Starting phenix.real_space_refine on Wed Apr 17 08:25:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaq_36131/04_2024/8jaq_36131.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaq_36131/04_2024/8jaq_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaq_36131/04_2024/8jaq_36131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaq_36131/04_2024/8jaq_36131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaq_36131/04_2024/8jaq_36131.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaq_36131/04_2024/8jaq_36131.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/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: 21.04, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.64 Conformation dependent library (CDL) restraints added in 7.3 seconds 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: 4.20 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: 14.77 Time building geometry restraints manager: 17.75 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: 99.59 - 106.52: 849 106.52 - 113.45: 21790 113.45 - 120.37: 15703 120.37 - 127.30: 15355 127.30 - 134.23: 385 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 2.440 nonbonded pdb=" OE1 GLU B 334 " pdb=" OG SER B 378 " model vdw 2.200 2.440 nonbonded pdb=" OG SER M 94 " pdb=" OD2 ASP N 25 " model vdw 2.202 2.440 ... (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 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: 19.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 46.270 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 112.180 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.820 ------------------------------------------------------------------------------- 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 40068 Z= 0.199 Angle : 0.554 8.990 54082 Z= 0.298 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 : 9.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (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 TRP 0.023 0.001 TRP K 159 HIS 0.009 0.001 HIS A 279 PHE 0.015 0.001 PHE J 60 TYR 0.020 0.001 TYR I 558 ARG 0.008 0.000 ARG G 37 *********************** 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 fitting. rotamer outliers: 3 poor density : 734 time to evaluate : 4.454 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: 0.5711 time to fit residues: 670.0036 Evaluate side-chains 448 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 448 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 0.7980 chunk 359 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 371 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 chunk 276 optimal weight: 2.9990 chunk 430 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN B 431 HIS B 578 GLN I 581 GLN I 590 ASN I 624 ASN 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 624 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 40068 Z= 0.235 Angle : 0.575 8.512 54082 Z= 0.305 Chirality : 0.039 0.297 5932 Planarity : 0.004 0.056 6889 Dihedral : 4.148 25.627 5282 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.84 % Allowed : 7.44 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.12), residues: 4769 helix: -0.10 (0.09), residues: 3210 sheet: -1.34 (0.53), residues: 101 loop : -1.13 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 159 HIS 0.006 0.001 HIS A 410 PHE 0.037 0.002 PHE B 186 TYR 0.028 0.001 TYR U 558 ARG 0.006 0.001 ARG G 37 *********************** 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 526 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 490 time to evaluate : 4.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ILE cc_start: 0.8439 (mp) cc_final: 0.8051 (mp) REVERT: E 167 ILE cc_start: 0.5908 (OUTLIER) cc_final: 0.5541 (pt) REVERT: D 70 LEU cc_start: 0.8341 (tp) cc_final: 0.8118 (tp) REVERT: J 165 CYS cc_start: 0.6163 (m) cc_final: 0.5954 (m) REVERT: J 364 ILE cc_start: 0.7852 (mm) cc_final: 0------------------------------------------------------------------------------- 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** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 490 ASN I 474 HIS I 581 GLN ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN N 51 GLN U 36 ASN ** U 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40068 Z= 0.237 Angle : 0.530 9.177 54082 Z= 0.280 Chirality : 0.038 0.219 5932 Planarity : 0.004 0.060 6889 Dihedral : 4.067 26.775 5282 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.22 % Allowed : 9.