Starting phenix.real_space_refine on Sun Dec 29 14:19:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ity_35712/12_2024/8ity_35712_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ity_35712/12_2024/8ity_35712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ity_35712/12_2024/8ity_35712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ity_35712/12_2024/8ity_35712.map" model { file = "/net/cci-nas-00/data/ceres_data/8ity_35712/12_2024/8ity_35712_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ity_35712/12_2024/8ity_35712_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 164 5.49 5 Mg 1 5.21 5 S 349 5.16 5 C 35688 2.51 5 N 9981 2.21 5 O 10946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 57140 Number of models: 1 Model: "" Number of chains: 32 Chain: "1" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1233 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "3" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3037 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 16, 'TRANS': 357} Chain breaks: 2 Chain: "4" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3058 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 10, 'TRANS': 354} Chain: "A" Number of atoms: 10814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1378, 10814 Classifications: {'peptide': 1378} Link IDs: {'PTRANS': 64, 'TRANS': 1313} Chain: "B" Number of atoms: 8741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8741 Classifications: {'peptide': 1105} Link IDs: {'PTRANS': 51, 'TRANS': 1053} Chain breaks: 1 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 435 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3167 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 22, 'TRANS': 371} Chain breaks: 2 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1837 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 754 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 12, 'TRANS': 74} Chain: "U" Number of atoms: 1396 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 176, 1391 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Conformer: "B" Number of residues, atoms: 176, 1391 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} bond proxies already assigned to first conformer: 1410 Chain: "V" Number of atoms: 2853 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 361, 2847 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 361, 2847 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 bond proxies already assigned to first conformer: 2891 Chain: "W" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 943 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "X" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1677 Classifications: {'DNA': 82} Link IDs: {'rna3p': 81} Chain: "Y" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1685 Classifications: {'DNA': 82} Link IDs: {'rna3p': 81} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7893 SG CYS A 72 110.500 136.552 153.918 1.00229.13 S ATOM 26470 SG CYS B1080 100.923 143.060 166.856 1.00185.38 S ATOM 26489 SG CYS B1083 98.315 142.034 164.227 1.00179.66 S ATOM 26555 SG CYS B1092 101.426 143.664 163.131 1.00180.90 S ATOM 26583 SG CYS B1095 98.930 145.755 164.963 1.00179.34 S ATOM 35493 SG CYS I 5 23.742 108.025 122.146 1.00124.68 S ATOM 35510 SG CYS I 8 26.674 109.850 120.450 1.00127.71 S ATOM 35640 SG CYS I 25 25.501 111.327 123.534 1.00129.56 S ATOM 35661 SG CYS I 28 22.962 111.143 120.659 1.00126.98 S ATOM 35942 SG CYS J 7 110.293 64.311 144.492 1.00 75.73 S ATOM 36230 SG CYS J 44 109.150 62.099 145.738 1.00 83.12 S ATOM 36236 SG CYS J 45 111.362 60.368 143.229 1.00 85.64 S ATOM 37298 SG CYS L 22 116.080 87.100 107.923 1.00119.56 S ATOM 37415 SG CYS L 36 117.788 90.877 108.213 1.00120.93 S ATOM 47606 SG CYS P 290 94.379 165.064 147.994 1.00268.17 S ATOM 47588 SG CYS P 287 92.231 167.503 153.862 1.00262.37 S ATOM 47730 SG CYS P 307 98.180 164.772 151.742 1.00255.50 S ATOM 47653 SG CYS P 296 94.244 161.803 154.048 1.00255.77 S ATOM 49983 SG CYS V 7 132.064 121.673 153.024 1.00178.33 S ATOM 50161 SG CYS V 31 134.765 118.628 155.274 1.00175.49 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS V 177 " occ=0.47 ... (10 atoms not shown) pdb=" SG BCYS V 177 " occ=0.53 residue: pdb=" N LYS V 364 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS V 364 " occ=0.00 residue: pdb=" N SER V 365 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER V 365 " occ=0.00 residue: pdb=" N PRO V 366 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO V 366 " occ=0.00 residue: pdb=" N LYS V 367 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS V 367 " occ=0.00 residue: pdb=" N ARG V 368 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG V 368 " occ=0.00 residue: pdb=" N ILE V 369 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE V 369 " occ=0.00 residue: pdb=" N CYS V 370 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS V 370 " occ=0.00 residue: pdb=" N PRO V 371 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO V 371 " occ=0.00 residue: pdb=" N SER V 376 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER V 376 " occ=0.00 residue: pdb=" N THR V 377 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR V 377 " occ=0.00 residue: pdb=" N VAL V 378 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL V 378 " occ=0.00 Time building chain proxies: 25.19, per 1000 atoms: 0.44 Number of scatterers: 57140 At special positions: 0 Unit cell: (162.748, 216.108, 228.114, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 349 16.00 P 164 15.00 Mg 1 11.99 O 10946 8.00 N 9981 7.00 C 35688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 156 " distance=2.04 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 159 " distance=2.13 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.94 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 296 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb=" ZN V 700 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 31 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 7 " Number of angles added : 12 