PRO I 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 244 Processing sheet with id=AA2, first strand: chain '2' and resid 331 through 334 removed outlier: 3.629A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA 2 453 " --> pdb=" O GLU 2 407 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE 2 409 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N SER 2 455 " --> pdb=" O ILE 2 409 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ARG 2 458 " --> pdb=" O GLU 2 423 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLU 2 423 " --> pdb=" O ARG 2 458 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL 2 324 " --> pdb=" O GLN 2 391 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN 2 391 " --> pdb=" O VAL 2 324 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG 2 326 " --> pdb=" O THR 2 389 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 346 through 347 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: 6.188A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA 2 566 " --> pdb=" O ASP 2 607 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY 2 543 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 6.728A 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 96 through 99 Processing sheet with id=AA9, first strand: chain '3' and resid 165 through 166 removed outlier: 3.764A pdb=" N GLU 3 183 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 178 through 189 current: chain '3' and resid 209 through 213 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 209 through 213 current: chain '3' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 273 through 279 current: chain '3' and resid 318 through 328 Processing sheet with id=AB1, first strand: chain '3' and resid 391 through 393 removed outlier: 3.873A pdb=" N LYS 3 391 " --> pdb=" O LEU 3 399 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 429 through 433 removed outlier: 6.445A pdb=" N ILE 3 430 " --> pdb=" O CYS 3 471 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASP 3 473 " --> pdb=" O ILE 3 430 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 6.233A 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 499 removed outlier: 3.501A pdb=" N THR 3 504 " --> pdb=" O ILE 3 497 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 241 through 244 removed outlier: 7.223A pdb=" N LEU 4 241 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N TYR 4 306 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU 4 243 " --> pdb=" O TYR 4 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '4' and resid 325 through 334 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 325 through 334 current: chain '4' and resid 354 through 359 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 354 through 359 current: chain '4' and resid 414 through 420 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 414 through 420 current: chain '4' and resid 458 through 468 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '4' and resid 453 through 454 Processing sheet with id=AB8, first strand: chain '4' and resid 590 through 591 removed outlier: 6.645A pdb=" N ILE 4 564 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA 4 675 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU 4 566 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 604 through 607 removed outlier: 3.683A pdb=" N GLU 4 617 " --> pdb=" O TYR 4 604 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 653 through 658 Processing sheet with id=AC2, first strand: chain '5' and resid 60 through 64 Processing sheet with id=AC3, first strand: chain '5' and resid 189 through 193 removed outlier: 6.586A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU 5 179 " --> pdb=" O SER 5 247 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N SER 5 247 " --> pdb=" O LEU 5 179 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ILE 5 181 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N HIS 5 245 " --> pdb=" O ILE 5 181 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N CYS 5 183 " --> pdb=" O ILE 5 243 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ILE 5 243 " --> pdb=" O CYS 5 183 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE 5 330 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N ASP 5 279 " --> pdb=" O GLY 5 332 " (cutoff:3.500A) removed outlier: 13.147A pdb=" N GLN 5 334 " --> pdb=" O ASP 5 279 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR 5 301 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE 5 328 " --> pdb=" O SER 5 299 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER 5 299 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE 5 330 " --> pdb=" O ILE 5 297 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE 5 297 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '5' and resid 398 through 399 removed outlier: 3.983A pdb=" N LYS 5 398 " --> pdb=" O LEU 5 406 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '5' and resid 436 through 440 removed outlier: 6.514A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASP 5 480 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR 5 439 " --> pdb=" O ASP 5 480 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 451 through 456 removed outlier: 3.748A pdb=" N GLU 5 461 " --> pdb=" O ASP 5 456 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 501 through 506 Processing sheet with id=AC8, first strand: chain '5' and resid 727 through 729 removed outlier: 3.745A pdb=" N THR 5 728 " --> pdb=" O ILE 5 770 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN 5 769 " --> pdb=" O ARG 5 764 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '6' and resid 150 through 154 Processing sheet with id=AD1, first strand: chain '6' and resid 287 through 296 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 287 through 296 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 381 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 376 through 381 current: chain '6' and resid 450 through 461 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain '6' and resid 557 through 558 removed outlier: 4.240A pdb=" N LYS 6 557 " --> pdb=" O LEU 6 565 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 596 through 599 removed outlier: 6.557A pdb=" N GLY 6 634 " --> pdb=" O SER 6 677 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU 6 679 " --> pdb=" O GLY 6 634 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE 6 571 " --> pdb=" O ALA 6 680 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ALA 6 682 " --> pdb=" O ILE 6 571 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL 6 573 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 610 through 613 Processing sheet with id=AD5, first strand: chain '6' and resid 660 through 665 Processing sheet with id=AD6, first strand: chain '7' and resid 78 through 81 removed outlier: 6.085A pdb=" N VAL 7 78 " --> pdb=" O TYR 7 203 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LYS 7 205 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE 7 80 " --> pdb=" O LYS 7 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '7' and resid 238 through 248 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 238 through 248 current: chain '7' and resid 270 through 272 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 270 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 373 through 382 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '7' and resid 480 through 483 removed outlier: 6.186A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP 7 517 " --> pdb=" O ARG 7 560 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N SER 7 562 " --> pdb=" O ASP 7 517 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY 7 519 " --> pdb=" O SER 7 562 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU 7 564 " --> pdb=" O GLY 7 519 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA 7 565 " --> pdb=" O VAL 7 456 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY 7 460 " --> pdb=" O ALA 7 567 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 43 through 47 Processing sheet with id=AE1, first strand: chain 'D' and resid 291 through 293 removed outlier: 3.691A pdb=" N ILE D 274 " --> pdb=" O LEU I 170 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 247 through 249 removed outlier: 4.076A pdb=" N ASN D 249 " --> pdb=" O LYS D 253 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 265 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 140 through 142 removed outlier: 6.604A pdb=" N LEU E 81 " --> pdb=" O TYR E 121 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU E 123 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU E 83 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 28 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU E 27 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL E 59 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE E 29 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE E 61 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL E 31 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 56 " --> pdb=" O PHE H 190 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 316 through 324 Processing sheet with id=AE5, first strand: chain 'E' and resid 520 through 521 removed outlier: 3.562A pdb=" N ALA E 570 " --> pdb=" O CYS E 528 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 580 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 171 through 174 removed outlier: 6.586A pdb=" N GLU F 538 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL F 640 " --> pdb=" O GLU F 538 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL F 540 " --> pdb=" O VAL F 640 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N CYS F 642 " --> pdb=" O VAL F 540 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE F 542 " --> pdb=" O CYS F 642 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET F 639 " --> pdb=" O ILE F 659 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 181 through 184 removed outlier: 3.751A pdb=" N GLN F 189 " --> pdb=" O ASN F 184 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 313 through 314 removed outlier: 6.810A pdb=" N ILE F 313 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLU F 329 " --> pdb=" O THR F 342 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET F 344 " --> pdb=" O LEU F 327 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU F 327 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL F 326 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY F 286 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TRP F 296 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 9.441A pdb=" N PHE F 339 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLU F 306 " --> pdb=" O PHE F 339 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL F 341 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP F 308 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N SER F 343 " --> pdb=" O ASP F 308 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 399 through 401 removed outlier: 7.112A pdb=" N VAL F 400 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLN F 435 " --> pdb=" O VAL F 400 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 523 through 525 current: chain 'F' and resid 669 through 676 removed outlier: 3.867A pdb=" N ALA F 670 " --> pdb=" O GLU F 686 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS F 680 " --> pdb=" O VAL F 676 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 1322 through 1324 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1322 through 1324 current: chain 'G' and resid 1335 through 1341 Processing sheet with id=AF2, first strand: chain 'G' and resid 1355 through 1359 Processing sheet with id=AF3, first strand: chain 'G' and resid 1500 through 1503 removed outlier: 3.602A pdb=" N PHE G1502 " --> pdb=" O TYR G1486 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY G1485 " --> pdb=" O LEU G1591 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLN G1593 " --> pdb=" O GLY G1485 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU G1487 " --> pdb=" O GLN G1593 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU G1590 " --> pdb=" O VAL G1613 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 1721 through 1722 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1721 through 1722 current: chain 'G' and resid 1865 through 1869 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1865 through 1869 current: chain 'G' and resid 1916 through 1922 Processing sheet with id=AF5, first strand: chain 'G' and resid 2102 through 2107 removed outlier: 3.631A pdb=" N ASP G2105 " --> pdb=" O SER G2115 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N SER G2115 " --> pdb=" O ASP G2105 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 2162 through 2163 Processing sheet with id=AF7, first strand: chain 'H' and resid 173 through 176 Processing sheet with id=AF8, first strand: chain 'I' and resid 24 through 27 removed outlier: 3.510A pdb=" N THR I 69 " --> pdb=" O ILE I 27 " (cutoff:3.500A) 2177 hydrogen bonds defined for protein. 6264 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: 24.99 Time building geometry restraints manager: 14.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17433 1.34 - 1.46: 10753 1.46 - 1.58: 25301 1.58 - 1.70: 41 1.70 - 1.81: 385 Bond restraints: 53913 Sorted by residual: bond pdb=" CB PRO F 634 " pdb=" CG PRO F 634 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.42e+00 bond pdb=" CB PRO I 4 " pdb=" CG PRO I 4 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.60e+00 bond pdb=" C LEU I 3 " pdb=" N PRO I 4 " ideal model delta sigma weight residual 1.334 1.364 -0.031 2.34e-02 1.83e+03 1.70e+00 bond pdb=" CG PRO F 634 " pdb=" CD PRO F 634 " ideal model delta sigma weight residual 1.503 1.544 -0.041 3.40e-02 8.65e+02 1.49e+00 bond pdb=" CG PRO I 4 " pdb=" CD PRO I 4 " ideal model delta sigma weight residual 1.503 1.541 -0.038 3.40e-02 8.65e+02 1.22e+00 ... (remaining 53908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 72158 2.14 - 4.27: 719 4.27 - 6.41: 101 6.41 - 8.54: 7 8.54 - 10.68: 5 Bond angle restraints: 72990 Sorted by residual: angle pdb=" C TRP I 119 " pdb=" N LEU I 120 " pdb=" CA LEU I 120 " ideal model delta sigma weight residual 121.54 127.78 -6.24 1.91e+00 2.74e-01 1.07e+01 angle pdb=" N GLU G1537 " pdb=" CA GLU G1537 " pdb=" CB GLU G1537 " ideal model delta sigma weight residual 110.39 115.48 -5.09 1.66e+00 3.63e-01 9.39e+00 angle pdb=" C SER 7 677 " pdb=" N LYS 7 678 " pdb=" CA LYS 7 678 " ideal model delta sigma weight residual 121.54 127.35 -5.81 1.91e+00 2.74e-01 9.25e+00 angle pdb=" CA PRO F 634 " pdb=" N PRO F 634 " pdb=" CD PRO F 634 " ideal model delta sigma weight residual 112.00 107.75 4.25 1.40e+00 5.10e-01 9.20e+00 angle pdb=" C ASN 5 561 " pdb=" N GLU 5 562 " pdb=" CA GLU 5 562 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.86e+00 ... (remaining 72985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 31741 28.35 - 56.71: 1178 56.71 - 85.06: 112 85.06 - 113.41: 10 113.41 - 141.76: 1 Dihedral angle restraints: 33042 sinusoidal: 13644 harmonic: 19398 Sorted by residual: dihedral pdb=" O2A ADP 61101 " pdb=" O3A ADP 61101 " pdb=" PA ADP 61101 " pdb=" PB ADP 61101 " ideal model delta sinusoidal sigma weight residual 300.00 158.24 141.76 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" CA CYS F 633 " pdb=" C CYS F 633 " pdb=" N PRO F 634 " pdb=" CA PRO F 634 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" C4' ADP 61101 " pdb=" C5' ADP 61101 " pdb=" O5' ADP 61101 " pdb=" PA ADP 61101 " ideal model delta sinusoidal sigma weight residual 180.00 -104.57 -75.43 1 2.00e+01 2.50e-03 1.80e+01 ... (remaining 33039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 5771 0.036 - 0.072: 1809 0.072 - 0.108: 637 0.108 - 0.144: 159 0.144 - 0.180: 6 Chirality restraints: 8382 Sorted by residual: chirality pdb=" CA PRO I 4 " pdb=" N PRO I 4 " pdb=" C PRO I 4 " pdb=" CB PRO I 4 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA VAL 4 744 " pdb=" N VAL 4 744 " pdb=" C VAL 4 744 " pdb=" CB VAL 4 744 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CB ILE G2026 " pdb=" CA ILE