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 4769 helix: 0.21 (0.09), residues: 3219 sheet: -1.51 (0.51), residues: 111 loop : -1.05 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 159 HIS 0.014 0.001 HIS I 474 PHE 0.034 0.002 PHE K 186 TYR 0.022 0.001 TYR H 79 ARG 0.009 0.000 ARG R 46 *********************** 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 528 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 476 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7481 (mmtt) cc_final: 0.7134 (mmtp) REVERT: A 385 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8107 (mp) REVERT: A 451 MET cc_start: 0.7048 (mtt) cc_final: 0.6803 (mtp) REVERT: D 70 LEU cc_start: 0.8301 (tp) cc_final: 0.8030 (tp) REVERT: I 338 LEU cc_start: 0.8640 (mm) cc_final: 0.8316 (tp) REVERT: J 165 CYS cc_start: 0.6096 (m) cc_final: 0.5771 (m) REVERT: J 364 ILE cc_start: 0.7829 (mm) cc_final: 0.7612 (mm) REVERT: K 430 LYS cc_start: 0.7470 (ttmt) cc_final: 0.7138 (ttpt) REVERT: N 111 ASP cc_start: 0.7767 (t0) cc_final: 0.7559 (t0) REVERT: U 566 MET cc_start: 0.6114 (tpp) cc_final: 0.5907 (tpp) REVERT: U 582 MET cc_start: 0.7657 (ttm) cc_final: 0.7236 (ttt) REVERT: U 605 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.4929 (ppp) outliers start: 52 outliers final: 33 residues processed: 507 average time/residue: 0.3995 time to fit residues: 333.3455 Evaluate side-chains 467 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 432 time to evaluate : 3.853 ------------------------------------------------------------------------------- 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 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 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 G residue 94 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain I residue 186 ASN Chi-restraints excluded: chain I residue 454 GLU Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 223 ASP Chi-restraints excluded: chain J residue 344 GLN Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain K residue 460 GLU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain V residue 28 ASN 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 426 optimal weight: 5.9990 chunk 324 optimal weight: 0.1980 chunk 223 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 432 optimal weight: 0.9990 chunk 458 optimal weight: 0.7980 chunk 226 optimal weight: 9.9990 chunk 410 optimal weight: 0.0470 chunk 123 optimal weight: 0.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN G 49 GLN ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** U 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40068 Z= 0.181 Angle : 0.503 15.278 54082 Z= 0.264 Chirality : 0.038 0.340 5932 Planarity : 0.003 0.051 6889 Dihedral : 3.967 26.038 5282 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.24 % Allowed : 11.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 4769 helix: 0.49 (0.09), residues: 3220 sheet: -1.30 (0.58), residues: 87 loop : -1.05 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP J 159 HIS 0.007 0.001 HIS U 283 PHE 0.031 0.001 PHE K 186 TYR 0.022 0.001 TYR H 18 ARG 0.006 0.000 ARG Q 37 *********************** 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 522 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 469 time to evaluate : 4.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7395 (mmtt) cc_final: 0.7084 (mmtp) REVERT: A 385 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8016 (mp) REVERT: D 70 LEU cc_start: 0.8289 (tp) cc_final: 0.8040 (tp) REVERT: I 335 MET cc_start: 0.7298 (tpp) cc_final: 0.7051 (tpp) REVERT: I 338 LEU cc_start: 0.8580 (mm) cc_final: 0.8265 (tp) REVERT: J 165 CYS cc_start: 0.6046 (m) cc_final: 0.5805 (m) REVERT: J 468 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6568 (t80) REVERT: K 430 LYS cc_start: 0.7309 (ttmt) cc_final: 0.7072 (ttpt) REVERT: N 111 ASP cc_start: 0.7842 (t0) cc_final: 0.7556 (t0) REVERT: U 338 LEU cc_start: 0.8610 (mm) cc_final: 0.8330 (tp) REVERT: U 582 MET cc_start: 0.7569 (ttm) cc_final: 0.7171 (ttt) REVERT: U 605 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.4888 (ppp) outliers start: 53 outliers final: 33 residues processed: 503 average time/residue: 0.5438 time to fit residues: 448.7771 Evaluate side-chains 463 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 427 time to evaluate : 4.835 ------------------------------------------------------------------------------- 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 A residue 470 VAL 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 C residue 7 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 71 SER 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 R residue 28 ASN Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 223 ASP 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 V residue 28 ASN Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 344 LEU Chi-restraints excluded: chain U residue 345 GLU 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 381 optimal weight: 0.5980 chunk 260 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 390 optimal weight: 6.9990 chunk 316 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 411 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 158 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 490 ASN B 578 GLN H 58 ASN I 362 GLN J 24 ASN J 328 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 ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 255 HIS ** U 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 40068 Z= 0.325 Angle : 0.562 12.265 54082 Z= 0.295 Chirality : 0.040 0.341 5932 Planarity : 0.004 0.060 6889 Dihedral : 4.100 25.286 5282 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.28 % Favored : 95.70 % Rotamer: Outliers : 1.85 % Allowed : 11.51 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.12), residues: 4769 helix: 0.32 (0.09), residues: 3221 sheet: -1.30 (0.59), residues: 87 loop : -1.01 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 159 HIS 0.007 0.001 HIS J 284 PHE 0.037 0.002 PHE B 186 TYR 0.026 0.002 TYR I 558 ARG 0.009 0.000 ARG R 46 *********************** 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 531 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 452 time to evaluate : 4.