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12676 Finding SS restraints... Secondary structure from input PDB file: 269 helices and 66 sheets defined 45.5% alpha, 15.0% beta 53 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 18.82 Creating SS restraints... Processing helix chain '1' and resid 4 through 21 removed outlier: 3.769A pdb=" N THR 1 9 " --> pdb=" O PRO 1 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU 1 12 " --> pdb=" O GLN 1 8 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER 1 16 " --> pdb=" O GLU 1 12 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 34 removed outlier: 3.849A pdb=" N ARG 1 34 " --> pdb=" O THR 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 48 through 65 removed outlier: 3.728A pdb=" N TYR 1 65 " --> pdb=" O LEU 1 61 " (cutoff:3.500A) Processing helix chain '1' and resid 71 through 88 Processing helix chain '1' and resid 102 through 104 No H-bonds generated for 'chain '1' and resid 102 through 104' Processing helix chain '1' and resid 105 through 117 removed outlier: 3.791A pdb=" N LYS 1 109 " --> pdb=" O ASP 1 105 " (cutoff:3.500A) Processing helix chain '1' and resid 119 through 133 removed outlier: 3.718A pdb=" N PHE 1 126 " --> pdb=" O ALA 1 122 " (cutoff:3.500A) Processing helix chain '3' and resid 44 through 55 removed outlier: 3.989A pdb=" N GLY 3 48 " --> pdb=" O VAL 3 44 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU 3 49 " --> pdb=" O GLY 3 45 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG 3 52 " --> pdb=" O GLY 3 48 " (cutoff:3.500A) Processing helix chain '3' and resid 77 through 90 removed outlier: 4.737A pdb=" N ARG 3 88 " --> pdb=" O ALA 3 84 " (cutoff:3.500A) Processing helix chain '3' and resid 99 through 106 Processing helix chain '3' and resid 127 through 143 removed outlier: 3.558A pdb=" N THR 3 143 " --> pdb=" O HIS 3 139 " (cutoff:3.500A) Processing helix chain '3' and resid 150 through 162 removed outlier: 4.042A pdb=" N VAL 3 156 " --> pdb=" O GLN 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 170 through 174 removed outlier: 3.556A pdb=" N MET 3 174 " --> pdb=" O SER 3 171 " (cutoff:3.500A) Processing helix chain '3' and resid 211 through 219 removed outlier: 3.791A pdb=" N LEU 3 215 " --> pdb=" O LYS 3 211 " (cutoff:3.500A) Processing helix chain '3' and resid 221 through 226 Processing helix chain '3' and resid 242 through 247 Processing helix chain '3' and resid 270 through 280 removed outlier: 4.254A pdb=" N ILE 3 274 " --> pdb=" O LEU 3 270 " (cutoff:3.500A) Processing helix chain '3' and resid 297 through 300 Processing helix chain '3' and resid 380 through 389 removed outlier: 3.537A pdb=" N MET 3 386 " --> pdb=" O VAL 3 382 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS 3 388 " --> pdb=" O PHE 3 384 " (cutoff:3.500A) Processing helix chain '3' and resid 406 through 410 Processing helix chain '4' and resid 163 through 171 removed outlier: 3.749A pdb=" N GLU 4 167 " --> pdb=" O GLU 4 163 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN 4 171 " --> pdb=" O GLU 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 185 through 222 Proline residue: 4 207 - end of helix Processing helix chain '4' and resid 224 through 247 Processing helix chain '4' and resid 251 through 255 removed outlier: 3.585A pdb=" N LEU 4 254 " --> pdb=" O GLU 4 251 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 269 removed outlier: 3.510A pdb=" N ILE 4 266 " --> pdb=" O ASP 4 262 " (cutoff:3.500A) Processing helix chain '4' and resid 276 through 286 removed outlier: 3.782A pdb=" N PHE 4 283 " --> pdb=" O GLU 4 279 " (cutoff:3.500A) Processing helix chain '4' and resid 301 through 313 Processing helix chain '4' and resid 316 through 325 Processing helix chain '4' and resid 329 through 341 removed outlier: 3.726A pdb=" N GLN 4 335 " --> pdb=" O PHE 4 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS 4 336 " --> pdb=" O GLN 4 332 " (cutoff:3.500A) Processing helix chain '4' and resid 351 through 365 removed outlier: 3.827A pdb=" N ARG 4 355 " --> pdb=" O GLU 4 351 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET 4 356 " --> pdb=" O GLU 4 352 " (cutoff:3.500A) Processing helix chain '4' and resid 371 through 379 removed outlier: 3.792A pdb=" N ILE 4 375 " --> pdb=" O PRO 4 371 " (cutoff:3.500A) Processing helix chain '4' and resid 385 through 387 No H-bonds generated for 'chain '4' and resid 385 through 387' Processing helix chain '4' and resid 388 through 393 Processing helix chain '4' and resid 407 through 412 Processing helix chain '4' and resid 413 through 419 removed outlier: 4.228A pdb=" N ALA 4 417 " --> pdb=" O LEU 4 413 " (cutoff:3.500A) Processing helix chain '4' and resid 423 through 430 removed outlier: 3.927A pdb=" N ARG 4 428 " --> pdb=" O PHE 4 425 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU 4 429 " --> pdb=" O LYS 4 426 " (cutoff:3.500A) Processing helix chain '4' and resid 435 through 448 removed outlier: 3.921A pdb=" N ASP 4 441 " --> pdb=" O ALA 4 437 " (cutoff:3.500A) Processing helix chain '4' and resid 459 through 469 removed outlier: 3.879A pdb=" N GLN 4 463 " --> pdb=" O LYS 4 459 " (cutoff:3.500A) Processing helix chain '4' and resid 477 through 482 Processing helix chain '4' and resid 487 through 499 removed outlier: 5.368A pdb=" N SER 4 493 " --> pdb=" O SER 4 489 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS 4 494 " --> pdb=" O GLN 4 490 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE 4 497 " --> pdb=" O SER 4 493 " (cutoff:3.500A) Processing helix chain '4' and resid 505 through 510 Processing helix chain '4' and resid 511 through 513 No H-bonds generated for 'chain '4' and resid 511 through 513' Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 94 through 108 removed outlier: 4.524A pdb=" N ARG A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 205 through 212 Proline residue: A 209 - end of helix removed outlier: 4.332A pdb=" N GLY A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 233 through 238 removed outlier: 4.382A pdb=" N LEU A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 277 through 300 Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.556A pdb=" N LEU A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.600A pdb=" N ILE A 389 " --> pdb=" O HIS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.797A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 571 through 572 No H-bonds generated for 'chain 'A' and resid 571 through 572' Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.728A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.819A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 662 through 695 removed outlier: 8.033A pdb=" N GLN A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N ASN A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU A 675 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 733 Processing helix chain 'A' and resid 743 through 771 Processing helix chain 'A' and resid 775 through 783 Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 828 through 832 Processing helix chain 'A' and resid 843 through 880 removed outlier: 4.087A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 920 through 932 Processing helix chain 'A' and resid 941 through 954 Processing helix chain 'A' and resid 955 through 961 removed outlier: 3.526A pdb=" N PHE A 958 " --> pdb=" O LYS A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 987 removed outlier: 3.743A pdb=" N TYR A 987 " --> pdb=" O THR A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1007 through 1025 Processing helix chain 'A' and resid 1032 through 1048 Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1066 through 1076 Processing helix chain 'A' and resid 1094 through 1106 Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1133 through 1140 Processing helix chain 'A' and resid 1145 through 1153 Processing helix chain 'A' and resid 1187 through 1196 removed outlier: 4.209A pdb=" N PHE A1191 " --> pdb=" O TYR A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1238 Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.550A pdb=" N THR A1246 " --> pdb=" O GLY A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1259 Processing helix chain 'A' and resid 1259 through 1278 removed outlier: 3.590A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.991A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1312 Processing helix chain 'A' and resid 1314 through 1322 removed outlier: 3.799A pdb=" N GLU A1322 " --> pdb=" O LEU A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1334 Processing helix chain 'A' and resid 1342 through 1350 Processing helix chain 'A' and resid 1355 through 1359 removed outlier: 3.850A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 removed outlier: 4.426A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.748A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.536A pdb=" N ILE B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Proline residue: B 267 - end of helix Processing helix chain 'B' and resid 279 through 291 Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.559A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.548A pdb=" N LYS B 404 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 removed outlier: 4.030A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 508 through 518 removed outlier: 3.801A pdb=" N VAL B 512 " --> pdb=" O ASP B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 removed outlier: 3.612A pdb=" N GLU B 530 " --> pdb=" O CYS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 566 Processing helix chain 'B' and resid 607 through 617 Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.853A pdb=" N ASP B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.562A pdb=" N LEU B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.883A pdb=" N LEU B 671 " --> pdb=" O VAL B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 679 through 691 Processing helix chain 'B' and resid 722 through 728 removed outlier: 3.523A pdb=" N GLU B 726 " --> pdb=" O THR B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 733 Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 804 through 807 Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 932 through 938 removed outlier: 4.398A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.932A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 980 removed outlier: 3.528A pdb=" N VAL B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1038 through 1042 Processing helix chain 'B' and resid 1048 through 1059 Processing helix chain 'B' and resid 1060 through 1070 Processing helix chain 'B' and resid 1108 through 1120 removed outlier: 3.506A pdb=" N MET B1120 " --> pdb=" O GLU B1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 82 Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.781A pdb=" N LEU C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 285 through 289 removed outlier: 3.732A pdb=" N PHE C 288 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 295 removed outlier: 3.930A pdb=" N LYS C 295 " --> pdb=" O LYS C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 344 Processing helix chain 'D' and resid 12 through 30 Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 40 through 56 Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.714A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 93 through 99 removed outlier: 4.340A pdb=" N ILE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 removed outlier: 4.266A pdb=" N ALA D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.683A pdb=" N LEU E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 132 through 136' Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 removed outlier: 3.547A pdb=" N ILE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'G' and resid 197 through 201 removed outlier: 4.127A pdb=" N TRP G 201 " --> pdb=" O LEU G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.511A pdb=" N GLN H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.461A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 3.552A pdb=" N ALA J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.887A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 62 removed outlier: 4.260A pdb=" N