G2026 " pdb=" CG1 ILE G2026 " pdb=" CG2 ILE G2026 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 8379 not shown) Planarity restraints: 9295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 633 " -0.088 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO F 634 " 0.231 5.00e-02 4.00e+02 pdb=" CA PRO F 634 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO F 634 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 3 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO I 4 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO I 4 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO I 4 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 6 368 " 0.056 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO 6 369 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO 6 369 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO 6 369 " 0.047 5.00e-02 4.00e+02 ... (remaining 9292 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 341 2.57 - 3.15: 42590 3.15 - 3.73: 79861 3.73 - 4.32: 103721 4.32 - 4.90: 175198 Nonbonded interactions: 401711 Sorted by model distance: nonbonded pdb="MG MG 31001 " pdb=" O3B ATP 31002 " model vdw 1.983 2.170 nonbonded pdb="MG MG 7 902 " pdb=" O1B ATP 7 903 " model vdw 2.007 2.170 nonbonded pdb="MG MG 31001 " pdb=" O1A ATP 31002 " model vdw 2.047 2.170 nonbonded pdb=" O1G ATP 51701 " pdb="MG MG 51703 " model vdw 2.051 2.170 nonbonded pdb=" O LYS 7 295 " pdb="ZN ZN 7 901 " model vdw 2.140 2.230 ... (remaining 401706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.960 Check model and map are aligned: 0.390 Set scattering table: 0.470 Process input model: 119.780 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 53913 Z= 0.143 Angle : 0.540 10.679 72990 Z= 0.276 Chirality : 0.041 0.180 8382 Planarity : 0.004 0.133 9295 Dihedral : 14.173 141.765 20438 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: 0.08 (0.11), residues: 6516 helix: 1.13 (0.10), residues: 2637 sheet: -0.05 (0.16), residues: 1027 loop : -0.89 (0.12), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G1798 HIS 0.007 0.001 HIS 4 465 PHE 0.023 0.001 PHE D 105 TYR 0.025 0.001 TYR H 53 ARG 0.006 0.000 ARG 5 764 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 6.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 387 ARG cc_start: 0.7003 (ptt90) cc_final: 0.6800 (ptp-110) REVERT: 2 438 LEU cc_start: 0.7929 (tp) cc_final: 0.7528 (tp) REVERT: 3 193 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7425 (mmt-90) REVERT: 3 447 THR cc_start: 0.7655 (t) cc_final: 0.7417 (p) REVERT: 5 469 MET cc_start: 0.8670 (ttt) cc_final: 0.8459 (ttt) REVERT: 6 621 TYR cc_start: 0.6777 (m-80) cc_final: 0.6509 (m-80) REVERT: 6 645 ASP cc_start: 0.7861 (t0) cc_final: 0.7292 (p0) REVERT: 7 148 LEU cc_start: 0.7755 (mt) cc_final: 0.7498 (tp) REVERT: 7 277 THR cc_start: 0.8927 (m) cc_final: 0.8659 (p) REVERT: 7 360 TYR cc_start: 0.7711 (t80) cc_final: 0.7026 (t80) REVERT: 7 411 TYR cc_start: 0.8367 (p90) cc_final: 0.8138 (p90) REVERT: 7 652 MET cc_start: 0.5836 (ppp) cc_final: 0.5243 (ppp) REVERT: C 186 ASP cc_start: 0.8213 (m-30) cc_final: 0.7982 (m-30) REVERT: D 108 MET cc_start: 0.3859 (tmm) cc_final: 0.3022 (mmt) REVERT: D 129 MET cc_start: 0.8855 (mpp) cc_final: 0.8151 (mpp) REVERT: F 187 LYS cc_start: 0.8146 (mppt) cc_final: 0.7320 (mtpt) REVERT: F 266 MET cc_start: 0.4128 (mtt) cc_final: 0.2283 (tmm) REVERT: F 544 ASP cc_start: 0.7811 (p0) cc_final: 0.7463 (t0) REVERT: F 673 MET cc_start: 0.7474 (tmm) cc_final: 0.7268 (tmm) REVERT: G 1386 ASN cc_start: 0.8337 (t0) cc_final: 0.7860 (t0) REVERT: G 1649 LEU cc_start: 0.8847 (tt) cc_final: 0.8641 (mt) REVERT: G 1798 TRP cc_start: 0.7705 (m-10) cc_final: 0.7326 (m-10) REVERT: G 1899 ASP cc_start: 0.7530 (m-30) cc_final: 0.7318 (m-30) REVERT: H 49 LYS cc_start: 0.8092 (ptpt) cc_final: 0.7768 (pptt) REVERT: H 51 THR cc_start: 0.8142 (p) cc_final: 0.7745 (p) REVERT: H 110 MET cc_start: 0.0958 (mmt) cc_final: 0.0675 (mmt) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.6283 time to fit residues: 581.4242 Evaluate side-chains 309 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 5.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 553 optimal weight: 2.9990 chunk 497 optimal weight: 0.9990 chunk 275 optimal weight: 0.0570 chunk 169 optimal weight: 10.0000 chunk 335 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 514 optimal weight: 6.9990 chunk 198 optimal weight: 0.7980 chunk 312 optimal weight: 6.9990 chunk 382 optimal weight: 3.9990 chunk 595 optimal weight: 0.5980 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 29 GLN 3 210 HIS 3 308 GLN 3 638 ASN ** 4 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 274 GLN 4 685 ASN 5 632 GLN 5 636 ASN 6 786 GLN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN G1489 HIS ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.088 53913 Z= 0.157 Angle : 0.555 11.819 72990 Z= 0.286 Chirality : 0.042 0.184 8382 Planarity : 0.004 0.132 9295 Dihedral : 7.461 143.382 7452 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 0.63 % Allowed : 6.62 % Favored : 92.74 % 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: 0.24 (0.11), residues: 6516 helix: 1.27 (0.10), residues: 2705 sheet: 0.05 (0.16), residues: 1040 loop : -0.87 (0.12), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 102 HIS 0.006 0.001 HIS G1489 PHE 0.053 0.001 PHE H 73 TYR 0.019 0.001 TYR 7 641 ARG 0.018 0.000 ARG D 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 359 time to evaluate : 6.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 438 LEU cc_start: 0.7702 (tp) cc_final: 0.7379 (tp) REVERT: 3 384 MET cc_start: 0.8758 (tmm) cc_final: 0.8556 (ttp) REVERT: 3 447 THR cc_start: 0.7642 (t) cc_final: 0.7324 (p) REVERT: 3 583 ARG cc_start: 0.5543 (tpp-160) cc_final: 0.5191 (tpt170) REVERT: 4 342 MET cc_start: 0.7600 (tpt) cc_final: 0.7300 (tpt) REVERT: 5 348 MET cc_start: 0.7517 (mmm) cc_final: 0.7024 (mmp) REVERT: 6 621 TYR cc_start: 0.6772 (m-80) cc_final: 0.6490 (m-80) REVERT: 6 645 ASP cc_start: 0.7921 (t0) cc_final: 0.7466 (p0) REVERT: 7 148 LEU cc_start: 0.7837 (mt) cc_final: 0.7602 (tp) REVERT: 7 277 THR cc_start: 0.8953 (m) cc_final: 0.8692 (p) REVERT: 7 360 TYR cc_start: 0.7777 (t80) cc_final: 0.7083 (t80) REVERT: 7 411 TYR cc_start: 0.8338 (p90) cc_final: 0.7968 (p90) REVERT: 7 652 MET cc_start: 0.5641 (ppp) cc_final: 0.5238 (ppp) REVERT: C 90 THR cc_start: 0.8855 (m) cc_final: 0.8566 (m) REVERT: C 186 ASP cc_start: 0.8205 (m-30) cc_final: 0.7952 (m-30) REVERT: D 108 MET cc_start: 0.3716 (tmm) cc_final: 0.3028 (mmt) REVERT: D 129 MET cc_start: 0.9004 (mpp) cc_final: 0.8237 (mpp) REVERT: F 43 GLU cc_start: 0.6874 (pp20) cc_final: 0.6664 (mm-30) REVERT: F 434 TRP cc_start: 0.7388 (m100) cc_final: 0.7013 (m100) REVERT: F 544 ASP cc_start: 0.7772 (p0) cc_final: 0.7568 (t0) REVERT: G 1386 ASN cc_start: 0.8425 (t0) cc_final: 0.7998 (t0) REVERT: G 1482 MET cc_start: 0.4270 (OUTLIER) cc_final: 0.3881 (mmm) REVERT: G 1537 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6748 (pm20) REVERT: G 1610 MET cc_start: 0.4921 (ptt) cc_final: 0.4649 (pmm) REVERT: G 1649 LEU cc_start: 0.8812 (tt) cc_final: 0.8603 (mt) REVERT: G 1794 MET cc_start: 0.7505 (ttm) cc_final: 0.6995 (ttm) REVERT: G 1798 TRP cc_start: 0.7693 (m-10) cc_final: 0.7415 (m-10) REVERT: H 53 TYR cc_start: 0.7303 (m-80) cc_final: 0.7056 (m-80) REVERT: H 138 ILE cc_start: 0.8457 (mm) cc_final: 0.8222 (mm) outliers start: 37 outliers final: 16 residues processed: 380 average time/residue: 0.6355 time to fit residues: 418.1133 Evaluate side-chains 319 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 301 time to evaluate : 6.