Starting phenix.real_space_refine on Tue Aug 26 22:03:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jaq_36131/08_2025/8jaq_36131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jaq_36131/08_2025/8jaq_36131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jaq_36131/08_2025/8jaq_36131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jaq_36131/08_2025/8jaq_36131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jaq_36131/08_2025/8jaq_36131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jaq_36131/08_2025/8jaq_36131.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4765 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 233 5.16 5 C 25051 2.51 5 N 6678 2.21 5 O 7263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39233 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4622 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 6, 'TRANS': 565} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1616 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 1 Chain: "S" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4622 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 6, 'TRANS': 565} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "G" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 782 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 8, 'TRANS': 90} Chain: "H" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5223 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 618} Chain breaks: 1 Chain: "R" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 666 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 4619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4619 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 565} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4613 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 6, 'TRANS': 564} Chain: "L" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1176 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain breaks: 1 Chain: "M" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 1 Chain: "N" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 718 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 1 Chain: "O" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "P" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "Q" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "T" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 722 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 1 Chain: "V" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 666 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5223 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 618} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 410 SG CYS A 54 122.947 170.365 72.761 1.00 0.89 S ATOM 8178 SG CYS B 54 125.704 170.644 75.407 1.00 7.35 S ATOM 19406 SG CYS R 53 117.651 81.272 76.903 1.00 19.51 S ATOM 19429 SG CYS R 56 121.303 81.904 76.930 1.00 24.38 S ATOM 19513 SG CYS R 68 119.921 78.354 77.329 1.00 30.02 S ATOM 19320 SG CYS R 42 111.124 77.321 78.441 1.00 13.15 S ATOM 19339 SG CYS R 45 112.229 78.699 75.052 1.00 12.94 S ATOM 19634 SG CYS R 83 113.266 80.533 78.161 1.00 14.78 S ATOM 19563 SG CYS R 75 105.846 72.647 88.520 1.00 15.99 S ATOM 19730 SG CYS R 94 105.237 75.121 86.312 1.00 13.19 S ATOM 20264 SG CYS J 54 73.674 78.925 72.752 1.00 5.00 S ATOM 24883 SG CYS K 54 71.371 80.103 75.735 1.00 0.43 S ATOM 33554 SG CYS V 53 79.275 168.094 76.806 1.00 26.04 S ATOM 33577 SG CYS V 56 75.539 168.013 76.641 1.00 31.85 S ATOM 33661 SG CYS V 68 77.443 171.358 77.172 1.00 32.66 S ATOM 33468 SG CYS V 42 85.351 172.006 78.502 1.00 17.26 S ATOM 33487 SG CYS V 45 84.639 170.308 75.164 1.00 16.46 S ATOM 33782 SG CYS V 83 83.314 168.744 78.277 1.00 19.50 S ATOM 33711 SG CYS V 75 90.890 176.575 88.496 1.00 21.58 S ATOM 33878 SG CYS V 94 91.602 174.200 86.340 1.00 17.02 S Time building chain proxies: 7.77, per 1000 atoms: 0.20 Number of scatterers: 39233 At special positions: 0 Unit cell: (198.44, 250.92, 139.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 233 16.00 O 7263 8.00 N 6678 7.00 C 25051 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: 2.40 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 9.8 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 89 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS A 89 " pdb="ZN ZN B 601 " - pdb=" SG CYS A 54 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 54 " pdb=" ZN J 601 " pdb="ZN ZN J 601 " - pdb=" NE2 HIS K 89 " pdb="ZN ZN J 601 " - pdb=" NE2 HIS J 89 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 54 " pdb="ZN ZN J 601 " - pdb=" SG CYS K 54 " pdb=" ZN R 200 " pdb="ZN ZN R 200 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 68 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb=" ZN V 200 " pdb="ZN ZN V 200 " - pdb=" ND1 HIS V 82 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 53 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 68 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 56 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1 HIS V 80 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 45 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 83 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 42 " pdb=" ZN V 202 " pdb="ZN ZN V 202 " - pdb=" SG CYS V 75 " pdb="ZN ZN V 202 " - pdb=" SG CYS V 94 " pdb="ZN ZN V 202 " - pdb=" ND1 HIS V 77 " Number of angles added : 16 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9248 Finding SS restraints... Secondary structure from input PDB file: 223 helices and 20 sheets defined 70.5% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 25 through 29 removed outlier: 3.935A pdb=" N ARG A 29 " --> pdb=" O ILE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.527A pdb=" N PHE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.794A pdb=" N SER A 58 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.874A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.503A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 133 Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.642A pdb=" N LYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.530A pdb=" N TRP A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE A 160 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 200 removed outlier: 3.746A pdb=" N HIS A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.563A pdb=" N GLU A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 removed outlier: 3.638A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 259 removed outlier: 3.752A pdb=" N VAL A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 280 removed outlier: 3.829A pdb=" N GLN A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 307 through 322 removed outlier: 3.546A pdb=" N ILE A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 Processing helix chain 'A' and resid 350 through 368 removed outlier: 3.684A pdb=" N ALA A 360 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 392 removed outlier: 3.946A pdb=" N SER A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.679A pdb=" N GLU A 399 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 443 removed outlier: 3.784A pdb=" N SER A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 463 removed outlier: 4.048A pdb=" N GLU A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 484 removed outlier: 3.750A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 506 removed outlier: 3.766A pdb=" N ALA A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 492 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 removed outlier: 3.581A pdb=" N ASP A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 550 removed outlier: 3.551A pdb=" N VAL A 533 " --> pdb=" O ASN A 529 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 541 " --> pdb=" O HIS A 537 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 561 removed outlier: 3.599A pdb=" N SER A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 578 removed outlier: 3.559A pdb=" N VAL A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 removed outlier: 3.589A pdb=" N THR E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.611A pdb=" N CYS E 46 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 47 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 3.857A pdb=" N ILE E 63 " --> pdb=" O THR E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.559A pdb=" N ARG E 89 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.716A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 173 removed outlier: 3.759A pdb=" N MET E 162 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 171 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 186 removed outlier: 4.220A pdb=" N VAL E 184 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 185 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 191 Processing helix chain 'E' and resid 200 through 207 Processing helix chain 'C' and resid 23 through 36 removed outlier: 3.693A pdb=" N LEU C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 39 through 47 removed outlier: 3.747A pdb=" N LYS D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 83 removed outlier: 3.514A pdb=" N THR D 78 " --> pdb=" O CYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 28 through 33 removed outlier: 3.866A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 removed outlier: 3.536A pdb=" N ASP B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.693A pdb=" N SER B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.599A pdb=" N HIS B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 135 through 152 removed outlier: 4.310A pdb=" N LYS B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 175 removed outlier: 3.964A pdb=" N VAL B 163 " --> pdb=" O TRP B 159 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 199 removed outlier: 3.632A pdb=" N GLU B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 234 removed outlier: 3.562A pdb=" N LYS