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 451 MET cc_start: 0.7105 (mtt) cc_final: 0.6792 (mtp) REVERT: B 480 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6731 (tp) REVERT: I 338 LEU cc_start: 0.8605 (mm) cc_final: 0.8267 (tp) REVERT: I 566 MET cc_start: 0.5948 (tpp) cc_final: 0.5256 (tpp) REVERT: J 165 CYS cc_start: 0.6189 (m) cc_final: 0.5976 (m) REVERT: J 205 LYS cc_start: 0.6790 (mmtt) cc_final: 0.6169 (mmtp) REVERT: J 468 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6726 (t80) REVERT: U 338 LEU cc_start: 0.8627 (mm) cc_final: 0.8321 (tp) REVERT: U 582 MET cc_start: 0.7664 (ttm) cc_final: 0.7251 (ttt) REVERT: U 605 MET cc_start: 0.6037 (OUTLIER) cc_final: 0.4863 (ppp) outliers start: 79 outliers final: 55 residues processed: 509 average time/residue: 0.5144 time to fit residues: 429.0963 Evaluate side-chains 487 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 428 time to evaluate : 3.555 ------------------------------------------------------------------------------- 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 385 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 158 ILE 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 442 MET Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 71 SER 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 186 ASN Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 454 GLU Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain J residue 31 ASP 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 344 GLN Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain J residue 490 ASN Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 378 SER 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 75 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain V residue 28 ASN Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain U residue 25 VAL 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 345 GLU 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 154 optimal weight: 2.9990 chunk 412 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 269 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 458 optimal weight: 0.0040 chunk 380 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 300 ASN B 490 ASN ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 300 ASN ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 581 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40068 Z= 0.188 Angle : 0.502 10.795 54082 Z= 0.263 Chirality : 0.038 0.330 5932 Planarity : 0.003 0.050 6889 Dihedral : 3.985 24.205 5282 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.38 % Allowed : 12.58 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 4769 helix: 0.60 (0.09), residues: 3224 sheet: -1.27 (0.59), residues: 87 loop : -0.99 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP J 159 HIS 0.006 0.001 HIS U 283 PHE 0.026 0.001 PHE K 186 TYR 0.030 0.001 TYR K 226 ARG 0.008 0.000 ARG U 251 *********************** 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 518 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 459 time to evaluate : 4.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8059 (mp) REVERT: A 451 MET cc_start: 0.6975 (mtt) cc_final: 0.6663 (mtp) REVERT: D 70 LEU cc_start: 0.8332 (tp) cc_final: 0.8083 (tp) REVERT: H 17 MET cc_start: 0.7215 (tpp) cc_final: 0.7009 (tpp) REVERT: I 338 LEU cc_start: 0.8602 (mm) cc_final: 0.8265 (tp) REVERT: I 566 MET cc_start: 0.5822 (tpp) cc_final: 0.5207 (tpp) REVERT: J 165 CYS cc_start: 0.6114 (m) cc_final: 0.5901 (m) REVERT: J 468 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6675 (t80) REVERT: N 45 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6469 (mmm) REVERT: U 338 LEU cc_start: 0.8640 (mm) cc_final: 0.8333 (tp) REVERT: U 566 MET cc_start: 0.6475 (tpp) cc_final: 0.6102 (tpp) REVERT: U 582 MET cc_start: 0.7694 (ttm) cc_final: 0.7290 (ttt) REVERT: U 605 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.4940 (ppp) outliers start: 59 outliers final: 43 residues processed: 495 average time/residue: 0.5362 time to fit residues: 434.5532 Evaluate side-chains 471 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 424 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 105 CYS 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 A residue 470 