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 745 LEU Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 5 residue 498 GLU Chi-restraints excluded: chain 7 residue 202 LEU Chi-restraints excluded: chain 7 residue 608 ASP Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain G residue 1368 LEU Chi-restraints excluded: chain G residue 1470 MET Chi-restraints excluded: chain G residue 1482 MET Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 2153 ASP Chi-restraints excluded: chain G residue 2186 GLU Chi-restraints excluded: chain G residue 2215 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 63 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 331 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 495 optimal weight: 4.9990 chunk 405 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 596 optimal weight: 0.6980 chunk 644 optimal weight: 5.9990 chunk 531 optimal weight: 0.8980 chunk 591 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 478 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 746 GLN 4 240 ASN ** 5 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1396 GLN G1489 HIS ** G1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1742 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 53913 Z= 0.249 Angle : 0.589 13.779 72990 Z= 0.303 Chirality : 0.043 0.205 8382 Planarity : 0.005 0.133 9295 Dihedral : 7.482 140.304 7452 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 1.18 % Allowed : 9.29 % Favored : 89.54 % 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: 0.14 (0.10), residues: 6516 helix: 1.24 (0.10), residues: 2711 sheet: -0.05 (0.16), residues: 1037 loop : -0.96 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G1688 HIS 0.007 0.001 HIS G1489 PHE 0.026 0.002 PHE H 73 TYR 0.022 0.002 TYR G1879 ARG 0.014 0.001 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 318 time to evaluate : 6.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 438 LEU cc_start: 0.7740 (tp) cc_final: 0.7441 (tp) REVERT: 3 360 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.6162 (p90) REVERT: 4 273 ASP cc_start: 0.6550 (m-30) cc_final: 0.6174 (t0) REVERT: 5 348 MET cc_start: 0.7499 (mmm) cc_final: 0.7089 (mmp) REVERT: 5 398 LYS cc_start: 0.7979 (tptt) cc_final: 0.7388 (ttmt) REVERT: 6 621 TYR cc_start: 0.6821 (m-80) cc_final: 0.6521 (m-80) REVERT: 6 645 ASP cc_start: 0.7809 (t0) cc_final: 0.7343 (p0) REVERT: 7 148 LEU cc_start: 0.7870 (mt) cc_final: 0.7637 (tp) REVERT: 7 258 ILE cc_start: 0.7849 (mt) cc_final: 0.7567 (mt) REVERT: 7 402 MET cc_start: 0.8282 (mmm) cc_final: 0.8045 (mmm) REVERT: 7 411 TYR cc_start: 0.8337 (p90) cc_final: 0.8117 (p90) REVERT: 7 652 MET cc_start: 0.5839 (ppp) cc_final: 0.5401 (ppp) REVERT: C 186 ASP cc_start: 0.8144 (m-30) cc_final: 0.7888 (m-30) REVERT: D 108 MET cc_start: 0.3613 (tmm) cc_final: 0.3119 (mmt) REVERT: F 20 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8510 (tt) REVERT: F 544 ASP cc_start: 0.7739 (p0) cc_final: 0.7423 (t0) REVERT: G 1386 ASN cc_start: 0.8554 (t0) cc_final: 0.8117 (t0) REVERT: G 1465 MET cc_start: 0.5615 (mmm) cc_final: 0.4984 (mtp) REVERT: G 1537 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6617 (pm20) REVERT: G 1610 MET cc_start: 0.4927 (ptt) cc_final: 0.4596 (pmm) outliers start: 69 outliers final: 42 residues processed: 365 average time/residue: 0.6047 time to fit residues: 385.3626 Evaluate side-chains 326 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 2 residue 764 MET Chi-restraints excluded: chain 3 residue 329 LEU Chi-restraints excluded: chain 3 residue 360 PHE Chi-restraints excluded: chain 3 residue 389 VAL Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 365 ILE Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 295 VAL Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 498 GLU Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 303 GLU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 678 ILE Chi-restraints excluded: chain 6 residue 835 ILE Chi-restraints excluded: chain 7 residue 202 LEU Chi-restraints excluded: chain 7 residue 494 THR Chi-restraints excluded: chain 7 residue 608 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1470 MET Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 2153 ASP Chi-restraints excluded: chain G residue 2186 GLU Chi-restraints excluded: chain G residue 2215 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 63 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 589 optimal weight: 10.0000 chunk 448 optimal weight: 7.9990 chunk 309 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 400 optimal weight: 6.9990 chunk 598 optimal weight: 0.7980 chunk 634 optimal weight: 8.9990 chunk 312 optimal weight: 0.8980 chunk 567 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 376 ASN ** 3 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 625 ASN D 249 ASN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 667 ASN ** G1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 53913 Z= 0.233 Angle : 0.570 14.337 72990 Z= 0.294 Chirality : 0.043 0.215 8382 Planarity : 0.004 0.132 9295 Dihedral : 7.490 138.874 7452 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 1.79 % Allowed : 11.57 % Favored : 86.63 % 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: 0.13 (0.10), residues: 6516 helix: 1.25 (0.10), residues: 2713 sheet: -0.08 (0.16), residues: 1029 loop : -0.99 (0.12), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G1798 HIS 0.006 0.001 HIS G1434 PHE 0.023 0.002 PHE H 73 TYR 0.019 0.001 TYR H 53 ARG 0.005 0.000 ARG 5 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 303 time to evaluate : 6.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 385 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7229 (p90) REVERT: 2 438 LEU cc_start: 0.7669 (tp) cc_final: 0.7401 (tp) REVERT: 3 360 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6537 (p90) REVERT: 4 272 MET cc_start: 0.4207 (tpt) cc_final: 0.3946 (mmm) REVERT: 5 172 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8777 (pp) REVERT: 5 398 LYS cc_start: 0.8031 (tptt) cc_final: 0.7488 (ttmt) REVERT: 6 621 TYR cc_start: 0.6888 (m-80) cc_final: 0.6585 (m-80) REVERT: 6 645 ASP cc_start: 0.7817 (t0) cc_final: 0.7338 (p0) REVERT: 7 258 ILE cc_start: 0.7948 (mt) cc_final: 0.7671 (mt) REVERT: 7 652 MET cc_start: 0.5882 (ppp) cc_final: 0.5387 (ppp) REVERT: C 74 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7784 (tp) REVERT: C 186 ASP cc_start: 0.8124 (m-30) cc_final: 0.7882 (m-30) REVERT: D 108 MET cc_start: 0.3697 (tmm) cc_final: 0.3220 (mmt) REVERT: E 129 TRP cc_start: 0.6592 (OUTLIER) cc_final: 0.5770 (p90) REVERT: E 380 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7513 (tmm) REVERT: F 20 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8508 (tt) REVERT: G 1386 ASN cc_start: 0.8576 (t0) cc_final: 0.8114 (t0) REVERT: G 1465 MET cc_start: 0.5715 (mmm) cc_final: 0.5498 (mmm) REVERT: G 1537 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: G 1610 MET cc_start: 0.4758 (ptt) cc_final: 0.4420 (pmm) REVERT: G 1798 TRP cc_start: 0.7818 (m-10) cc_final: 0.7567 (m-10) REVERT: G 1957 MET cc_start: 0.8733 (ttm) cc_final: 0.8387 (tpp) outliers start: 105 outliers final: 54 residues processed: 385 average time/residue: 0.6005 time to fit residues: 409.7002 Evaluate side-chains 334 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 272 time to evaluate : 7.