B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 259 removed outlier: 3.735A pdb=" N VAL B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 removed outlier: 3.870A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 301 Processing helix chain 'B' and resid 303 through 322 removed outlier: 3.862A pdb=" N ALA B 309 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 removed outlier: 3.524A pdb=" N TYR B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 368 removed outlier: 4.114A pdb=" N HIS B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 392 removed outlier: 3.734A pdb=" N SER B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 421 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 444 through 463 removed outlier: 3.656A pdb=" N ALA B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 484 removed outlier: 4.007A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 506 removed outlier: 3.516A pdb=" N ALA B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU B 492 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYS B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 510 removed outlier: 4.032A pdb=" N TYR B 510 " --> pdb=" O GLY B 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 511 through 525 removed outlier: 4.543A pdb=" N TYR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 551 removed outlier: 4.144A pdb=" N VAL B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 577 Processing helix chain 'G' and resid 23 through 36 Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 39 through 47 Processing helix chain 'H' and resid 66 through 83 removed outlier: 4.231A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.565A pdb=" N ASN H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.723A pdb=" N THR I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL I 25 " --> pdb=" O ILE I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 47 removed outlier: 3.688A pdb=" N PHE I 39 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 78 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.766A pdb=" N GLU I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 112 Processing helix chain 'I' and resid 138 through 151 removed outlier: 4.136A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 172 removed outlier: 3.906A pdb=" N ARG I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 191 removed outlier: 3.621A pdb=" N PHE I 188 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL I 189 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 191 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 207 Processing helix chain 'I' and resid 207 through 230 removed outlier: 3.719A pdb=" N GLN I 228 " --> pdb=" O SER I 224 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU I 229 " --> pdb=" O ASN I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 254 removed outlier: 3.684A pdb=" N MET I 236 " --> pdb=" O CYS I 232 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP I 245 " --> pdb=" O GLY I 241 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG I 251 " --> pdb=" O GLU I 247 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 257 No H-bonds generated for 'chain 'I' and resid 255 through 257' Processing helix chain 'I' and resid 258 through 269 removed outlier: 3.618A pdb=" N ILE I 263 " --> pdb=" O TYR I 259 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG I 269 " --> pdb=" O GLU I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 281 Processing helix chain 'I' and resid 281 through 288 removed outlier: 3.996A pdb=" N ILE I 285 " --> pdb=" O GLU I 281 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE I 286 " --> pdb=" O CYS I 282 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG I 287 " --> pdb=" O HIS I 283 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN I 288 " --> pdb=" O ASN I 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 281 through 288' Processing helix chain 'I' and resid 290 through 304 removed outlier: 3.746A pdb=" N MET I 297 " --> pdb=" O ASP I 293 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU I 300 " --> pdb=" O ASN I 296 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU I 301 " --> pdb=" O MET I 297 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA I 303 " --> pdb=" O VAL I 299 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL I 304 " --> pdb=" O LEU I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 327 removed outlier: 4.010A pdb=" N MET I 311 " --> pdb=" O GLY I 307 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS I 318 " --> pdb=" O GLU I 314 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE I 319 " --> pdb=" O LEU I 315 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU I 324 " --> pdb=" O HIS I 320 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG I 325 " --> pdb=" O ASP I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 357 removed outlier: 3.529A pdb=" N LEU I 338 " --> pdb=" O ASN I 334 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN I 352 " --> pdb=" O GLY I 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL I 357 " --> pdb=" O LEU I 353 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 377 Processing helix chain 'I' and resid 386 through 400 removed outlier: 3.819A pdb=" N LEU I 390 " --> pdb=" O LYS I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 424 removed outlier: 4.461A pdb=" N ASP I 413 " --> pdb=" O ASN I 409 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR I 420 " --> pdb=" O THR I 416 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL I 421 " --> pdb=" O SER I 417 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR I 424 " --> pdb=" O THR I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 427 through 445 removed outlier: 3.775A pdb=" N PHE I 431 " --> pdb=" O ASP I 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 465 Processing helix chain 'I' and resid 470 through 482 removed outlier: 3.525A pdb=" N HIS I 474 " --> pdb=" O THR I 470 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG I 475 " --> pdb=" O SER I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 482 through 496 removed outlier: 3.703A pdb=" N LYS I 489 " --> pdb=" O ASP I 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 530 through 548 removed outlier: 4.243A pdb=" N LYS I 535 " --> pdb=" O GLN I 531 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER I 536 " --> pdb=" O GLU I 532 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU I 541 " --> pdb=" O VAL I 537 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU I 542 " --> pdb=" O GLN I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 579 through 591 removed outlier: 4.286A pdb=" N VAL I 584 " --> pdb=" O TYR I 580 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN I 590 " --> pdb=" O LEU I 586 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER I 591 " --> pdb=" O ALA I 587 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 603 removed outlier: 3.517A pdb=" N THR I 603 " --> pdb=" O LEU I 599 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 620 removed outlier: 4.268A pdb=" N LYS I 615 " --> pdb=" O THR I 611 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU I 617 " --> pdb=" O THR I 613 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 68 removed outlier: 3.623A pdb=" N GLU R 67 " --> pdb=" O THR R 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS R 68 " --> pdb=" O SER R 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 64 through 68' Processing helix chain 'R' and resid 81 through 89 Processing helix chain 'J' and resid 12 through 24 Processing helix chain 'J' and resid 25 through 29 removed outlier: 4.035A pdb=" N ARG J 29 " --> pdb=" O ILE J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 35 Processing helix chain 'J' and resid 36 through 50 removed outlier: 3.699A pdb=" N PHE J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 61 removed outlier: 3.579A pdb=" N SER J 58 " --> pdb=" O CYS J 54 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU J 59 " --> pdb=" O GLN J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 71 removed outlier: 4.614A pdb=" N LYS J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.704A pdb=" N HIS J 81 " --> pdb=" O HIS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 111 removed outlier: 3.587A pdb=" N ARG J 104 " --> pdb=" O SER J 100 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER J 106 " --> pdb=" O SER J 102 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR J 107 " --> pdb=" O ARG J 103 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU J 110 " --> pdb=" O SER J 106 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER J 111 " --> pdb=" O TYR J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 134 Processing helix chain 'J' and resid 135 through 153 removed outlier: 3.985A pdb=" N LYS J 141 " --> pdb=" O SER J 137 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL J 142 " --> pdb=" O ASP J 138 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS J 153 " --> pdb=" O LEU J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 175 removed outlier: 4.021A pdb=" N PHE J 160 " --> pdb=" O MET J 156 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG J 161 " --> pdb=" O LEU J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 199 removed outlier: 4.350A pdb=" N GLU J 184 " --> pdb=" O HIS J 180 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE J 186 " --> pdb=" O GLY J 182 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS J 187 " --> pdb=" O GLU J 183 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS J 199 " --> pdb=" O LYS J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 210 Processing helix chain 'J' and resid 211 through 219 removed outlier: 3.728A pdb=" N LEU J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 235 removed outlier: 3.561A pdb=" N LYS J 227 " --> pdb=" O ASP J 223 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU J 231 " --> pdb=" O LYS J 227 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU J 235 " --> pdb=" O GLU J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 259 removed outlier: 3.649A pdb=" N VAL J 258 " --> pdb=" O LYS J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 281 removed outlier: 3.614A pdb=" N ALA J 265 " --> pdb=" O GLU J 261 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN J 267 " --> pdb=" O LYS J 263 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS J 271 " --> pdb=" O GLN J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 300 Processing helix chain 'J' and resid 304 through 322 removed outlier: 4.420A pdb=" N ALA J 309 " --> pdb=" O CYS J 305 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE J 310 " --> pdb=" O GLN J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 344 Processing helix chain 'J' and resid 351 through 368 removed outlier: 3.759A pdb=" N ALA J 360 " --> pdb=" O HIS J 356 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS J 366 " --> pdb=" O GLY J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 393 removed outlier: 3.995A pdb=" N SER J 377 " --> pdb=" O LEU J 373 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE J 391 " --> pdb=" O GLU J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 422 removed outlier: 3.589A pdb=" N GLN J 400 " --> pdb=" O LYS J 396 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 403 " --> pdb=" O GLU J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 443 removed outlier: 3.503A pdb=" N ASN J 434 " --> pdb=" O LYS J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 463 removed outlier: 3.664A pdb=" N GLU J 449 " --> pdb=" O PHE J 445 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU J 450 " --> pdb=" O LYS J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 484 removed outlier: 3.609A pdb=" N ALA J 471 " --> pdb=" O ASP J 467 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER J 473 " --> pdb=" O GLU J 469 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP J 484 " --> pdb=" O LEU J 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 506 removed outlier: 3.617A pdb=" N GLU J 492 " --> pdb=" O TYR J 488 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS J 493 " --> pdb=" O GLU J 489 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 526 removed outlier: 4.485A pdb=" N TYR J 515 " --> pdb=" O SER J 511 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY J 519 " --> pdb=" O TYR J 515 " (cutoff:3.500A) Processing helix chain 'J' and resid 530 through 551 removed outlier: 3.607A pdb=" N PHE J 534 " --> pdb=" O TYR J 530 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU J 535 " --> pdb=" O GLU J 531 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER J 541 " --> pdb=" O HIS J 537 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN J 542 " --> pdb=" O ASN J 538 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG J 549 " --> pdb=" O ARG J 545 " (cutoff:3.500A) Processing helix chain 'J' and resid 566 through 577 removed outlier: 3.738A pdb=" N LEU J 575 " --> pdb=" O VAL J 571 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER J 577 " --> pdb=" O SER J 573 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 24 Processing helix chain 'K' and resid 28 through 33 removed outlier: 3.961A pdb=" N ARG K 33 " --> pdb=" O ARG K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 61 removed outlier: 4.005A pdb=" N GLU K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 70 Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.892A pdb=" N HIS K 81 " --> pdb=" O HIS K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 106 Processing helix chain 'K' and resid 112 through 134 removed outlier: 3.856A pdb=" N ILE K 120 " --> pdb=" O LYS K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 151 removed outlier: 4.050A pdb=" N LYS K 141 " --> pdb=" O SER K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 175 removed outlier: 3.770A pdb=" N TRP K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE K 160 " --> pdb=" O MET K 156 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL K 163 " --> pdb=" O TRP K 159 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU K 164 " --> pdb=" O PHE K 160 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG K 168 " --> pdb=" O GLU K 164 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG K 173 " --> pdb=" O LEU K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 199 removed outlier: 4.412A pdb=" N GLU K 184 " --> pdb=" O HIS K 180 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR K 192 " --> pdb=" O LEU K 188 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS K 199 " --> pdb=" O LYS K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 219 removed outlier: 3.875A pdb=" N LEU K 212 " --> pdb=" O LEU K 208 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE K 217 " --> pdb=" O CYS K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 234 Processing helix chain 'K' and resid 241 through 258 removed outlier: 3.657A pdb=" N VAL K 258 " --> pdb=" O LYS K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 280 removed outlier: 4.210A pdb=" N GLN K 267 " --> pdb=" O LYS K 263 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS K 279 " --> pdb=" O LEU K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 301 Processing helix chain 'K' and resid 306 through 322 Processing helix chain 'K' and resid 326 through 344 Processing helix chain 'K' and resid 351 through 368 removed outlier: 3.985A pdb=" N HIS K 366 " --> pdb=" O GLY K 362 " (cutoff:3.500A) Processing helix chain 'K' and resid 373 through 393 removed outlier: 4.000A pdb=" N SER K 377 " --> pdb=" O LEU K 373 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE K 391 " --> pdb=" O GLU K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 422 removed outlier: 4.009A pdb=" N GLN K 404 " --> pdb=" O GLN K 400 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU K 409 " --> pdb=" O GLU K 405 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU K 411 " --> pdb=" O HIS K 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 425 through 442 Processing helix chain 'K' and resid 444 through 463 removed outlier: 3.616A pdb=" N GLU K 450 " --> pdb=" O LYS K 446 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN K 461 " --> pdb=" O GLN K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 484 removed outlier: 3.832A pdb=" N HIS K 476 " --> pdb=" O LEU K 472 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP K 484 " --> pdb=" O LEU K 480 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 507 removed outlier: 3.793A pdb=" N GLU K 492 " --> pdb=" O TYR K 488 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS K 493 " --> pdb=" O GLU K 489 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU K 494 " --> pdb=" O ASN K 490 " (cutoff:3.500A) Processing helix chain 'K' and resid 508 through 511 removed outlier: 5.963A pdb=" N SER K 511 " --> pdb=" O GLU K 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 508 through 511' Processing helix chain 'K' and resid 512 through 525 removed outlier: 3.528A pdb=" N GLY K 519 " --> pdb=" O TYR K 515 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 548 removed outlier: 3.953A pdb=" N VAL K 533 " --> pdb=" O ASN K 529 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE K 534 " --> pdb=" O TYR K 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 569 through 577 removed outlier: 3.590A pdb=" N SER K 577 " --> pdb=" O SER K 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 25 removed outlier: 3.508A pdb=" N THR L 13 " --> pdb=" O ASP L 9 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN L 15 " --> pdb=" O ASP L 11 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR L 20 " --> pdb=" O LYS L 16 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 47 removed outlier: 3.629A pdb=" N ARG L 38 " --> pdb=" O THR L 34 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE L 39 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER L 40 " --> pdb=" O ASN L 36 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA L 44 " --> pdb=" O SER L 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL L 47 " --> pdb=" O TYR L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 79 removed outlier: 4.299A pdb=" N ARG L 75 " --> pdb=" O HIS L 71 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL L 76 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 105 removed outlier: 4.407A pdb=" N GLU L 93 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR L 94 " --> pdb=" O TYR L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 112 Processing helix chain 'L' and resid 138 through 151 removed outlier: 3.508A pdb=" N ALA L 143 " --> pdb=" O ILE L 139 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU L 144 " --> pdb=" O GLY L 140 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET L 151 " --> pdb=" O TRP L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 156 Processing helix chain 'M' and resid 23 through 36 removed outlier: 3.886A pdb=" N ILE M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 61 removed outlier: 3.603A pdb=" N GLY M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 67 Processing helix chain 'N' and resid 33 through 37 Processing helix chain 'N' and resid 39 through 47 Processing helix chain 'N' and resid 48 through 51 Processing helix chain 'N' and resid 66 through 83 removed outlier: 4.273A pdb=" N LYS N 72 " --> pdb=" O HIS N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 111 removed outlier: 4.621A pdb=" N LEU N 101 " --> pdb=" O PRO N 97 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU N 102 " --> pdb=" O GLU N 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 33 removed outlier: 3.876A pdb=" N LEU Q 27 " --> pdb=" O THR Q 23 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS Q 28 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 49 Processing helix chain 'T' and resid 