LYS J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 61 removed outlier: 3.513A pdb=" N LYS K 61 " --> pdb=" O TYR K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 126 removed outlier: 3.535A pdb=" N ALA K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 139 through 154 removed outlier: 3.687A pdb=" N ASP M 143 " --> pdb=" O PHE M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 202 Processing helix chain 'M' and resid 215 through 223 removed outlier: 3.591A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 226 No H-bonds generated for 'chain 'M' and resid 224 through 226' Processing helix chain 'M' and resid 241 through 250 Processing helix chain 'M' and resid 269 through 275 removed outlier: 3.840A pdb=" N THR M 275 " --> pdb=" O ALA M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 290 Processing helix chain 'M' and resid 293 through 302 removed outlier: 3.506A pdb=" N SER M 299 " --> pdb=" O ALA M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 317 removed outlier: 3.733A pdb=" N GLN M 315 " --> pdb=" O LEU M 311 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS M 316 " --> pdb=" O ARG M 312 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL M 317 " --> pdb=" O GLY M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 333 removed outlier: 3.529A pdb=" N LEU M 332 " --> pdb=" O LYS M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 363 removed outlier: 3.685A pdb=" N THR M 361 " --> pdb=" O MET M 357 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN M 362 " --> pdb=" O TRP M 358 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 376 Processing helix chain 'M' and resid 378 through 389 removed outlier: 3.664A pdb=" N MET M 389 " --> pdb=" O PHE M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 412 removed outlier: 3.790A pdb=" N ILE M 409 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 435 Processing helix chain 'N' and resid 249 through 259 Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 388 through 396 Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 19 through 32 Processing helix chain 'O' and resid 36 through 44 Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.880A pdb=" N HIS O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 78 through 85 removed outlier: 3.799A pdb=" N MET O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 99 Processing helix chain 'O' and resid 100 through 114 Processing helix chain 'O' and resid 117 through 132 removed outlier: 3.846A pdb=" N GLU O 131 " --> pdb=" O ASP O 127 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 154 removed outlier: 3.890A pdb=" N VAL O 144 " --> pdb=" O ASP O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 187 removed outlier: 3.537A pdb=" N ASP O 186 " --> pdb=" O ASN O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 259 Processing helix chain 'O' and resid 260 through 274 Processing helix chain 'O' and resid 290 through 297 Processing helix chain 'O' and resid 304 through 317 Processing helix chain 'O' and resid 337 through 359 Processing helix chain 'O' and resid 359 through 372 Processing helix chain 'O' and resid 376 through 385 Processing helix chain 'O' and resid 390 through 401 Processing helix chain 'O' and resid 427 through 457 removed outlier: 3.512A pdb=" N ALA O 431 " --> pdb=" O ASN O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 473 removed outlier: 3.903A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 487 removed outlier: 3.543A pdb=" N GLN O 483 " --> pdb=" O GLU O 480 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLN O 485 " --> pdb=" O ALA O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 491 through 530 removed outlier: 4.417A pdb=" N GLU O 495 " --> pdb=" O ILE O 491 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN O 497 " --> pdb=" O ALA O 493 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 103 Processing helix chain 'P' and resid 104 through 106 No H-bonds generated for 'chain 'P' and resid 104 through 106' Processing helix chain 'P' and resid 119 through 134 removed outlier: 3.900A pdb=" N ILE P 123 " --> pdb=" O PRO P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 199 removed outlier: 3.654A pdb=" N LYS P 199 " --> pdb=" O ALA P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 210 Processing helix chain 'P' and resid 213 through 224 Processing helix chain 'P' and resid 231 through 245 Processing helix chain 'P' and resid 307 through 316 Processing helix chain 'Q' and resid 51 through 71 removed outlier: 3.505A pdb=" N GLU Q 66 " --> pdb=" O GLN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 91 removed outlier: 3.574A pdb=" N LYS Q 89 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 111 removed outlier: 3.546A pdb=" N MET Q 111 " --> pdb=" O ARG Q 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 179 through 186 Processing helix chain 'U' and resid 226 through 244 Processing helix chain 'U' and resid 269 through 277 removed outlier: 3.597A pdb=" N LEU U 273 " --> pdb=" O ARG U 269 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL U 274 " --> pdb=" O LEU U 270 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 281 Processing helix chain 'U' and resid 317 through 334 Proline residue: U 330 - end of helix Processing helix chain 'V' and resid 43 through 48 Processing helix chain 'V' and resid 54 through 60 Processing helix chain 'V' and resid 66 through 83 Processing helix chain 'V' and resid 86 through 101 removed outlier: 3.537A pdb=" N GLU V 90 " --> pdb=" O PRO V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 103 through 108 Processing helix chain 'V' and resid 110 through 129 removed outlier: 3.705A pdb=" N HIS V 129 " --> pdb=" O THR V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 140 Processing helix chain 'V' and resid 145 through 161 Processing helix chain 'V' and resid 168 through 178 removed outlier: 3.870A pdb=" N SER V 178 " --> pdb=" O LYS V 174 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 194 Processing helix chain 'V' and resid 196 through 214 Processing helix chain 'V' and resid 221 