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 172 THR Chi-restraints excluded: chain 3 residue 329 LEU Chi-restraints excluded: chain 3 residue 360 PHE Chi-restraints excluded: chain 3 residue 389 VAL Chi-restraints excluded: chain 3 residue 487 HIS Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 548 VAL Chi-restraints excluded: chain 3 residue 650 LEU Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 172 LEU Chi-restraints excluded: chain 5 residue 261 ILE Chi-restraints excluded: chain 5 residue 540 ILE Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 303 GLU Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 516 LEU Chi-restraints excluded: chain 6 residue 678 ILE Chi-restraints excluded: chain 6 residue 797 VAL Chi-restraints excluded: chain 7 residue 77 SER Chi-restraints excluded: chain 7 residue 202 LEU Chi-restraints excluded: chain 7 residue 335 VAL Chi-restraints excluded: chain 7 residue 584 ILE Chi-restraints excluded: chain 7 residue 608 ASP Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 129 TRP Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain G residue 1401 THR Chi-restraints excluded: chain G residue 1463 PHE Chi-restraints excluded: chain G residue 1470 MET Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 2047 VAL Chi-restraints excluded: chain G residue 2153 ASP Chi-restraints excluded: chain G residue 2186 GLU Chi-restraints excluded: chain G residue 2215 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 63 MET Chi-restraints excluded: chain I residue 93 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 528 optimal weight: 6.9990 chunk 359 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 472 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 541 optimal weight: 20.0000 chunk 438 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 569 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 353 GLN 3 175 HIS 3 330 HIS 3 417 GLN ** 3 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 716 GLN 6 514 ASN 7 297 GLN ** 7 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS ** G1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 53913 Z= 0.344 Angle : 0.649 15.175 72990 Z= 0.333 Chirality : 0.045 0.215 8382 Planarity : 0.005 0.133 9295 Dihedral : 7.716 139.477 7452 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.83 % Rotamer: Outliers : 2.19 % Allowed : 12.94 % Favored : 84.88 % 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: -0.18 (0.10), residues: 6516 helix: 1.02 (0.10), residues: 2719 sheet: -0.27 (0.16), residues: 1026 loop : -1.17 (0.11), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G1688 HIS 0.008 0.001 HIS 3 201 PHE 0.021 0.002 PHE 3 735 TYR 0.033 0.002 TYR H 53 ARG 0.007 0.001 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 276 time to evaluate : 5.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 385 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7447 (p90) REVERT: 2 438 LEU cc_start: 0.7688 (tp) cc_final: 0.7423 (tp) REVERT: 3 360 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6706 (p90) REVERT: 4 312 LYS cc_start: 0.6669 (mmmt) cc_final: 0.6401 (mmtm) REVERT: 5 172 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8784 (pp) REVERT: 5 348 MET cc_start: 0.7688 (mmm) cc_final: 0.7246 (mmp) REVERT: 5 398 LYS cc_start: 0.8112 (tptt) cc_final: 0.7895 (tptt) REVERT: 5 576 HIS cc_start: 0.5951 (OUTLIER) cc_final: 0.5326 (t-90) REVERT: 6 621 TYR cc_start: 0.6974 (m-80) cc_final: 0.6739 (m-80) REVERT: 6 645 ASP cc_start: 0.7849 (t0) cc_final: 0.7340 (p0) REVERT: 7 258 ILE cc_start: 0.8013 (mt) cc_final: 0.7746 (mt) REVERT: 7 621 MET cc_start: 0.8670 (tmm) cc_final: 0.8428 (tmm) REVERT: 7 652 MET cc_start: 0.5829 (ppp) cc_final: 0.5291 (ppp) REVERT: D 108 MET cc_start: 0.3836 (tmm) cc_final: 0.3246 (mmt) REVERT: E 129 TRP cc_start: 0.6503 (OUTLIER) cc_final: 0.5591 (p90) REVERT: E 380 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7687 (tmm) REVERT: F 20 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8583 (tt) REVERT: G 1386 ASN cc_start: 0.8552 (t0) cc_final: 0.8049 (t0) REVERT: G 1465 MET cc_start: 0.5689 (mmm) cc_final: 0.5466 (mmm) REVERT: G 1537 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6574 (pm20) REVERT: G 1610 MET cc_start: 0.4752 (ptt) cc_final: 0.4287 (pmm) REVERT: H 49 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8153 (pptt) outliers start: 128 outliers final: 85 residues processed: 387 average time/residue: 0.5639 time to fit residues: 387.4618 Evaluate side-chains 352 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 258 time to evaluate : 6.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 240 GLU Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 130 THR Chi-restraints excluded: chain 3 residue 172 THR Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 321 ILE Chi-restraints excluded: chain 3 residue 329 LEU Chi-restraints excluded: chain 3 residue 360 PHE Chi-restraints excluded: chain 3 residue 389 VAL Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 487 HIS Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 548 VAL Chi-restraints excluded: chain 3 residue 650 LEU Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 365 ILE Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 92 THR Chi-restraints excluded: chain 5 residue 172 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 295 VAL Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 512 VAL Chi-restraints excluded: chain 5 residue 540 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 303 GLU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 668 ILE Chi-restraints excluded: chain 6 residue 678 ILE Chi-restraints excluded: chain 6 residue 797 VAL Chi-restraints excluded: chain 6 residue 835 ILE Chi-restraints excluded: chain 7 residue 77 SER Chi-restraints excluded: chain 7 residue 202 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 422 ILE Chi-restraints excluded: chain 7 residue 584 ILE Chi-restraints excluded: chain 7 residue 608 ASP Chi-restraints excluded: chain 7 residue 622 HIS Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 129 TRP Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1401 THR Chi-restraints excluded: chain G residue 1463 PHE Chi-restraints excluded: chain G residue 1470 MET Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 1613 VAL Chi-restraints excluded: chain G residue 1630 THR Chi-restraints excluded: chain G residue 1663 LEU Chi-restraints excluded: chain G residue 2047 VAL Chi-restraints excluded: chain G residue 2074 THR Chi-restraints excluded: chain G residue 2098 SER Chi-restraints excluded: chain G residue 2153 ASP Chi-restraints excluded: chain G residue 2186 GLU Chi-restraints excluded: chain G residue 2215 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 63 MET Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 93 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 213 optimal weight: 9.9990 chunk 571 optimal weight: 0.9980 chunk 125 optimal weight: 0.3980 chunk 372 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 634 optimal weight: 10.0000 chunk 526 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 209 optimal weight: 0.7980 chunk 333 optimal weight: 0.6980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 417 GLN ** 3 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS ** 7 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN G1534 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 53913 Z= 0.180 Angle : 0.558 14.617 72990 Z= 0.285 Chirality : 0.042 0.199 8382 Planarity : 0.004 0.129 9295 Dihedral : 7.487 139.487 7452 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.93 % Rotamer: Outliers : 1.93 % Allowed : 14.07 % Favored : 84.00 % 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: 0.06 (0.11), residues: 6516 helix: 1.27 (0.10), residues: 2723 sheet: -0.18 (0.16), residues: 1024 loop : -1.10 (0.12), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G1798 HIS 0.028 0.001 HIS 7 622 PHE 0.024 0.001 PHE F 44 TYR 0.019 0.001 TYR 5 753 ARG 0.008 0.000 ARG I 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 284 time to evaluate : 6.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 385 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7481 (p90) REVERT: 2 438 LEU cc_start: 0.7658 (tp) cc_final: 0.7423 (tp) REVERT: 5 348 MET cc_start: 0.7719 (mmm) cc_final: 0.7289 (mmp) REVERT: 5 398 LYS cc_start: 0.8090 (tptt) cc_final: 0.7833 (tptt) REVERT: 5 576 HIS cc_start: 0.5756 (OUTLIER) cc_final: 0.4934 (t-90) REVERT: 5 753 TYR cc_start: 0.7835 (t80) cc_final: 0.7360 (t80) REVERT: 6 621 TYR cc_start: 0.6973 (m-80) cc_final: 0.6672 (m-80) REVERT: 6 645 ASP cc_start: 0.7732 (t0) cc_final: 0.7441 (p0) REVERT: 7 258 ILE cc_start: 0.8086 (mt) cc_final: 0.7833 (mt) REVERT: 7 652 MET cc_start: 0.5752 (ppp) cc_final: 0.5259 (ppp) REVERT: C 74 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7860 (tp) REVERT: D 108 MET cc_start: 0.3587 (tmm) cc_final: 0.3044 (mmt) REVERT: E 129 TRP cc_start: 0.6513 (OUTLIER) cc_final: 0.5678 (p90) REVERT: F 20 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8610 (tt) REVERT: F 309 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8018 (mp) REVERT: G 1386 ASN cc_start: 0.8566 (t0) cc_final: 0.8081 (t0) REVERT: G 1534 GLN cc_start: 0.5881 (OUTLIER) cc_final: 0.5655 (pp30) REVERT: G 1537 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6648 (pm20) REVERT: G 1610 MET cc_start: 0.4835 (ptt) cc_final: 0.4381 (pmm) REVERT: G 1957 MET cc_start: 0.8686 (ttm) cc_final: 0.8374 (tpp) REVERT: G 2040 LEU cc_start: 0.8756 (tt) cc_final: 0.8107 (mt) outliers start: 113 outliers final: 75 residues processed: 381 average time/residue: 0.5899 time to fit residues: 397.7655 Evaluate side-chains 348 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 265 time to evaluate : 6.