32 through 37 Processing helix chain 'T' and resid 39 through 47 Processing helix chain 'T' and resid 66 through 84 removed outlier: 4.329A pdb=" N LYS T 72 " --> pdb=" O HIS T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 110 removed outlier: 3.808A pdb=" N ASN T 108 " --> pdb=" O LEU T 104 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE T 109 " --> pdb=" O MET T 105 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 3.522A pdb=" N ASN V 59 " --> pdb=" O GLU V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 89 Processing helix chain 'U' and resid 9 through 25 removed outlier: 3.829A pdb=" N THR U 20 " --> pdb=" O LYS U 16 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA U 23 " --> pdb=" O THR U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 47 removed outlier: 3.722A pdb=" N PHE U 39 " --> pdb=" O TRP U 35 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER U 40 " --> pdb=" O ASN U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 78 removed outlier: 3.873A pdb=" N ARG U 70 " --> pdb=" O GLU U 66 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS U 71 " --> pdb=" O ASN U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 105 removed outlier: 3.650A pdb=" N GLU U 93 " --> pdb=" O ARG U 89 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS U 96 " --> pdb=" O GLU U 92 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY U 97 " --> pdb=" O GLU U 93 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS U 103 " --> pdb=" O ASP U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 112 Processing helix chain 'U' and resid 138 through 151 removed outlier: 4.033A pdb=" N LEU U 144 " --> pdb=" O GLY U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 155 through 172 removed outlier: 3.903A pdb=" N ARG U 161 " --> pdb=" O ALA U 157 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 191 removed outlier: 3.743A pdb=" N PHE U 188 " --> pdb=" O VAL U 184 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL U 189 " --> pdb=" O ILE U 185 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL U 191 " --> pdb=" O SER U 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 201 through 207 Processing helix chain 'U' and resid 207 through 230 removed outlier: 3.735A pdb=" N GLN U 228 " --> pdb=" O SER U 224 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU U 229 " --> pdb=" O ASN U 225 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 254 removed outlier: 3.682A pdb=" N MET U 236 " --> pdb=" O CYS U 232 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU U 237 " --> pdb=" O SER U 233 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP U 245 " --> pdb=" O GLY U 241 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG U 251 " --> pdb=" O GLU U 247 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR U 253 " --> pdb=" O ARG U 249 " (cutoff:3.500A) Processing helix chain 'U' and resid 255 through 257 No H-bonds generated for 'chain 'U' and resid 255 through 257' Processing helix chain 'U' and resid 258 through 269 removed outlier: 3.548A pdb=" N ILE U 263 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG U 269 " --> pdb=" O GLU U 265 " (cutoff:3.500A) Processing helix chain 'U' and resid 274 through 280 Processing helix chain 'U' and resid 281 through 288 removed outlier: 3.590A pdb=" N GLN U 288 " --> pdb=" O ASN U 284 " (cutoff:3.500A) Processing helix chain 'U' and resid 290 through 304 removed outlier: 3.596A pdb=" N ASN U 296 " --> pdb=" O ASN U 292 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET U 297 " --> pdb=" O ASP U 293 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU U 301 " --> pdb=" O MET U 297 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA U 303 " --> pdb=" O VAL U 299 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL U 304 " --> pdb=" O LEU U 300 " (cutoff:3.500A) Processing helix chain 'U' and resid 307 through 329 removed outlier: 4.072A pdb=" N MET U 311 " --> pdb=" O GLY U 307 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU U 324 " --> pdb=" O HIS U 320 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG U 325 " --> pdb=" O ASP U 321 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA U 326 " --> pdb=" O GLU U 322 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR U 327 " --> pdb=" O GLY U 323 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN U 329 " --> pdb=" O ARG U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 334 through 357 removed outlier: 3.576A pdb=" N LEU U 338 " --> pdb=" O ASN U 334 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE U 339 " --> pdb=" O MET U 335 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN U 352 " --> pdb=" O GLY U 348 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL U 357 " --> pdb=" O LEU U 353 " (cutoff:3.500A) Processing helix chain 'U' and resid 361 through 377 Processing helix chain 'U' and resid 386 through 400 Processing helix chain 'U' and resid 407 through 424 removed outlier: 3.994A pdb=" N ASP U 413 " --> pdb=" O ASN U 409 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR U 420 " --> pdb=" O THR U 416 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL U 421 " --> pdb=" O SER U 417 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR U 424 " --> pdb=" O THR U 420 " (cutoff:3.500A) Processing helix chain 'U' and resid 427 through 445 removed outlier: 3.808A pdb=" N PHE U 431 " --> pdb=" O ASP U 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS U 445 " --> pdb=" O LYS U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 450 through 466 Processing helix chain 'U' and resid 470 through 496 removed outlier: 3.525A pdb=" N MET U 480 " --> pdb=" O MET U 476 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA U 484 " --> pdb=" O MET U 480 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP U 485 " --> pdb=" O SER U 481 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS U 489 " --> pdb=" O ASP U 485 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 548 removed outlier: 4.180A pdb=" N LYS U 535 " --> pdb=" O GLN U 531 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER U 536 " --> pdb=" O GLU U 532 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU U 541 " --> pdb=" O VAL U 537 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU U 542 " --> pdb=" O GLN U 538 " (cutoff:3.500A) Processing helix chain 'U' and resid 579 through 591 removed outlier: 4.039A pdb=" N VAL U 584 " --> pdb=" O TYR U 580 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE U 588 " --> pdb=" O VAL U 584 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN U 590 " --> pdb=" O LEU U 586 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER U 591 " --> pdb=" O ALA U 587 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 603 removed outlier: 3.632A pdb=" N ASP U 601 " --> pdb=" O LYS U 597 " (cutoff:3.500A) Processing helix chain 'U' and resid 607 through 620 removed outlier: 3.849A pdb=" N THR U 611 " --> pdb=" O GLU U 607 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS U 612 " --> pdb=" O LYS U 608 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE U 614 " --> pdb=" O LEU U 610 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS U 615 " --> pdb=" O THR U 611 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU U 617 " --> pdb=" O THR U 613 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL U 620 " --> pdb=" O SER U 616 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 14 through 15 Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AA3, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.764A pdb=" N ALA G 73 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G 75 " --> pdb=" O MET G 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'H' and resid 20 through 22 Processing sheet with id=AA7, first strand: chain 'I' and resid 508 through 513 removed outlier: 6.644A pdb=" N GLN I 508 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA R 31 " --> pdb=" O GLN I 508 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR I 510 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TRP R 33 " --> pdb=" O TYR I 510 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU I 512 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N TRP R 35 " --> pdb=" O LEU I 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 561 through 562 removed outlier: 3.545A pdb=" N VAL I 577 " --> pdb=" O GLY I 562 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL I 574 " --> pdb=" O PHE I 651 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 593 through 595 removed outlier: 3.888A pdb=" N VAL I 594 " --> pdb=" O PHE I 638 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE I 638 " --> pdb=" O VAL I 594 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 70 through 71 Processing sheet with id=AB2, first strand: chain 'M' and resid 14 through 18 removed outlier: 3.587A pdb=" N ILE M 7 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR M 16 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N PHE M 4 " --> pdb=" O ALA M 73 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N VAL M 75 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N MET M 6 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU M 77 " --> pdb=" O MET M 6 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG M 8 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 31 through 32 removed outlier: 9.181A pdb=" N VAL N 60 " --> pdb=" O TYR N 18 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LYS N 20 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 12 through 13 removed outlier: 3.841A pdb=" N THR Q 16 " --> pdb=" O LEU Q 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 12 through 13 removed outlier: 3.669A pdb=" N ALA Q 73 " --> pdb=" O PHE Q 4 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL Q 75 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 42 through 43 Processing sheet with id=AB7, first strand: chain 'T' and resid 20 through 22 Processing sheet with id=AB8, first strand: chain 'U' and resid 508 through 513 removed outlier: 3.885A pdb=" N TYR U 510 " --> pdb=" O ALA V 29 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA V 31 " --> pdb=" O TYR U 510 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'V' and resid 70 through 71 Processing sheet with id=AC1, first strand: chain 'U' and resid 561 through 563 removed outlier: 3.767A pdb=" N VAL U 577 " --> pdb=" O GLY U 562 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL U 574 " --> pdb=" O PHE U 651 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 593 through 594 removed outlier: 3.615A pdb=" N VAL U 594 " --> pdb=" O PHE U 638 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE U 638 " --> pdb=" O VAL U 594 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER U 639 " --> pdb=" O ASN U 624 " (cutoff:3.500A) 2250 hydrogen bonds defined for protein. 