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 158 ILE 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 C residue 47 ASP Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 71 SER 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 R residue 28 ASN Chi-restraints excluded: chain J residue 31 ASP 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 300 ASN Chi-restraints excluded: chain K residue 378 SER 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 T residue 71 SER Chi-restraints excluded: chain V residue 28 ASN 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 345 GLU 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 442 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 334 optimal weight: 0.8980 chunk 259 optimal weight: 6.9990 chunk 386 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 456 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** 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 55 GLN ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 362 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 40068 Z= 0.207 Angle : 0.506 11.375 54082 Z= 0.264 Chirality : 0.038 0.305 5932 Planarity : 0.003 0.051 6889 Dihedral : 3.945 23.943 5282 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.68 % Allowed : 12.98 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.12), residues: 4769 helix: 0.67 (0.09), residues: 3220 sheet: -1.17 (0.59), residues: 85 loop : -0.96 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP J 159 HIS 0.005 0.001 HIS U 283 PHE 0.035 0.001 PHE K 186 TYR 0.026 0.001 TYR I 558 ARG 0.007 0.000 ARG Q 37 *********************** 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 516 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 444 time to evaluate : 4.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.6365 (ptt) cc_final: 0.5979 (ptt) REVERT: A 385 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8068 (mp) REVERT: A 451 MET cc_start: 0.7007 (mtt) cc_final: 0.6690 (mtp) REVERT: B 480 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6750 (tp) REVERT: I 338 LEU cc_start: 0.8592 (mm) cc_final: 0.8229 (tp) REVERT: I 566 MET cc_start: 0.5787 (tpp) cc_final: 0.5194 (tpp) REVERT: J 385 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8274 (mp) REVERT: J 468 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.6661 (t80) REVERT: K 87 MET cc_start: 0.8215 (mmm) cc_final: 0.8001 (mmm) REVERT: M 104 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7855 (tttp) REVERT: N 45 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6505 (mmm) REVERT: U 338 LEU cc_start: 0.8627 (mm) cc_final: 0.8293 (tp) REVERT: U 566 MET cc_start: 0.6475 (tpp) cc_final: 0.6076 (tpp) REVERT: U 582 MET cc_start: 0.7704 (ttm) cc_final: 0.7078 (ttt) REVERT: U 605 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.4922 (ppp) outliers start: 72 outliers final: 55 residues processed: 490 average time/residue: 0.5292 time to fit residues: 427.5076 Evaluate side-chains 483 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 421 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 105 CYS 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 A residue 470 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 71 SER 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 I residue 454 GLU Chi-restraints excluded: chain I residue 605 MET Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 65 VAL 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 378 SER 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 75 VAL Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain V residue 28 ASN 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 345 GLU Chi-restraints excluded: chain U residue 406 MET 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 282 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 272 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 311 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 359 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 300 ASN B 490 ASN ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 496 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 40068 Z= 0.255 Angle : 0.531 10.715 54082 Z= 0.276 Chirality : 0.039 0.280 5932 Planarity : 0.003 0.051 6889 Dihedral : 3.987 25.322 5282 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.89 % Allowed : 13.10 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.12), residues: 4769 helix: 0.60 (0.09), residues: 3225 sheet: -1.17 (0.60), residues: 85 loop : -0.97 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP J 159 HIS 0.005 0.001 HIS J 89 PHE 0.052 0.002 PHE K 186 TYR 0.020 0.001 TYR K 226 ARG 0.007 0.000 ARG Q 37 *********************** 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 524 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 443 time to evaluate : 4.