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 240 GLU Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 329 LEU Chi-restraints excluded: chain 3 residue 389 VAL Chi-restraints excluded: chain 3 residue 424 ASN Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 487 HIS Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 650 LEU Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 261 ILE Chi-restraints excluded: chain 5 residue 295 VAL Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 512 VAL Chi-restraints excluded: chain 5 residue 540 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 303 GLU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 668 ILE Chi-restraints excluded: chain 6 residue 678 ILE Chi-restraints excluded: chain 6 residue 797 VAL Chi-restraints excluded: chain 7 residue 77 SER Chi-restraints excluded: chain 7 residue 202 LEU Chi-restraints excluded: chain 7 residue 335 VAL Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 584 ILE Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 129 TRP Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1368 LEU Chi-restraints excluded: chain G residue 1401 THR Chi-restraints excluded: chain G residue 1463 PHE Chi-restraints excluded: chain G residue 1470 MET Chi-restraints excluded: chain G residue 1534 GLN Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 1663 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 2047 VAL Chi-restraints excluded: chain G residue 2153 ASP Chi-restraints excluded: chain G residue 2186 GLU Chi-restraints excluded: chain G residue 2215 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 63 MET Chi-restraints excluded: chain I residue 93 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 611 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 361 optimal weight: 5.9990 chunk 463 optimal weight: 7.9990 chunk 359 optimal weight: 10.0000 chunk 534 optimal weight: 9.9990 chunk 354 optimal weight: 0.9980 chunk 632 optimal weight: 0.0670 chunk 395 optimal weight: 4.9990 chunk 385 optimal weight: 6.9990 chunk 291 optimal weight: 0.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS ** 7 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 53913 Z= 0.259 Angle : 0.596 15.070 72990 Z= 0.304 Chirality : 0.043 0.229 8382 Planarity : 0.005 0.129 9295 Dihedral : 7.544 139.450 7452 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 2.29 % Allowed : 14.58 % Favored : 83.13 % 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: -0.04 (0.10), residues: 6516 helix: 1.20 (0.10), residues: 2721 sheet: -0.27 (0.16), residues: 1016 loop : -1.16 (0.11), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G1798 HIS 0.006 0.001 HIS G1434 PHE 0.018 0.001 PHE G1361 TYR 0.016 0.001 TYR H 53 ARG 0.009 0.000 ARG I 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 263 time to evaluate : 6.172 Fit side-chains revert: symmetry clash REVERT: 2 276 MET cc_start: 0.8158 (tpp) cc_final: 0.7887 (tpp) REVERT: 2 385 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7381 (p90) REVERT: 2 438 LEU cc_start: 0.7709 (tp) cc_final: 0.7471 (tp) REVERT: 3 360 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6578 (p90) REVERT: 3 456 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6734 (ptt90) REVERT: 3 478 MET cc_start: 0.7512 (ttp) cc_final: 0.7214 (ttp) REVERT: 4 312 LYS cc_start: 0.6695 (mmmt) cc_final: 0.6426 (mmtm) REVERT: 5 348 MET cc_start: 0.7730 (mmm) cc_final: 0.7326 (mmp) REVERT: 5 398 LYS cc_start: 0.8074 (tptt) cc_final: 0.7836 (tptt) REVERT: 5 576 HIS cc_start: 0.5942 (OUTLIER) cc_final: 0.5016 (t-90) REVERT: 6 621 TYR cc_start: 0.6995 (m-80) cc_final: 0.6786 (m-80) REVERT: 7 258 ILE cc_start: 0.8147 (mt) cc_final: 0.7901 (mt) REVERT: 7 498 MET cc_start: 0.5538 (mmp) cc_final: 0.5152 (mmm) REVERT: 7 652 MET cc_start: 0.5830 (ppp) cc_final: 0.5249 (ppp) REVERT: C 74 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7915 (tp) REVERT: D 108 MET cc_start: 0.3530 (tmm) cc_final: 0.3082 (mmt) REVERT: D 129 MET cc_start: 0.9155 (mpp) cc_final: 0.8510 (mpp) REVERT: E 129 TRP cc_start: 0.6640 (OUTLIER) cc_final: 0.5735 (p90) REVERT: F 20 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8590 (tt) REVERT: F 673 MET cc_start: 0.7436 (tmm) cc_final: 0.7047 (tmm) REVERT: G 1386 ASN cc_start: 0.8591 (t0) cc_final: 0.8061 (t0) REVERT: G 1537 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6863 (pm20) REVERT: G 2040 LEU cc_start: 0.8771 (tt) cc_final: 0.8095 (mt) outliers start: 134 outliers final: 93 residues processed: 383 average time/residue: 0.5857 time to fit residues: 396.6770 Evaluate side-chains 355 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 254 time to evaluate : 6.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 240 GLU Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 2 residue 764 MET Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 329 LEU Chi-restraints excluded: chain 3 residue 360 PHE Chi-restraints excluded: chain 3 residue 389 VAL Chi-restraints excluded: chain 3 residue 424 ASN Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 456 ARG Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 487 HIS Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 3 residue 586 LEU Chi-restraints excluded: chain 3 residue 650 LEU Chi-restraints excluded: chain 3 residue 671 LEU Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 365 ILE Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 92 THR Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 261 ILE Chi-restraints excluded: chain 5 residue 295 VAL Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 512 VAL Chi-restraints excluded: chain 5 residue 540 ILE Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 635 ILE Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 303 GLU Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 668 ILE Chi-restraints excluded: chain 6 residue 678 ILE Chi-restraints excluded: chain 6 residue 715 ILE Chi-restraints excluded: chain 6 residue 797 VAL Chi-restraints excluded: chain 7 residue 77 SER Chi-restraints excluded: chain 7 residue 202 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 335 VAL Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 584 ILE Chi-restraints excluded: chain 7 residue 622 HIS Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 129 TRP Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1368 LEU Chi-restraints excluded: chain G residue 1401 THR Chi-restraints excluded: chain G residue 1463 PHE Chi-restraints excluded: chain G residue 1470 MET Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 1630 THR Chi-restraints excluded: chain G residue 1663 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 2047 VAL Chi-restraints excluded: chain G residue 2098 SER Chi-restraints excluded: chain G residue 2153 ASP Chi-restraints excluded: chain G residue 2186 GLU Chi-restraints excluded: chain G residue 2215 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 63 MET Chi-restraints excluded: chain I residue 93 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 391 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 377 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 401 optimal weight: 0.6980 chunk 430 optimal weight: 4.9990 chunk 312 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 496 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 682 ASN 5 694 GLN ** 6 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS ** 7 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN ** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 53913 Z= 0.140 Angle : 0.542 13.922 72990 Z= 0.276 Chirality : 0.041 0.195 8382 Planarity : 0.004 0.124 9295 Dihedral : 7.296 138.735 7452 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 1.57 % Allowed : 15.47 % Favored : 82.96 % 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: 0.25 (0.11), residues: 6516 helix: 1.45 (0.10), residues: 2712 sheet: -0.13 (0.16), residues: 1021 loop : -1.00 (0.12), residues: 2783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP G1798 HIS 0.011 0.001 HIS 7 622 PHE 0.017 0.001 PHE F 44 TYR 0.022 0.001 TYR 5 753 ARG 0.010 0.000 ARG 6 832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 287 time to evaluate : 6.