6642 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: 7.74 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10017 1.33 - 1.45: 7711 1.45 - 1.57: 21986 1.57 - 1.69: 0 1.69 - 1.81: 354 Bond restraints: 40068 Sorted by residual: bond pdb=" CA ALA I 48 " pdb=" C ALA I 48 " ideal model delta sigma weight residual 1.528 1.486 0.042 1.38e-02 5.25e+03 9.37e+00 bond pdb=" CA ALA U 48 " pdb=" C ALA U 48 " ideal model delta sigma weight residual 1.528 1.488 0.040 1.38e-02 5.25e+03 8.46e+00 bond pdb=" CA ALA U 48 " pdb=" CB ALA U 48 " ideal model delta sigma weight residual 1.528 1.492 0.036 1.54e-02 4.22e+03 5.56e+00 bond pdb=" CA ALA I 48 " pdb=" CB ALA I 48 " ideal model delta sigma weight residual 1.528 1.493 0.035 1.54e-02 4.22e+03 5.24e+00 bond pdb=" C VAL I 47 " pdb=" O VAL I 47 " ideal model delta sigma weight residual 1.236 1.214 0.023 1.19e-02 7.06e+03 3.62e+00 ... (remaining 40063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 53173 1.80 - 3.60: 772 3.60 - 5.39: 97 5.39 - 7.19: 34 7.19 - 8.99: 6 Bond angle restraints: 54082 Sorted by residual: angle pdb=" C GLN I 521 " pdb=" CA GLN I 521 " pdb=" CB GLN I 521 " ideal model delta sigma weight residual 116.34 110.00 6.34 1.40e+00 5.10e-01 2.05e+01 angle pdb=" C VAL R 39 " pdb=" N ASP R 40 " pdb=" CA ASP R 40 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C VAL V 39 " pdb=" N ASP V 40 " pdb=" CA ASP V 40 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C THR T 84 " pdb=" N ASN T 85 " pdb=" CA ASN T 85 " ideal model delta sigma weight residual 121.54 128.48 -6.94 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C THR D 84 " pdb=" N ASN D 85 " pdb=" CA ASN D 85 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.28e+01 ... (remaining 54077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 21760 18.00 - 36.00: 1955 36.00 - 53.99: 285 53.99 - 71.99: 81 71.99 - 89.99: 45 Dihedral angle restraints: 24126 sinusoidal: 9831 harmonic: 14295 Sorted by residual: dihedral pdb=" CA VAL B 301 " pdb=" C VAL B 301 " pdb=" N ASP B 302 " pdb=" CA ASP B 302 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA MET I 26 " pdb=" C MET I 26 " pdb=" N LEU I 27 " pdb=" CA LEU I 27 " ideal model delta harmonic sigma weight residual -180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA LYS A 195 " pdb=" C LYS A 195 " pdb=" N LEU A 196 " pdb=" CA LEU A 196 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 24123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5559 0.071 - 0.142: 358 0.142 - 0.213: 12 0.213 - 0.284: 0 0.284 - 0.355: 3 Chirality restraints: 5932 Sorted by residual: chirality pdb=" CB VAL I 47 " pdb=" CA VAL I 47 " pdb=" CG1 VAL I 47 " pdb=" CG2 VAL I 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB VAL U 47 " pdb=" CA VAL U 47 " pdb=" CG1 VAL U 47 " pdb=" CG2 VAL U 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB ILE D 99 " pdb=" CA ILE D 99 " pdb=" CG1 ILE D 99 " pdb=" CG2 ILE D 99 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 5929 not shown) Planarity restraints: 6889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE U 529 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO U 530 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO U 530 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO U 530 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS U 46 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C CYS U 46 " -0.036 2.00e-02 2.50e+03 pdb=" O CYS U 46 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL U 47 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 529 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO I 530 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO I 530 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 530 " -0.028 5.00e-02 4.00e+02 ... (remaining 6886 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 323 2.60 - 3.18: 33677 3.18 - 3.75: 63901 3.75 - 4.33: 88179 4.33 - 4.90: 145000 Nonbonded interactions: 331080 Sorted by model distance: nonbonded pdb=" OD1 ASP V 97 " pdb="ZN ZN V 202 " model vdw 2.028 2.230 nonbonded pdb=" OD1 ASP R 97 " pdb="ZN ZN R 202 " model vdw 2.037 2.230 nonbonded pdb=" OG SER A 220 " pdb=" OD1 ASN A 425 " model vdw 2.180 3.040 nonbonded pdb=" OE1 GLU B 334 " pdb=" OG SER B 378 " model vdw 2.200 3.040 nonbonded pdb=" OG SER M 94 " pdb=" OD2 ASP N 25 " model vdw 2.202 3.040 ... (remaining 331075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) selection = (chain 'B' and (resid 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) selection = (chain 'J' and resid 7 through 577) selection = (chain 'K' and (resid 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) } ncs_group { reference = (chain 'C' and resid 2 through 100) selection = (chain 'G' and (resid 2 through 79 or resid 88 through 100)) selection = (chain 'M' and resid 2 through 100) } ncs_group { reference = (chain 'D' and (resid 17 through 50 or resid 58 through 112)) selection = (chain 'H' and (resid 17 through 50 or resid 58 through 112)) selection = (chain 'N' and (resid 17 through 50 or resid 58 through 112)) selection = (chain 'T' and (resid 17 through 50 or resid 58 through 112)) } ncs_group { reference = chain 'F' selection = chain 'O' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'R' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.040 Extract box with map and model: 0.800 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 33.850 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 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 : 0.003 0.054 40098 Z= 0.138 Angle : 0.561 12.369 54098 Z= 0.299 Chirality : 0.039 0.355 5932 Planarity : 0.004 0.054 6889 Dihedral : 14.200 89.988 14878 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.07 % Allowed : 0.19 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.11), residues: 4769 helix: -0.82 (0.09), residues: 3103 sheet: -1.54 (0.48), residues: 120 loop : -1.13 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 37 TYR 0.020 0.001 TYR I 558 PHE 0.015 0.001 PHE J 60 TRP 0.023 0.001 TRP K 159 HIS 0.009 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00307 (40068) covalent geometry : angle 0.55376 (54082) hydrogen bonds : bond 0.23722 ( 2246) hydrogen bonds : angle 7.97366 ( 6642) metal coordination : bond 0.01213 ( 30) metal coordination : angle 5.30184 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 734 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.7360 (t0) cc_final: 0.7153 (t0) REVERT: J 165 CYS cc_start: 0.6196 (m) cc_final: 0.5920 (m) REVERT: J 240 LEU cc_start: 0.7303 (mt) cc_final: 0.6994 (mt) REVERT: U 566 MET cc_start: 0.6211 (tpp) cc_final: 0.5934 (tpp) outliers start: 3 outliers final: 0 residues processed: 737 average time/residue: 0.2281 time to fit residues: 269.9353 Evaluate side-chains 448 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.2980 chunk 388 optimal weight: 0.0020 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 7.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN B 431 HIS I 581 GLN J 81 HIS J 84 GLN ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 GLN K 199 HIS N 108 ASN ** U 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.203259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.177736 restraints weight = 49641.107| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.53 r_work: 0.3817 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40098 Z= 0.152 Angle : 0.582 10.196 54098 Z= 0.309 Chirality : 0.039 0.279 5932 Planarity : 0.004 0.056 6889 Dihedral : 4.132 23.722 5282 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.63 % Allowed : 7.41 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.12), residues: 4769 helix: -0.08 (0.09), residues: 3216 sheet: -1.55 (0.53), residues: 105 loop : -1.15 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 161 TYR 0.027 0.001 TYR U 558 PHE 0.034 0.002 PHE B 186 TRP 0.030 0.002 TRP K 159 HIS 0.005 0.001 HIS K 180 Details of bonding type rmsd covalent geometry : bond 0.00326 (40068) covalent geometry : angle 0.57793 (54082) hydrogen bonds : bond 0.05661 ( 2246) hydrogen bonds : angle 4.96089 ( 6642) metal coordination : bond 0.01135 ( 30) metal coordination : angle 4.25573 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 512 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ILE cc_start: 0.8668 (mp) cc_final: 0.8159 (mp) REVERT: A 451 MET cc_start: 0.7117 (mtt) cc_final: 0.6877 (mtp) REVERT: E 167 ILE cc_start: 0.5638 (OUTLIER) cc_final: 0.5249 (pt) REVERT: C 31 VAL cc_start: 0.5910 (p) cc_final: 0.5688 (t) REVERT: D 111 ASP cc_start: 0.8352 (t0) cc_final: 0.8110 (t0) REVERT: J 165 CYS cc_start: 0.6949 (m) cc_final: 0.6512 (m) REVERT: J 364 ILE cc_start: 0.8078 (mm) cc_final: 0.7855 (mm) REVERT: J 451 MET cc_start: 0.7607 (mmt) cc_final: 0.6935 (mmt) REVERT: K 359 ARG cc_start: 0.7385 (tpt90) cc_final: 0.7180 (mmm160) REVERT: N 111 ASP cc_start: 0.8331 (t0) cc_final: 0.8093 (t0) REVERT: U 406 MET cc_start: 0.5834 (mpp) cc_final: 0.5182 (mtm) REVERT: U 463 GLN