through 237 removed outlier: 4.075A pdb=" N VAL V 225 " --> pdb=" O HIS V 221 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 243 Processing helix chain 'V' and resid 246 through 255 Processing helix chain 'V' and resid 261 through 278 Processing helix chain 'V' and resid 280 through 287 Processing helix chain 'V' and resid 293 through 295 No H-bonds generated for 'chain 'V' and resid 293 through 295' Processing helix chain 'V' and resid 296 through 303 Processing helix chain 'V' and resid 303 through 314 removed outlier: 3.509A pdb=" N ASP V 314 " --> pdb=" O SER V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 386 through 393 removed outlier: 3.522A pdb=" N GLU V 390 " --> pdb=" O ASP V 386 " (cutoff:3.500A) Processing helix chain 'V' and resid 395 through 406 removed outlier: 3.541A pdb=" N GLN V 406 " --> pdb=" O PHE V 402 " (cutoff:3.500A) Processing helix chain 'W' and resid 304 through 319 Processing helix chain 'W' and resid 321 through 328 Processing helix chain 'W' and resid 333 through 358 removed outlier: 3.608A pdb=" N GLY W 349 " --> pdb=" O GLU W 345 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TRP W 350 " --> pdb=" O LYS W 346 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG W 351 " --> pdb=" O THR W 347 " (cutoff:3.500A) Processing helix chain 'W' and resid 364 through 384 Processing sheet with id=AA1, first strand: chain '1' and resid 97 through 100 removed outlier: 6.820A pdb=" N ILE 1 97 " --> pdb=" O HIS 1 136 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR 1 138 " --> pdb=" O ILE 1 97 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL 1 99 " --> pdb=" O THR 1 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '3' and resid 32 through 34 removed outlier: 3.512A pdb=" N LEU 3 34 " --> pdb=" O ASN 3 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain '3' and resid 203 through 207 removed outlier: 4.097A pdb=" N VAL 3 320 " --> pdb=" O LEU 3 187 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU 3 310 " --> pdb=" O TYR 3 253 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR 3 253 " --> pdb=" O LEU 3 310 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS 3 312 " --> pdb=" O PHE 3 251 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE 3 252 " --> pdb=" O TYR 3 259 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR 3 259 " --> pdb=" O PHE 3 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 203 through 207 Processing sheet with id=AA6, first strand: chain '3' and resid 378 through 379 Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.357A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS G 45 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU G 48 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL G 75 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS G 71 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU G 54 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LYS G 69 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP G 56 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS G 67 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA D 9 " --> pdb=" O LEU G 4 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.357A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS G 45 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALA G 57 " --> pdb=" O HIS A1364 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A1362 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1337 through 1339 removed outlier: 7.135A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE A 20 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE B1123 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.578A pdb=" N ILE A 34 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ASP A 87 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N LEU A 88 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 11.480A pdb=" N LEU A 256 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N LEU A 90 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG A 254 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AB3, first strand: chain 'A' and resid 265 through 268 removed outlier: 4.356A pdb=" N GLY A 273 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.812A pdb=" N LYS A 359 " --> pdb=" O LEU B1047 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 6.030A pdb=" N VAL A 380 " --> pdb=" O ARG A 479 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS A 481 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 382 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 488 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.947A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB8, first strand: chain 'A' and resid 617 through 619 removed outlier: 6.462A pdb=" N THR A 639 " --> pdb=" O MET A 646 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 883 through 884 removed outlier: 3.961A pdb=" N CYS A 883 " --> pdb=" O ARG A 891 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 891 " --> pdb=" O CYS A 883 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1085 through 1088 Processing sheet with id=AC2, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 3.818A pdb=" N GLN A1202 " --> pdb=" O THR A1108 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1165 through 1166 removed outlier: 3.503A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A1119 " --> pdb=" O ASN I 40 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN I 40 " --> pdb=" O GLU A1119 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL I 38 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 64 through 65 removed outlier: 7.483A pdb=" N LEU B 75 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N THR B 120 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N TYR B 77 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU B 118 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 79 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA B 111 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY B 134 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE B 113 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 