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 276 MET cc_start: 0.8132 (tpp) cc_final: 0.7879 (tpp) REVERT: 2 385 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7516 (p90) REVERT: 2 438 LEU cc_start: 0.7635 (tp) cc_final: 0.7414 (tp) REVERT: 3 456 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6640 (ptt90) REVERT: 3 478 MET cc_start: 0.7314 (ttp) cc_final: 0.7001 (ttp) REVERT: 4 780 MET cc_start: 0.7523 (tmm) cc_final: 0.7187 (tmm) REVERT: 5 348 MET cc_start: 0.7657 (mmm) cc_final: 0.7295 (mmp) REVERT: 5 398 LYS cc_start: 0.8081 (tptt) cc_final: 0.7456 (ttmt) REVERT: 5 753 TYR cc_start: 0.7882 (t80) cc_final: 0.7429 (t80) REVERT: 6 621 TYR cc_start: 0.6966 (m-80) cc_final: 0.6661 (m-80) REVERT: 6 645 ASP cc_start: 0.7942 (t0) cc_final: 0.7401 (p0) REVERT: 7 258 ILE cc_start: 0.8138 (mt) cc_final: 0.7904 (mt) REVERT: 7 402 MET cc_start: 0.7509 (mmm) cc_final: 0.7189 (mmm) REVERT: 7 652 MET cc_start: 0.5846 (ppp) cc_final: 0.5286 (ppp) REVERT: C 74 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7842 (tp) REVERT: D 108 MET cc_start: 0.3551 (tmm) cc_final: 0.2970 (mmt) REVERT: E 129 TRP cc_start: 0.6546 (OUTLIER) cc_final: 0.5636 (p90) REVERT: E 539 TYR cc_start: 0.7913 (m-80) cc_final: 0.7594 (m-80) REVERT: E 580 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7812 (tt) REVERT: G 1386 ASN cc_start: 0.8594 (t0) cc_final: 0.8084 (t0) REVERT: G 1537 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6538 (pm20) REVERT: G 1798 TRP cc_start: 0.7757 (m-10) cc_final: 0.7539 (m100) REVERT: G 1957 MET cc_start: 0.8602 (ttm) cc_final: 0.8248 (tpp) REVERT: G 2040 LEU cc_start: 0.8724 (tt) cc_final: 0.8099 (mt) outliers start: 92 outliers final: 69 residues processed: 366 average time/residue: 0.5957 time to fit residues: 397.0423 Evaluate side-chains 338 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 263 time to evaluate : 6.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 321 ILE Chi-restraints excluded: chain 3 residue 329 LEU Chi-restraints excluded: chain 3 residue 456 ARG Chi-restraints excluded: chain 3 residue 487 HIS Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 548 VAL Chi-restraints excluded: chain 3 residue 650 LEU Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 261 ILE Chi-restraints excluded: chain 5 residue 635 ILE Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 303 GLU Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 668 ILE Chi-restraints excluded: chain 6 residue 678 ILE Chi-restraints excluded: chain 6 residue 797 VAL Chi-restraints excluded: chain 6 residue 835 ILE Chi-restraints excluded: chain 7 residue 77 SER Chi-restraints excluded: chain 7 residue 202 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 335 VAL Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 584 ILE Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 129 TRP Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1368 LEU Chi-restraints excluded: chain G residue 1401 THR Chi-restraints excluded: chain G residue 1463 PHE Chi-restraints excluded: chain G residue 1470 MET Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 1663 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 2047 VAL Chi-restraints excluded: chain G residue 2098 SER Chi-restraints excluded: chain G residue 2153 ASP Chi-restraints excluded: chain G residue 2215 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 63 MET Chi-restraints excluded: chain I residue 93 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 575 optimal weight: 9.9990 chunk 605 optimal weight: 5.9990 chunk 552 optimal weight: 9.9990 chunk 589 optimal weight: 8.9990 chunk 354 optimal weight: 3.9990 chunk 256 optimal weight: 8.9990 chunk 462 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 532 optimal weight: 0.7980 chunk 557 optimal weight: 7.9990 chunk 587 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 641 ASN 5 273 ASN 6 649 GLN 7 622 HIS ** 7 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN G1534 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 53913 Z= 0.301 Angle : 0.628 14.729 72990 Z= 0.319 Chirality : 0.044 0.322 8382 Planarity : 0.005 0.127 9295 Dihedral : 7.498 138.467 7452 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 1.81 % Allowed : 15.50 % Favored : 82.69 % 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: 0.00 (0.11), residues: 6516 helix: 1.26 (0.10), residues: 2716 sheet: -0.22 (0.16), residues: 1017 loop : -1.16 (0.12), residues: 2783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G1798 HIS 0.007 0.001 HIS 3 201 PHE 0.017 0.002 PHE 3 735 TYR 0.032 0.002 TYR F 672 ARG 0.007 0.000 ARG I 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 261 time to evaluate : 6.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 385 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7541 (p90) REVERT: 2 438 LEU cc_start: 0.7854 (tp) cc_final: 0.7581 (tp) REVERT: 3 456 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6730 (ptt90) REVERT: 3 478 MET cc_start: 0.7495 (ttp) cc_final: 0.7181 (ttp) REVERT: 4 280 MET cc_start: 0.7782 (ttt) cc_final: 0.7441 (ppp) REVERT: 4 312 LYS cc_start: 0.6729 (mmmt) cc_final: 0.6459 (mmtm) REVERT: 5 398 LYS cc_start: 0.8121 (tptt) cc_final: 0.7583 (ttmt) REVERT: 5 576 HIS cc_start: 0.5791 (OUTLIER) cc_final: 0.4621 (t-90) REVERT: 6 416 LYS cc_start: 0.3729 (pttp) cc_final: 0.2606 (tttm) REVERT: 6 621 TYR cc_start: 0.7083 (m-80) cc_final: 0.6772 (m-80) REVERT: 6 645 ASP cc_start: 0.8033 (t0) cc_final: 0.7347 (p0) REVERT: 7 258 ILE cc_start: 0.8189 (mt) cc_final: 0.7961 (mt) REVERT: 7 402 MET cc_start: 0.7555 (mmm) cc_final: 0.7253 (mmm) REVERT: 7 413 ARG cc_start: 0.8441 (mtt90) cc_final: 0.8144 (mmm160) REVERT: 7 459 MET cc_start: 0.7589 (mmm) cc_final: 0.7309 (mmm) REVERT: 7 498 MET cc_start: 0.5887 (mmm) cc_final: 0.5435 (mmp) REVERT: 7 652 MET cc_start: 0.5888 (ppp) cc_final: 0.5238 (ppp) REVERT: C 74 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7931 (tp) REVERT: D 108 MET cc_start: 0.3610 (tmm) cc_final: 0.3026 (mmt) REVERT: E 129 TRP cc_start: 0.6784 (OUTLIER) cc_final: 0.5840 (p90) REVERT: E 580 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7890 (tt) REVERT: F 20 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8599 (tt) REVERT: G 1386 ASN cc_start: 0.8481 (t0) cc_final: 0.8031 (t0) REVERT: G 1534 GLN cc_start: 0.6190 (OUTLIER) cc_final: 0.5941 (pp30) REVERT: G 1537 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6629 (pm20) REVERT: G 2040 LEU cc_start: 0.8778 (tt) cc_final: 0.8121 (mt) REVERT: I 189 MET cc_start: 0.8951 (mtt) cc_final: 0.8625 (mtt) outliers start: 106 outliers final: 82 residues processed: 356 average time/residue: 0.6053 time to fit residues: 380.3698 Evaluate side-chains 347 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 256 time to evaluate : 6.