cc_start: 0.8013 (pp30) cc_final: 0.7754 (pp30) REVERT: U 566 MET cc_start: 0.6197 (tpp) cc_final: 0.5861 (tpp) REVERT: U 582 MET cc_start: 0.7933 (ttm) cc_final: 0.7677 (ttt) outliers start: 27 outliers final: 12 residues processed: 523 average time/residue: 0.2233 time to fit residues: 190.2808 Evaluate side-chains 441 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 428 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain U residue 510 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 201 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 413 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 444 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS D 61 ASN I 474 HIS I 624 ASN J 24 ASN ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 482 ASN N 51 GLN U 463 GLN U 624 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.204064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.178388 restraints weight = 49166.708| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.47 r_work: 0.3831 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 40098 Z= 0.173 Angle : 0.559 10.317 54098 Z= 0.295 Chirality : 0.039 0.202 5932 Planarity : 0.004 0.059 6889 Dihedral : 4.122 24.271 5282 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.19 % Allowed : 9.54 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.12), residues: 4769 helix: 0.15 (0.09), residues: 3206 sheet: -1.33 (0.55), residues: 99 loop : -1.10 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 46 TYR 0.021 0.001 TYR I 558 PHE 0.030 0.002 PHE A 186 TRP 0.048 0.002 TRP J 159 HIS 0.014 0.001 HIS I 474 Details of bonding type rmsd covalent geometry : bond 0.00400 (40068) covalent geometry : angle 0.55320 (54082) hydrogen bonds : bond 0.04654 ( 2246) hydrogen bonds : angle 4.61000 ( 6642) metal coordination : bond 0.01226 ( 30) metal coordination : angle 4.52858 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 494 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7650 (mmtt) cc_final: 0.7339 (mmtp) REVERT: A 385 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8270 (mp) REVERT: A 451 MET cc_start: 0.7152 (mtt) cc_final: 0.6902 (mtp) REVERT: B 183 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7483 (mt-10) REVERT: I 338 LEU cc_start: 0.8611 (mm) cc_final: 0.8276 (tp) REVERT: I 582 MET cc_start: 0.7584 (ttm) cc_final: 0.7329 (ttt) REVERT: J 165 CYS cc_start: 0.6881 (m) cc_final: 0.6489 (m) REVERT: J 205 LYS cc_start: 0.7536 (mmtt) cc_final: 0.7220 (mmtt) REVERT: J 364 ILE cc_start: 0.8159 (mm) cc_final: 0.7945 (mm) REVERT: J 468 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7144 (t80) REVERT: N 111 ASP cc_start: 0.8503 (t0) cc_final: 0.8223 (t0) REVERT: U 582 MET cc_start: 0.7884 (ttm) cc_final: 0.7408 (ttt) REVERT: U 605 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.4910 (ppp) outliers start: 51 outliers final: 28 residues processed: 518 average time/residue: 0.2244 time to fit residues: 191.0399 Evaluate side-chains 472 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 441 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 223 ASP Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain K residue 378 SER Chi-restraints excluded: chain K residue 399 GLU Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 344 LEU Chi-restraints excluded: chain U residue 510 TYR Chi-restraints excluded: chain U residue 605 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 30 optimal weight: 0.2980 chunk 47 optimal weight: 10.0000 chunk 293 optimal weight: 0.9990 chunk 405 optimal weight: 0.6980 chunk 458 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 387 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 416 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN D 61 ASN J 50 GLN J 158 HIS ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 300 ASN ** K 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 581 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.204942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.177271 restraints weight = 49127.745| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.50 r_work: 0.3682 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40098 Z= 0.141 Angle : 0.527 14.254 54098 Z= 0.277 Chirality : 0.038 0.331 5932 Planarity : 0.003 0.053 6889 Dihedral : 4.052 24.460 5282 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.38 % Allowed : 11.04 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.12), residues: 4769 helix: 0.35 (0.09), residues: 3217 sheet: -1.32 (0.54), residues: 99 loop : -1.07 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 37 TYR 0.026 0.001 TYR K 510 PHE 0.032 0.001 PHE K 186 TRP 0.034 0.001 TRP B 159 HIS 0.011 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00322 (40068) covalent geometry : angle 0.52251 (54082) hydrogen bonds : bond 0.04218 ( 2246) hydrogen bonds : angle 4.41377 ( 6642) metal coordination : bond 0.01107 ( 30) metal coordination : angle 4.13294 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 474 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7426 (mmtp) REVERT: A 385 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8116 (mp) REVERT: A 529 ASN cc_start: 0.7499 (t0) cc_final: 0.7216 (t0) REVERT: D 20 LYS cc_start: 0.7369 (pptt) cc_final: 0.6990 (pptt) REVERT: D 111 ASP cc_start: 0.8294 (t0) cc_final: 0.8065 (t0) REVERT: I 338 LEU cc_start: 0.8803 (mm) cc_final: 0.8396 (tp) REVERT: I 438 MET cc_start: 0.8050 (ttm) cc_final: 0.7750 (ttm) REVERT: I 566 MET cc_start: 0.5953 (tpp) cc_final: 0.4958 (tpp) REVERT: I 582 MET cc_start: 0.7764 (ttm) cc_final: 0.7495 (ttt) REVERT: J 159 TRP cc_start: 0.7861 (m-10) cc_final: 0.7336 (m-90) REVERT: J 165 CYS cc_start: 0.6889 (m) cc_final: 0.6484 (m) REVERT: J 205 LYS cc_start: 0.7610 (mmtt) cc_final: 0.7114 (mmtt) REVERT: J 403 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.6987 (mm) REVERT: J 468 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7186 (t80) REVERT: K 430 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7586 (ttpt) REVERT: N 111 ASP cc_start: 0.8537 (t0) cc_final: 0.8275 (t0) REVERT: U 338 LEU cc_start: 0.8767 (mm) cc_final: 0.8364 (tp) REVERT: U 438 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7966 (ttm) REVERT: U 582 MET cc_start: 0.8073 (ttm) cc_final: 0.7671 (ttt) REVERT: U 605 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.5142 (ppp) REVERT: U 638 PHE cc_start: 0.5806 (m-80) cc_final: 0.5330 (m-80) outliers start: 59 outliers final: 34 residues processed: 509 average time/residue: 0.2084 time to fit residues: 176.4897 Evaluate side-chains 470 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 431 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 223 ASP Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 399 GLU Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain U residue 71 HIS Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 344 LEU Chi-restraints excluded: chain U residue 438 MET Chi-restraints excluded: chain U residue 510 TYR Chi-restraints excluded: chain U residue 605 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 256 optimal weight: 0.6980 chunk 334 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 392 optimal weight: 6.9990 chunk 275 optimal weight: 0.5980 chunk 281 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 470 optimal weight: 6.9990 chunk 83 optimal weight: 0.4980 chunk 60 optimal weight: 8.9990 chunk 149 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 333 HIS G 49 GLN ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 GLN ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 300 ASN ** K 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 255 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.205778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.179425 restraints weight = 48825.459| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.43 r_work: 0.3836 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 40098 Z= 0.125 Angle : 0.511 13.097 54098 Z= 0.267 Chirality : 0.038 0.348 5932 Planarity : 0.003 0.050 6889 Dihedral : 3.975 18.942 5282 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.45 % Allowed : 11.74 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.12), residues: 4769 helix: 0.52 (0.09), residues: 3218 sheet: -1.23 (0.54), residues: 99 loop : -1.05 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 37 TYR 0.026 0.001 TYR U 558 PHE 0.054 0.001 PHE B 186 TRP 0.027 0.001 TRP K 159 HIS 0.008 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00279 (40068) covalent geometry : angle 0.50661 (54082) hydrogen bonds : bond 0.03969 ( 2246) hydrogen bonds : angle 4.28688 ( 6642) metal coordination : bond 0.01044 ( 30) metal coordination : angle 3.95423 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 476 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7589 (mmtt) cc_final: 0.7318 (mmtp) REVERT: A 385 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8149 (mp) REVERT: D 111 ASP cc_start: 0.8411 (t0) cc_final: 0.8205 (t0) REVERT: B 302 ASP cc_start: 0.7036 (m-30) cc_final: 0.6818 (t0) REVERT: B 480 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7157 (tp) REVERT: I 338 LEU cc_start: 0.8577 (mm) cc_final: 0.8222 (tp) REVERT: I 566 MET cc_start: 0.5789 (tpp) cc_final: 0.5165 (tpp) REVERT: I 582 MET cc_start: 0.7625 (ttm) cc_final: 0.7178 (ttt) REVERT: J 159 TRP cc_start: 0.7497 (m-10) cc_final: 0.7176 (m-10) REVERT: J 165 CYS cc_start: 0.6785 (m) cc_final: 0.6463 (m) REVERT: J 205 LYS cc_start: 0.7566 (mmtt) cc_final: 0.7292 (mmtt) REVERT: J 403 LEU cc_start: 0.7026 (mm) cc_final: 0.6747 (mm) REVERT: J 468 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7189 (t80) REVERT: K 430 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7554 (ttpt) REVERT: U 153 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: U 338 LEU cc_start: 0.8588 (mm) cc_final: 0.8276 (tp) REVERT: U 566 MET cc_start: 0.6525 (tpp) cc_final: 0.6099 (tpp) REVERT: U 582 MET cc_start: 0.7918 (ttm) cc_final: 0.7488 (ttt) REVERT: U 605 MET cc_start: 0.6228 (OUTLIER) cc_final: 0.4962 (ppp) outliers start: 62 outliers final: 42 residues processed: 512 average time/residue: 0.2187 time to fit residues: 185.6088 Evaluate side-chains 480 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 433 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain U residue 71 HIS Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain U residue 153 GLU Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 344 LEU Chi-restraints excluded: chain U residue 510 TYR Chi-restraints excluded: chain U residue 605 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 240 optimal weight: 3.9990 chunk 395 optimal weight: 0.6980 chunk 247 optimal weight: 0.6980 chunk 179 optimal weight: 0.5980 chunk 271 optimal weight: 0.8980 chunk 457 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 291 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 239 optimal weight: 0.4980 chunk 180 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN I 362 GLN J 158 HIS ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 496 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.206376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.179097 restraints weight = 49200.826| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.50 r_work: 0.3829 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 40098 Z= 0.120 Angle : 0.511 13.161 54098 Z= 0.265 Chirality : 0.038 0.378 5932 Planarity : 0.003 0.068 6889 Dihedral : 3.935 20.283 5282 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.17 % Allowed : 12.98 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.12), residues: 4769 helix: 0.66 (0.09), residues: 3218 sheet: -1.10 (0.61), residues: 75 loop : -1.03 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 46 TYR 0.026 0.001 TYR K 510 PHE 0.031 0.001 PHE B 186 TRP 0.061 0.001 TRP B 159 HIS 0.007 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00269 (40068) covalent geometry : angle 0.50631 (54082) hydrogen bonds : bond 0.03824 ( 2246) hydrogen bonds : angle 4.21971 ( 6642) metal coordination : bond 0.01001 ( 30) metal coordination : angle 3.86857 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 469 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8096 (mp) REVERT: B 302 ASP cc_start: 0.7009 (m-30) cc_final: 0.6775 (t0) REVERT: B 480 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7175 (tp) REVERT: I 26 MET cc_start: 0.8631 (ppp) cc_final: 0.8181 (ppp) REVERT: I 338 LEU cc_start: 0.8622 (mm) cc_final: 0.8239 (tp) REVERT: I 566 MET cc_start: 0.5714 (tpp) cc_final: 0.5154 (tpp) REVERT: I 582 MET cc_start: 0.7714 (ttm) cc_final: 0.7335 (ttt) REVERT: J 159 TRP cc_start: 0.7557 (m-10) cc_final: 0.7218 (m-10) REVERT: J 165 CYS cc_start: 0.6823 (m) cc_final: 0.6507 (m) REVERT: J 205 LYS cc_start: 0.7501 (mmtt) cc_final: 0.7268 (mmtt) REVERT: J 403 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6712 (mm) REVERT: J 468 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7213 (t80) REVERT: K 430 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7583 (ttpt) REVERT: M 101 ASP cc_start: 0.7640 (t0) cc_final: 0.7435 (t0) REVERT: U 338 LEU cc_start: 0.8585 (mm) cc_final: 0.8258 (tp) REVERT: U 406 MET cc_start: 0.6187 (mpp) cc_final: 0.5905 (mpp) REVERT: U 566 MET cc_start: 0.6446 (tpp) cc_final: 0.5990 (tpp) REVERT: U 582 MET cc_start: 0.7883 (ttm) cc_final: 0.7463 (ttt) REVERT: U 605 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.4878 (ppp) outliers start: 50 outliers final: 35 residues processed: 497 average time/residue: 0.2509 time to fit residues: 205.7721 Evaluate side-chains 474 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 434 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 162 MET Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 344 LEU Chi-restraints excluded: chain U residue 510 TYR Chi-restraints excluded: chain U residue 605 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 343 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 318 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 295 optimal weight: 0.0970 chunk 329 optimal weight: 0.5980 chunk 305 optimal weight: 1.9990 chunk 415 optimal weight: 0.3980 chunk 168 optimal weight: 0.8980 chunk 254 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 300 ASN ** K 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.207191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.180667 restraints weight = 48991.465| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.50 r_work: 0.3845 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40098 Z= 0.117 Angle : 0.507 11.290 54098 Z= 0.263 Chirality : 0.038 0.356 5932 Planarity : 0.003 0.058 6889 Dihedral : 3.889 20.170 5282 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.33 % Allowed : 13.45 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.12), residues: 4769 helix: 0.78 (0.09), residues: 3213 sheet: -1.10 (0.62), residues: 75 loop : -1.04 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG U 251 TYR 0.025 0.001 TYR U 558 PHE 0.039 0.001 PHE B 186 TRP 0.029 0.001 TRP B 159 HIS 0.007 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00261 (40068) covalent geometry : angle 0.50313 (54082) hydrogen bonds : bond 0.03725 ( 2246) hydrogen bonds : angle 4.15528 ( 6642) metal coordination : bond 0.00981 ( 30) metal coordination : angle 3.80121 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 461 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.6736 (ptt) cc_final: 0.6452 (ptt) REVERT: A 205 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7279 (mmtp) REVERT: A 385 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8078 (mp) REVERT: C 53 ASP cc_start: 0.7441 (t70) cc_final: 0.6921 (t0) REVERT: B 302 ASP cc_start: 0.7071 (m-30) cc_final: 0.6830 (t0) REVERT: B 480 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7137 (tp) REVERT: I 338 LEU cc_start: 0.8589 (mm) cc_final: 0.8209 (tp) REVERT: I 566 MET cc_start: 0.5677 (tpp) cc_final: 0.5157 (tpp) REVERT: I 582 MET cc_start: 0.7648 (ttm) cc_final: 0.7321 (ttt) REVERT: J 159 TRP cc_start: 0.7460 (m-10) cc_final: 0.7185 (m-10) REVERT: J 165 CYS cc_start: 0.6882 (m) cc_final: 0.6576 (m) REVERT: J 403 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6740 (mm) REVERT: J 468 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7136 (t80) REVERT: K 351 ASP cc_start: 0.7107 (m-30) cc_final: 0.6882 (m-30) REVERT: K 430 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7556 (ttpt) REVERT: M 101 ASP cc_start: 0.7687 (t0) cc_final: 0.7468 (t0) REVERT: N 45 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6446 (mmm) REVERT: N 111 ASP cc_start: 0.8337 (t0) cc_final: 0.8120 (t0) REVERT: U 338 LEU cc_start: 0.8556 (mm) cc_final: 0.8225 (tp) REVERT: U 406 MET cc_start: 0.6097 (mpp) cc_final: 0.5825 (mpp) REVERT: U 566 MET cc_start: 0.6400 (tpp) cc_final: 0.5971 (tpp) REVERT: U 582 MET cc_start: 0.7866 (ttm) cc_final: 0.7453 (ttt) REVERT: U 605 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.4886 (ppp) outliers start: 57 outliers final: 38 residues processed: 494 average time/residue: 0.2148 time to fit residues: 176.8746 Evaluate side-chains 479 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 435 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 399 GLU Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 344 LEU Chi-restraints excluded: chain U residue 510 TYR Chi-restraints excluded: chain U residue 605 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 186 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 411 optimal weight: 3.9990 chunk 329 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 412 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 337 optimal weight: 3.9990 chunk 303 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 300 ASN ** K 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.200357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.172943 restraints weight = 49312.091| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.62 r_work: 0.3776 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40098 Z= 0.145 Angle : 0.530 10.538 54098 Z= 0.274 Chirality : 0.039 0.331 5932 Planarity : 0.003 0.059 6889 Dihedral : 3.920 20.444 5282 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.36 % Allowed : 14.10 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.12), residues: 4769 helix: 0.74 (0.09), residues: 3208 sheet: -1.08 (0.62), residues: 75 loop : -1.02 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 46 TYR 0.023 0.001 TYR K 510 PHE 0.053 0.001 PHE K 186 TRP 0.078 0.002 TRP B 159 HIS 0.007 0.001 HIS U 283 Details of bonding type rmsd covalent geometry : bond 0.00337 (40068) covalent geometry : angle 0.52535 (54082) hydrogen bonds : bond 0.03801 ( 2246) hydrogen bonds : angle 4.19230 ( 6642) metal coordination : bond 0.01186 ( 30) metal coordination : angle 4.03504 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 456 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.6967 (ptt) cc_final: 0.6658 (ptt) REVERT: A 205 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7393 (mmtp) REVERT: A 385 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8091 (mp) REVERT: C 53 ASP cc_start: 0.7568 (t70) cc_final: 0.6977 (t0) REVERT: B 302 ASP cc_start: 0.7144 (m-30) cc_final: 0.6882 (t0) REVERT: B 480 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7090 (tp) REVERT: I 338 LEU cc_start: 0.8703 (mm) cc_final: 0.8292 (tp) REVERT: I 566 MET cc_start: 0.5683 (tpp) cc_final: 0.5108 (tpp) REVERT: I 582 MET cc_start: 0.7829 (ttm) cc_final: 0.7489 (ttt) REVERT: J 165 CYS cc_start: 0.6936 (m) cc_final: 0.6594 (m) REVERT: J 205 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7294 (mmtt) REVERT: J 385 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8375 (mp) REVERT: J 403 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6836 (mm) REVERT: J 468 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7145 (t80) REVERT: K 430 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7568 (ttpt) REVERT: N 45 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6508 (mmm) REVERT: N 111 ASP cc_start: 0.8444 (t0) cc_final: 0.8229 (t0) REVERT: U 338 LEU cc_start: 0.8666 (mm) cc_final: 0.8252 (tp) REVERT: U 406 MET cc_start: 0.6381 (mpp) cc_final: 0.6075 (mpp) REVERT: U 566 MET cc_start: 0.6335 (tpp) cc_final: 0.5813 (tpp) REVERT: U 582 MET cc_start: 0.7945 (ttm) cc_final: 0.7248 (ttt) REVERT: U 605 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.5078 (ppp) outliers start: 58 outliers final: 42 residues processed: 491 average time/residue: 0.2245 time to fit residues: 180.3899 Evaluate side-chains 484 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 435 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 399 GLU Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 344 LEU Chi-restraints excluded: chain U residue 510 TYR Chi-restraints excluded: chain U residue 605 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 161 optimal weight: 5.9990 chunk 318 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 366 optimal weight: 0.4980 chunk 412 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 457 optimal weight: 0.6980 chunk 302 optimal weight: 0.6980 chunk 466 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 300 ASN ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.200710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.173571 restraints weight = 49382.265| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.53 r_work: 0.3824 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40098 Z= 0.134 Angle : 0.524 10.401 54098 Z= 0.272 Chirality : 0.038 0.323 5932 Planarity : 0.003 0.057 6889 Dihedral : 3.915 20.454 5282 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.45 % Allowed : 14.03 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.12), residues: 4769 helix: 0.78 (0.09), residues: 3209 sheet: -1.20 (0.61), residues: 75 loop : -1.00 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 46 TYR 0.026 0.001 TYR U 558 PHE 0.044 0.001 PHE K 186 TRP 0.060 0.002 TRP B 159 HIS 0.006 0.001 HIS U 283 Details of bonding type rmsd covalent geometry : bond 0.00307 (40068) covalent geometry : angle 0.51982 (54082) hydrogen bonds : bond 0.03761 ( 2246) hydrogen bonds : angle 4.18021 ( 6642) metal coordination : bond 0.01179 ( 30) metal coordination : angle 3.92817 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 451 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.6749 (ptt) cc_final: 0.6485 (ptt) REVERT: A 205 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7555 (mmtp) REVERT: A 385 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 53 ASP cc_start: 0.7498 (t70) cc_final: 0.6903 (t0) REVERT: B 302 ASP cc_start: 0.7132 (m-30) cc_final: 0.6889 (t0) REVERT: B 480 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7136 (tp) REVERT: I 338 LEU cc_start: 0.8640 (mm) cc_final: 0.8243 (tp) REVERT: I 566 MET cc_start: 0.5559 (tpp) cc_final: 0.5098 (tpp) REVERT: I 582 MET cc_start: 0.7726 (ttm) cc_final: 0.7420 (ttt) REVERT: J 165 CYS cc_start: 0.6836 (m) cc_final: 0.6505 (m) REVERT: J 205 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7244 (mmtt) REVERT: J 385 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8382 (mp) REVERT: J 403 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6757 (mm) REVERT: J 468 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7026 (t80) REVERT: K 430 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7593 (ttpt) REVERT: M 101 ASP cc_start: 0.7784 (t0) cc_final: 0.7582 (t0) REVERT: N 45 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6621 (mmm) REVERT: N 111 ASP cc_start: 0.8530 (t0) cc_final: 0.8317 (t0) REVERT: U 338 LEU cc_start: 0.8601 (mm) cc_final: 0.8249 (tp) REVERT: U 406 MET cc_start: 0.6219 (mpp) cc_final: 0.5948 (mpp) REVERT: U 566 MET cc_start: 0.6206 (tpp) cc_final: 0.5894 (tpp) REVERT: U 582 MET cc_start: 0.7869 (ttm) cc_final: 0.7202 (ttt) REVERT: U 605 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5021 (ppp) outliers start: 62 outliers final: 46 residues processed: 486 average time/residue: 0.1991 time to fit residues: 160.4127 Evaluate side-chains 490 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 437 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 286 ILE Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 399 GLU Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain U residue 162 MET Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 344 LEU Chi-restraints excluded: chain U residue 510 TYR Chi-restraints excluded: chain U residue 605 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 166 optimal weight: 2.9990 chunk 299 optimal weight: 0.0670 chunk 371 optimal weight: 1.9990 chunk 445 optimal weight: 3.9990 chunk 459 optimal weight: 0.0030 chunk 281 optimal weight: 0.7980 chunk 454 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 overall best weight: 0.7732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 300 ASN ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.205313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.178874 restraints weight = 48909.657| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.47 r_work: 0.3828 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 40098 Z= 0.141 Angle : 0.544 11.355 54098 Z= 0.280 Chirality : 0.039 0.261 5932 Planarity : 0.003 0.068 6889 Dihedral : 3.948 20.598 5282 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.26 % Allowed : 14.36 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.12), residues: 4769 helix: 0.78 (0.09), residues: 3206 sheet: -1.25 (0.60), residues: 75 loop : -0.97 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 46 TYR 0.023 0.001 TYR K 510 PHE 0.065 0.001 PHE B 186 TRP 0.087 0.002 TRP J 159 HIS 0.006 0.001 HIS U 283 Details of bonding type rmsd covalent geometry : bond 0.00326 (40068) covalent geometry : angle 0.53958 (54082) hydrogen bonds : bond 0.03755 ( 2246) hydrogen bonds : angle 4.19548 ( 6642) metal coordination : bond 0.01204 ( 30) metal coordination : angle 4.01774 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 439 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.6680 (ptt) cc_final: 0.6419 (ptt) REVERT: A 205 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7429 (mmtp) REVERT: A 385 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8117 (mp) REVERT: C 53 ASP cc_start: 0.7518 (t70) cc_final: 0.6992 (t0) REVERT: B 302 ASP cc_start: 0.7070 (m-30) cc_final: 0.6837 (t0) REVERT: B 480 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7157 (tp) REVERT: I 338 LEU cc_start: 0.8670 (mm) cc_final: 0.8272 (tp) REVERT: I 566 MET cc_start: 0.5537 (tpp) cc_final: 0.5094 (tpp) REVERT: I 582 MET cc_start: 0.7728 (ttm) cc_final: 0.7418 (ttt) REVERT: J 165 CYS cc_start: 0.6859 (m) cc_final: 0.6459 (m) REVERT: J 205 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7239 (mmtt) REVERT: J 385 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8403 (mp) REVERT: J 468 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7036 (t80) REVERT: K 430 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7585 (ttpt) REVERT: M 101 ASP cc_start: 0.7775 (t0) cc_final: 0.7570 (t0) REVERT: N 45 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6658 (mmm) REVERT: N 111 ASP cc_start: 0.8571 (t0) cc_final: 0.8370 (t0) REVERT: U 338 LEU cc_start: 0.8588 (mm) cc_final: 0.8250 (tp) REVERT: U 406 MET cc_start: 0.6103 (mpp) cc_final: 0.5876 (mpp) REVERT: U 566 MET cc_start: 0.6214 (tpp) cc_final: 0.5924 (tpp) REVERT: U 582 MET cc_start: 0.7828 (ttm) cc_final: 0.7183 (ttt) REVERT: U 605 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5078 (ppp) outliers start: 54 outliers final: 46 residues processed: 473 average time/residue: 0.2379 time to fit residues: 185.4220 Evaluate side-chains 482 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 430 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 286 ILE Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 399 GLU Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain U residue 344 LEU Chi-restraints excluded: chain U residue 510 TYR Chi-restraints excluded: chain U residue 605 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 313 optimal weight: 0.8980 chunk 340 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 121 optimal weight: 0.1980 chunk 344 optimal weight: 4.9990 chunk 420 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 262 optimal weight: 0.9980 chunk 471 optimal weight: 30.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 300 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 362 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.205301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.178929 restraints weight = 49148.435| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.47 r_work: 0.3832 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 40098 Z= 0.185 Angle : 0.709 59.200 54098 Z= 0.411 Chirality : 0.040 0.482 5932 Planarity : 0.004 0.074 6889 Dihedral : 3.976 28.468 5282 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.29 % Allowed : 14.48 % Favored : 84.24 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.12), residues: 4769 helix: 0.78 (0.09), residues: 3206 sheet: -1.26 (0.60), residues: 75 loop : -0.97 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 46 TYR 0.018 0.001 TYR H 76 PHE 0.057 0.001 PHE B 186 TRP 0.078 0.002 TRP J 159 HIS 0.006 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00390 (40068) covalent geometry : angle 0.70544 (54082) hydrogen bonds : bond 0.03772 ( 2246) hydrogen bonds : angle 4.20114 ( 6642) metal coordination : bond 0.01200 ( 30) metal coordination : angle 4.01173 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8219.84 seconds wall clock time: 142 minutes 31.21 seconds (8551.21 seconds total)