115 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B 130 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG B 125 " --> pdb=" O ILE W 282 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AC7, first strand: chain 'B' and resid 360 through 363 removed outlier: 6.434A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 190 through 193 Processing sheet with id=AC9, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AD1, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AD2, first strand: chain 'B' and resid 603 through 604 Processing sheet with id=AD3, first strand: chain 'B' and resid 544 through 549 removed outlier: 6.685A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE B 537 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.716A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.716A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET L 44 " --> pdb=" O ILE B 871 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 896 through 897 removed outlier: 6.240A pdb=" N LEU B 755 " --> pdb=" O CYS B 907 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 909 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 756 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 927 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD8, first strand: chain 'B' and resid 795 through 796 removed outlier: 3.510A pdb=" N LYS B 801 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 826 through 828 removed outlier: 6.454A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1028 through 1029 removed outlier: 6.578A pdb=" N ARG B1028 " --> pdb=" O THR V 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 3.508A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 21 through 22 removed outlier: 3.523A pdb=" N VAL C 15 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 21 through 22 removed outlier: 3.523A pdb=" N VAL C 15 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS C 305 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.130A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 209 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.590A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 167 through 169 Processing sheet with id=AE8, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AE9, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AF1, first strand: chain 'E' and resid 61 through 63 removed outlier: 3.698A pdb=" N LEU E 61 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP E 70 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.690A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.833A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 97 through 101 removed outlier: 5.409A pdb=" N HIS G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.941A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 13 through 16 Processing sheet with id=AF7, first strand: chain 'K' and resid 26 through 30 Processing sheet with id=AF8, first strand: chain 'M' and resid 10 through 17 removed outlier: 8.457A pdb=" N LEU M 124 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP M 14 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU M 126 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR M 16 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL N 348 " --> pdb=" O VAL N 337 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY N 324 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL M 15 " --> pdb=" O VAL N 326 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS N 328 " --> pdb=" O ILE M 13 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE M 13 " --> pdb=" O LYS N 328 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU N 330 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLN M 11 " --> pdb=" O LEU N 330 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 25 through 34 removed outlier: 6.838A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU M 57 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA M 47 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU M 59 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY N 371 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL N 375 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR N 370 " --> pdb=" O GLY N 366 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG M 33 " --> pdb=" O LEU N 357 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N GLU N 359 " --> pdb=" O PRO M 31 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N VAL N 361 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N GLN M 29 " --> pdb=" O VAL N 361 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N VAL N 363 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LEU M 27 " --> pdb=" O VAL N 363 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N LEU N 365 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N LEU M 25 " --> pdb=" O LEU N 365 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 291 through 292 removed outlier: 3.995A pdb=" N TRP M 325 " --> pdb=" O MET M 292 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 365 through 366 Processing sheet with id=AG3, first strand: chain 'O' and resid 34 through 35 Processing sheet with id=AG4, first strand: chain 'O' and resid 157 through 159 Processing sheet with id=AG5, first strand: chain 'O' and resid 288 through 289 Processing sheet with id=AG6, first strand: chain 'O' and resid 405 through 406 Processing sheet with id=AG7, first strand: chain 'O' and resid 409 through 410 Processing sheet with id=AG8, first strand: chain 'P' and resid 136 through 139 Processing sheet with id=AG9, first strand: chain 'P' and resid 167 through 168 Processing sheet with id=AH1, first strand: chain 'P' and resid 211 through 212 removed outlier: 3.544A pdb=" N LEU P 269 " --> pdb=" O THR P 251 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'U' and resid 190 through 192 removed outlier: 3.871A pdb=" N SER U 170 " --> pdb=" O CYS U 221 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY U 223 " --> pdb=" O ILE U 168 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE U 168 " --> pdb=" O