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.6410 (ptt) cc_final: 0.6062 (ptt) REVERT: A 385 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8105 (mp) REVERT: A 451 MET cc_start: 0.7030 (mtt) cc_final: 0.6688 (mtp) REVERT: B 480 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6736 (tp) REVERT: I 338 LEU cc_start: 0.8602 (mm) cc_final: 0.8229 (tp) REVERT: I 566 MET cc_start: 0.5777 (tpp) cc_final: 0.5201 (tpp) REVERT: J 385 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8289 (mp) REVERT: J 468 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6689 (t80) REVERT: K 183 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6305 (mp0) REVERT: L 94 TYR cc_start: 0.6803 (t80) cc_final: 0.6494 (t80) REVERT: M 104 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7878 (tttp) REVERT: N 45 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6593 (mmm) REVERT: U 338 LEU cc_start: 0.8621 (mm) cc_final: 0.8299 (tp) REVERT: U 566 MET cc_start: 0.6439 (tpp) cc_final: 0.6033 (tpp) REVERT: U 582 MET cc_start: 0.7692 (ttm) cc_final: 0.7075 (ttt) REVERT: U 605 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.4940 (ppp) outliers start: 81 outliers final: 58 residues processed: 498 average time/residue: 0.5319 time to fit residues: 434.1674 Evaluate side-chains 492 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 426 time to evaluate : 4.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 105 CYS 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 A residue 470 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 99 ILE 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 138 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 71 SER 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 454 GLU Chi-restraints excluded: chain I residue 605 MET Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 344 GLN Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain J residue 410 HIS Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain J residue 490 ASN 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 378 SER 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 75 VAL Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain T residue 71 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 345 GLU Chi-restraints excluded: chain U residue 406 MET 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 415 optimal weight: 0.9980 chunk 437 optimal weight: 4.9990 chunk 399 optimal weight: 0.8980 chunk 425 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 334 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 384 optimal weight: 0.9990 chunk 402 optimal weight: 0.6980 chunk 424 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 300 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40068 Z= 0.213 Angle : 0.521 11.328 54082 Z= 0.270 Chirality : 0.038 0.268 5932 Planarity : 0.003 0.050 6889 Dihedral : 3.965 24.370 5282 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.75 % Allowed : 13.42 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.12), residues: 4769 helix: 0.70 (0.09), residues: 3229 sheet: -1.13 (0.60), residues: 85 loop : -0.95 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP J 159 HIS 0.022 0.001 HIS B 476 PHE 0.043 0.002 PHE K 186 TYR 0.038 0.001 TYR K 226 ARG 0.007 0.000 ARG Q 37 *********************** 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 518 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 443 time to evaluate : 4.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8063 (mp) REVERT: A 451 MET cc_start: 0.7011 (mtt) cc_final: 0.6664 (mtp) REVERT: D 70 LEU cc_start: 0.8314 (tp) cc_final: 0.8068 (tp) REVERT: I 338 LEU cc_start: 0.8605 (mm) cc_final: 0.8228 (tp) REVERT: I 566 MET cc_start: 0.5766 (tpp) cc_final: 0.5202 (tpp) REVERT: J 385 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8298 (mp) REVERT: J 468 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6790 (t80) REVERT: K 183 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6297 (mp0) REVERT: N 45 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6590 (mmm) REVERT: U 338 LEU cc_start: 0.8607 (mm) cc_final: 0.8275 (tp) REVERT: U 566 MET cc_start: 0.6331 (tpp) cc_final: 0.5920 (tpp) REVERT: U 582 MET cc_start: 0.7672 (ttm) cc_final: 0.7063 (ttt) REVERT: U 605 MET cc_start: 0.6060 (OUTLIER) cc_final: 0.4993 (ppp) outliers start: 75 outliers final: 59 residues processed: 493 average time/residue: 0.5399 time to fit residues: 437.3441 Evaluate side-chains 487 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 422 time to evaluate : 4.