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 240 GLU Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 147 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 321 ILE Chi-restraints excluded: chain 3 residue 329 LEU Chi-restraints excluded: chain 3 residue 456 ARG Chi-restraints excluded: chain 3 residue 487 HIS Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 548 VAL Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 3 residue 650 LEU Chi-restraints excluded: chain 3 residue 671 LEU Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 365 ILE Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 295 VAL Chi-restraints excluded: chain 5 residue 512 VAL Chi-restraints excluded: chain 5 residue 540 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 635 ILE Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 303 GLU Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 563 ILE Chi-restraints excluded: chain 6 residue 668 ILE Chi-restraints excluded: chain 6 residue 678 ILE Chi-restraints excluded: chain 6 residue 715 ILE Chi-restraints excluded: chain 6 residue 797 VAL Chi-restraints excluded: chain 7 residue 77 SER Chi-restraints excluded: chain 7 residue 202 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 335 VAL Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 584 ILE Chi-restraints excluded: chain 7 residue 622 HIS Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 129 TRP Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1401 THR Chi-restraints excluded: chain G residue 1463 PHE Chi-restraints excluded: chain G residue 1470 MET Chi-restraints excluded: chain G residue 1534 GLN Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 1630 THR Chi-restraints excluded: chain G residue 1663 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 2047 VAL Chi-restraints excluded: chain G residue 2098 SER Chi-restraints excluded: chain G residue 2153 ASP Chi-restraints excluded: chain G residue 2186 GLU Chi-restraints excluded: chain G residue 2215 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 63 MET Chi-restraints excluded: chain I residue 93 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 386 optimal weight: 5.9990 chunk 623 optimal weight: 0.9980 chunk 380 optimal weight: 0.9990 chunk 295 optimal weight: 0.0070 chunk 433 optimal weight: 0.9990 chunk 653 optimal weight: 5.9990 chunk 601 optimal weight: 3.9990 chunk 520 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 401 optimal weight: 2.9990 chunk 319 optimal weight: 0.9990 overall best weight: 0.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 53913 Z= 0.149 Angle : 0.559 14.220 72990 Z= 0.282 Chirality : 0.041 0.278 8382 Planarity : 0.004 0.122 9295 Dihedral : 7.259 137.829 7452 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 1.43 % Allowed : 16.05 % Favored : 82.52 % 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: 0.22 (0.11), residues: 6516 helix: 1.46 (0.10), residues: 2710 sheet: -0.16 (0.17), residues: 1015 loop : -1.05 (0.12), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP G1798 HIS 0.008 0.001 HIS 7 622 PHE 0.021 0.001 PHE 6 177 TYR 0.023 0.001 TYR 4 728 ARG 0.006 0.000 ARG 6 832 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 274 time to evaluate : 5.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 385 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7647 (p90) REVERT: 2 438 LEU cc_start: 0.7658 (tp) cc_final: 0.7419 (tp) REVERT: 2 636 ILE cc_start: 0.7980 (mp) cc_final: 0.7557 (mt) REVERT: 3 456 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6653 (ptt90) REVERT: 3 478 MET cc_start: 0.7499 (ttp) cc_final: 0.7197 (ttp) REVERT: 4 280 MET cc_start: 0.7859 (ttt) cc_final: 0.7605 (ppp) REVERT: 5 348 MET cc_start: 0.7547 (mmm) cc_final: 0.7269 (mmp) REVERT: 5 398 LYS cc_start: 0.8082 (tptt) cc_final: 0.7456 (ttmt) REVERT: 5 753 TYR cc_start: 0.7931 (t80) cc_final: 0.7468 (t80) REVERT: 6 416 LYS cc_start: 0.3572 (pttp) cc_final: 0.2474 (tttm) REVERT: 6 621 TYR cc_start: 0.6981 (m-80) cc_final: 0.6696 (m-80) REVERT: 6 645 ASP cc_start: 0.8037 (t0) cc_final: 0.7378 (p0) REVERT: 7 258 ILE cc_start: 0.8189 (mt) cc_final: 0.7929 (mt) REVERT: 7 402 MET cc_start: 0.7538 (mmm) cc_final: 0.7242 (mmm) REVERT: 7 413 ARG cc_start: 0.8445 (mtt90) cc_final: 0.8127 (mmm160) REVERT: 7 652 MET cc_start: 0.5980 (ppp) cc_final: 0.5377 (ppp) REVERT: C 74 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7880 (tp) REVERT: D 108 MET cc_start: 0.3538 (tmm) cc_final: 0.3144 (mmt) REVERT: E 129 TRP cc_start: 0.6823 (OUTLIER) cc_final: 0.5891 (p90) REVERT: E 539 TYR cc_start: 0.7942 (m-80) cc_final: 0.7627 (m-80) REVERT: E 580 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7774 (tt) REVERT: G 1386 ASN cc_start: 0.8591 (t0) cc_final: 0.8098 (t0) REVERT: G 1537 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6719 (pm20) REVERT: G 1798 TRP cc_start: 0.7758 (m-10) cc_final: 0.7506 (m100) REVERT: G 2040 LEU cc_start: 0.8730 (tt) cc_final: 0.8087 (mt) outliers start: 84 outliers final: 72 residues processed: 346 average time/residue: 0.6023 time to fit residues: 368.9084 Evaluate side-chains 341 residues out of total 5935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 263 time to evaluate : 6.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 216 LEU Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 415 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 321 ILE Chi-restraints excluded: chain 3 residue 329 LEU Chi-restraints excluded: chain 3 residue 389 VAL Chi-restraints excluded: chain 3 residue 456 ARG Chi-restraints excluded: chain 3 residue 487 HIS Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 548 VAL Chi-restraints excluded: chain 3 residue 569 HIS Chi-restraints excluded: chain 3 residue 650 LEU Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 365 ILE Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 635 ILE Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 303 GLU Chi-restraints excluded: chain 6 residue 386 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 443 LEU Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 668 ILE Chi-restraints excluded: chain 6 residue 678 ILE Chi-restraints excluded: chain 6 residue 715 ILE Chi-restraints excluded: chain 6 residue 797 VAL Chi-restraints excluded: chain 7 residue 202 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 335 VAL Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 584 ILE Chi-restraints excluded: chain 7 residue 622 HIS Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 129 TRP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1401 THR Chi-restraints excluded: chain G residue 1463 PHE Chi-restraints excluded: chain G residue 1470 MET Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 1663 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 2047 VAL Chi-restraints excluded: chain G residue 2098 SER Chi-restraints excluded: chain G residue 2153 ASP Chi-restraints excluded: chain G residue 2215 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 63 MET Chi-restraints excluded: chain I residue 93 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 413 optimal weight: 0.9980 chunk 554 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 479 optimal weight: 0.0470 chunk 76 optimal weight: 0.0870 chunk 144 optimal weight: 5.9990 chunk 521 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 535 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.9858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 622 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.093088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.072382 restraints weight = 159009.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073690 restraints weight = 104144.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.074586 restraints weight = 70048.936| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 53913 Z= 0.154 Angle : 0.554 13.807 72990 Z= 0.279 Chirality : 0.041 0.278 8382 Planarity : 0.004 0.120 9295 Dihedral : 7.143 137.657 7452 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 1.60 % Allowed : 15.98 % Favored : 82.42 % 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 (0.11), residues: 6516 helix: 1.50 (0.10), residues: 2716 sheet: -0.10 (0.17), residues: 1013 loop : -1.00 (0.12), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP G1798 HIS 0.009 0.001 HIS 7 622 PHE 0.027 0.001 PHE 7 278 TYR 0.023 0.001 TYR H 53 ARG 0.005 0.000 ARG I 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9094.53 seconds wall clock time: 217 minutes 20.13 seconds (13040.13 seconds total)