GLY U 223 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU U 165 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N SER U 261 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR U 171 " --> pdb=" O ILE U 255 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE U 255 " --> pdb=" O THR U 171 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ASN U 173 " --> pdb=" O PHE U 253 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE U 253 " --> pdb=" O ASN U 173 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 15 through 19 removed outlier: 3.608A pdb=" N VAL V 27 " --> pdb=" O VAL V 16 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP V 18 " --> pdb=" O GLN V 25 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN V 25 " --> pdb=" O ASP V 18 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR V 36 " --> pdb=" O LEU V 26 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 2428 hydrogen bonds defined for protein. 6819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 246 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 36.22 Time building geometry restraints manager: 12.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 24384 1.43 - 1.65: 33654 1.65 - 1.86: 535 1.86 - 2.08: 0 2.08 - 2.30: 12 Bond restraints: 58585 Sorted by residual: bond pdb=" CA THR V 175 " pdb=" C THR V 175 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.32e-02 5.74e+03 1.28e+01 bond pdb=" CA GLN B 294 " pdb=" C GLN B 294 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.62e-02 3.81e+03 1.09e+01 bond pdb=" N GLU L 21 " pdb=" CA GLU L 21 " ideal model delta sigma weight residual 1.454 1.497 -0.042 1.31e-02 5.83e+03 1.04e+01 bond pdb=" CA ALA V 108 " pdb=" C ALA V 108 " ideal model delta sigma weight residual 1.526 1.491 0.036 1.11e-02 8.12e+03 1.04e+01 bond pdb=" N CYS L 22 " pdb=" CA CYS L 22 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.32e-02 5.74e+03 1.01e+01 ... (remaining 58580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 17.14: 79776 17.14 - 34.28: 5 34.28 - 51.42: 0 51.42 - 68.56: 0 68.56 - 85.70: 10 Bond angle restraints: 79791 Sorted by residual: angle pdb=" O3' DT Y 49 " pdb=" P DT Y 50 " pdb=" OP1 DT Y 50 " ideal model delta sigma weight residual 108.00 22.30 85.70 3.00e+00 1.11e-01 8.16e+02 angle pdb=" O3' DA Y 67 " pdb=" P DT Y 68 " pdb=" OP1 DT Y 68 " ideal model delta sigma weight residual 108.00 22.48 85.52 3.00e+00 1.11e-01 8.13e+02 angle pdb=" O3' DA Y 69 " pdb=" P DT Y 70 " pdb=" OP1 DT Y 70 " ideal model delta sigma weight residual 108.00 22.50 85.50 3.00e+00 1.11e-01 8.12e+02 angle pdb=" O3' DA X -70 " pdb=" P DT X -69 " pdb=" OP1 DT X -69 " ideal model delta sigma weight residual 108.00 22.62 85.38 3.00e+00 1.11e-01 8.10e+02 angle pdb=" O3' DT Y 50 " pdb=" P DT Y 51 " pdb=" OP1 DT Y 51 " ideal model delta sigma weight residual 108.00 22.98 85.02 3.00e+00 1.11e-01 8.03e+02 ... (remaining 79786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 34257 35.38 - 70.76: 1194 70.76 - 106.14: 54 106.14 - 141.52: 0 141.52 - 176.90: 3 Dihedral angle restraints: 35508 sinusoidal: 15909 harmonic: 19599 Sorted by residual: dihedral pdb=" C ARG B 295 " pdb=" N ARG B 295 " pdb=" CA ARG B 295 " pdb=" CB ARG B 295 " ideal model delta harmonic sigma weight residual -122.60 -148.89 26.29 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" N ARG B 295 " pdb=" C ARG B 295 " pdb=" CA ARG B 295 " pdb=" CB ARG B 295 " ideal model delta harmonic sigma weight residual 122.80 147.32 -24.52 0 2.50e+00 1.60e-01 9.62e+01 dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -4.67 -81.33 1 1.00e+01 1.00e-02 8.15e+01 ... (remaining 35505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 8791 0.227 - 0.455: 90 0.455 - 0.682: 6 0.682 - 0.910: 1 0.910 - 1.137: 1 Chirality restraints: 8889 Sorted by residual: chirality pdb=" CA ARG B 295 " pdb=" N ARG B 295 " pdb=" C ARG B 295 " pdb=" CB ARG B 295 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CA ALA O 416 " pdb=" N ALA O 416 " pdb=" C ALA O 416 " pdb=" CB ALA O 416 " both_signs ideal model delta sigma weight residual False 2.48 1.73 0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" P DT X -22 " pdb=" OP1 DT X -22 " pdb=" OP2 DT X -22 " pdb=" O5' DT X -22 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.57 2.00e-01 2.50e+01 8.21e+00 ... (remaining 8886 not shown) Planarity restraints: 9690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 293 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.87e+01 pdb=" C ARG B 293 " -0.093 2.00e-02 2.50e+03 pdb=" O ARG B 293 " 0.035 2.00e-02 2.50e+03 pdb=" N GLN B 294 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR O 412 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO O 413 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO O 413 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO O 413 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS L 23 " -0.027 2.00e-02 2.50e+03 2.19e-02 7.16e+00 pdb=" CG HIS L 23 " 0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS L 23 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS L 23 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS L 23 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS L 23 " -0.014 2.00e-02 2.50e+03 ... (remaining 9687 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 58 2.27 - 2.93: 24322 2.93 - 3.59: 87347 3.59 - 4.24: 134396 4.24 - 4.90: 220771 Nonbonded interactions: 466894 Sorted by model distance: nonbonded pdb=" O ASN A 154 " pdb="ZN ZN A1402 " model vdw 1.615 2.230 nonbonded pdb=" NZ LYS E 85 " pdb=" OP2 DG Y -8 " model vdw 1.709 3.120 nonbonded pdb=" NZ LYS B 404 " pdb=" O THR V 140 " model vdw 1.930 3.120 nonbonded pdb=" OE1 GLU 4 167 " pdb=" NZ LYS M 316 " model vdw 1.969 3.120 nonbonded pdb=" C3' DA X -46 " pdb=" OP1 DT X -45 " model vdw 1.988 2.776 ... (remaining 466889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.680 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: 0.070 Extract box with map and model: 1.600 Check model and map are aligned: 0.330 Set scattering table: 0.400 Process input model: 145.250 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.250 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: 0.030 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 0.055 58585 Z= 0.205 Angle : 1.236 85.699 79791 Z= 0.513 Chirality : 0.060 1.137 8889 Planarity : 0.004 0.108 9690 Dihedral : 16.228 176.903 22823 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 0.66 % Allowed : 2.54 % Favored : 96.80 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.10), residues: 6657 helix: 0.65 (0.10), residues: 2657 sheet: -0.74 (0.19), residues: 714 loop : -1.16 (0.11), residues: 3286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 235 HIS 0.013 0.001 HIS L 23 PHE 0.026 0.001 PHE Q 38 TYR 0.020 0.001 TYR G 40 ARG 0.007 0.000 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 294 time to evaluate : 4.