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 105 CYS 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 137 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 54 CYS 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 302 ASP Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 71 SER 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 605 MET Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 344 GLN Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain J residue 410 HIS 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 378 SER 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 75 VAL Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain P residue -4 THR Chi-restraints excluded: chain T residue 71 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 345 GLU Chi-restraints excluded: chain U residue 406 MET Chi-restraints excluded: chain U residue 510 TYR Chi-restraints excluded: chain U residue 526 THR 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 279 optimal weight: 3.9990 chunk 450 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 312 optimal weight: 0.6980 chunk 472 optimal weight: 20.0000 chunk 434 optimal weight: 0.6980 chunk 376 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 290 optimal weight: 0.8980 chunk 230 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 158 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 300 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN ** J 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 40068 Z= 0.314 Angle : 0.571 12.049 54082 Z= 0.295 Chirality : 0.040 0.267 5932 Planarity : 0.004 0.052 6889 Dihedral : 4.065 22.409 5282 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.64 % Allowed : 13.56 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 4769 helix: 0.52 (0.09), residues: 3225 sheet: -1.18 (0.60), residues: 85 loop : -0.98 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP J 159 HIS 0.023 0.001 HIS B 476 PHE 0.037 0.002 PHE K 186 TYR 0.028 0.001 TYR K 226 ARG 0.007 0.000 ARG Q 37 ********************** 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 503 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 433 time to evaluate : 4.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8129 (mp) REVERT: A 451 MET cc_start: 0.7006 (mtt) cc_final: 0.6682 (mtp) REVERT: I 338 LEU cc_start: 0.8659 (mm) cc_final: 0.8282 (tp) REVERT: I 566 MET cc_start: 0.5775 (tpp) cc_final: 0.5199 (tpp) REVERT: J 385 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8339 (mp) REVERT: J 468 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.6845 (t80) REVERT: K 183 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6324 (mp0) REVERT: N 45 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6678 (mmm) REVERT: U 338 LEU cc_start: 0.8658 (mm) cc_final: 0.8323 (tp) REVERT: U 566 MET cc_start: 0.6265 (tpp) cc_final: 0.5882 (tpp) REVERT: U 582 MET cc_start: 0.7674 (ttm) cc_final: 0.7076 (ttt) REVERT: U 605 MET cc_start: 0.6006 (OUTLIER) cc_final: 0.4969 (ppp) outliers start: 70 outliers final: 62 residues processed: 482 average time/residue: 0.5353 time to fit residues: 422.7406 Evaluate side-chains 489 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 421 time to evaluate : 4.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 223 ASP 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 137 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 71 SER 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 454 GLU Chi-restraints excluded: chain I residue 605 MET Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 344 GLN Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain J residue 410 HIS 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 378 SER Chi-restraints excluded: chain K residue 403 LEU 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 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 T residue 71 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 345 GLU Chi-restraints excluded: chain U residue 406 MET Chi-restraints excluded: chain U residue 510 TYR Chi-restraints excluded: chain U residue 526 THR 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 298 optimal weight: 0.7980 chunk 400 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 346 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 376 optimal weight: 0.0670 chunk 157 optimal weight: 0.7980 chunk 386 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 158 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 300 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN B 578 GLN ** I 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 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** ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.203709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.176725 restraints weight = 48930.182| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.49 r_work: 0.3845 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40068 Z= 0.194 Angle : 0.530 11.426 54082 Z= 0.274 Chirality : 0.038 0.263 5932 Planarity : 0.003 0.050 6889 Dihedral : 4.014 23.961 5282 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.59 % Allowed : 13.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.12), residues: 4769 helix: 0.72 (0.09), residues: 3221 sheet: -1.13 (0.60), residues: 85 loop : -0.95 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP J 159 HIS 0.022 0.001 HIS B 476 PHE 0.042 0.002 PHE K 186 TYR 0.029 0.001 TYR K 226 ARG 0.008 0.000 ARG Q 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9581.89 seconds wall clock time: 362 minutes 0.80 seconds (21720.80 seconds total)