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 108 LEU cc_start: 0.5302 (mt) cc_final: 0.5011 (tp) REVERT: 1 140 MET cc_start: 0.6965 (ptp) cc_final: 0.6748 (ttt) REVERT: 3 386 MET cc_start: 0.1855 (pp-130) cc_final: 0.1488 (ptt) REVERT: 4 264 GLU cc_start: 0.8931 (mp0) cc_final: 0.8695 (mm-30) REVERT: 4 385 MET cc_start: -0.0517 (tmm) cc_final: -0.2563 (tpt) REVERT: 4 499 MET cc_start: 0.1891 (ptp) cc_final: 0.0749 (tpp) REVERT: A 79 CYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7290 (t) REVERT: A 116 MET cc_start: 0.6449 (tmm) cc_final: 0.5644 (mtp) REVERT: A 523 MET cc_start: 0.8992 (mtm) cc_final: 0.8735 (mtm) REVERT: A 680 MET cc_start: 0.8847 (mmt) cc_final: 0.8640 (mmm) REVERT: A 912 MET cc_start: 0.8364 (tpp) cc_final: 0.8057 (tpp) REVERT: A 1317 MET cc_start: 0.8167 (tmm) cc_final: 0.7950 (tmm) REVERT: A 1349 MET cc_start: 0.8379 (tpt) cc_final: 0.8173 (mmm) REVERT: B 243 MET cc_start: 0.8468 (tpt) cc_final: 0.8191 (tpp) REVERT: B 262 MET cc_start: 0.9328 (mpp) cc_final: 0.8918 (mpp) REVERT: B 478 MET cc_start: 0.8682 (mpp) cc_final: 0.8026 (mpp) REVERT: B 929 MET cc_start: 0.8396 (ttt) cc_final: 0.8161 (ttp) REVERT: B 1069 MET cc_start: 0.8804 (tmm) cc_final: 0.8497 (tmm) REVERT: E 94 MET cc_start: 0.8376 (tpt) cc_final: 0.7926 (tpt) REVERT: E 121 MET cc_start: 0.8253 (mpp) cc_final: 0.7957 (mpp) REVERT: H 37 MET cc_start: 0.9178 (mmm) cc_final: 0.8822 (mmm) REVERT: K 28 GLU cc_start: 0.8378 (mp0) cc_final: 0.8151 (mp0) REVERT: K 60 MET cc_start: 0.9055 (tpp) cc_final: 0.8774 (tpt) REVERT: K 97 GLN cc_start: 0.8800 (pp30) cc_final: 0.8347 (pp30) REVERT: K 102 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8366 (mt-10) REVERT: L 25 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8138 (mm-30) REVERT: M 60 MET cc_start: 0.7591 (pmm) cc_final: 0.7337 (pmm) REVERT: M 298 MET cc_start: 0.8812 (mmt) cc_final: 0.8451 (mpp) REVERT: O 133 MET cc_start: 0.4112 (ptt) cc_final: 0.3866 (ptt) REVERT: O 333 MET cc_start: 0.7946 (tmm) cc_final: 0.7130 (tmm) REVERT: O 420 THR cc_start: 0.6320 (OUTLIER) cc_final: 0.5677 (t) REVERT: P 310 MET cc_start: 0.8509 (mmt) cc_final: 0.7668 (mpp) REVERT: U 252 ASP cc_start: 0.8869 (t70) cc_final: 0.8489 (p0) REVERT: U 258 MET cc_start: 0.6742 (ptp) cc_final: 0.6493 (ptm) REVERT: W 282 ILE cc_start: 0.7741 (mm) cc_final: 0.7339 (mm) outliers start: 39 outliers final: 10 residues processed: 329 average time/residue: 0.5659 time to fit residues: 315.6152 Evaluate side-chains 241 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 4.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain O residue 412 THR Chi-restraints excluded: chain O residue 418 SER Chi-restraints excluded: chain O residue 420 THR Chi-restraints excluded: chain V residue 19 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 571 optimal weight: 5.9990 chunk 513 optimal weight: 8.9990 chunk 284 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 chunk 346 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 530 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 322 optimal weight: 9.9990 chunk 394 optimal weight: 1.9990 chunk 614 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 48 ASN ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 116 ASN ** 3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 185 ASN 3 202 GLN ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 314 GLN 4 247 GLN 4 438 GLN A 48 HIS A 158 HIS A 427 GLN A 599 GLN B 124 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 412 HIS ** N 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN P 181 ASN P 200 GLN V 129 HIS V 212 ASN W 339 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 58585 Z= 0.270 Angle : 0.741 29.266 79791 Z= 0.352 Chirality : 0.078 2.079 8889 Planarity : 0.004 0.094 9690 Dihedral : 15.533 177.052 9201 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Rotamer: Outliers : 0.51 % Allowed : 6.62 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -0.26 (0.10), residues: 6657 helix: 0.94 (0.10), residues: 2691 sheet: -0.72 (0.18), residues: 756 loop : -0.97 (0.11), residues: 3210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 364 HIS 0.011 0.001 HIS O 415 PHE 0.021 0.001 PHE 1 120 TYR 0.020 0.001 TYR A1151 ARG 0.008 0.000 ARG 1 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 4.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 108 LEU cc_start: 0.5702 (mt) cc_final: 0.5375 (tp) REVERT: 1 140 MET cc_start: 0.7063 (ptp) cc_final: 0.6806 (ttt) REVERT: 3 47 PHE cc_start: -0.2590 (OUTLIER) cc_final: -0.3082 (m-80) REVERT: 3 386 MET cc_start: 0.2470 (pp-130) cc_final: 0.2031 (ptt) REVERT: 4 385 MET cc_start: -0.0353 (tmm) cc_final: -0.2170 (tpt) REVERT: 4 499 MET cc_start: 0.2382 (ptp) cc_final: 0.1356 (tpp) REVERT: A 60 MET cc_start: 0.7626 (ttt) cc_final: 0.6094 (tmm) REVERT: A 116 MET cc_start: 0.6612 (tmm) cc_final: 0.5729 (mtp) REVERT: A 523 MET cc_start: 0.9057 (mtm) cc_final: 0.8847 (mtm) REVERT: A 680 MET cc_start: 0.8886 (mmt) cc_final: 0.8624 (mmm) REVERT: A 1275 MET cc_start: 0.8936 (mmm) cc_final: 0.8103 (mmm) REVERT: A 1317 MET cc_start: 0.8365 (tmm) cc_final: 0.8159 (tmm) REVERT: B 254 MET cc_start: 0.9306 (ttt) cc_final: 0.9099 (ttt) REVERT: B 478 MET cc_start: 0.8839 (mpp) cc_final: 0.8185 (mpp) REVERT: B 870 MET cc_start: 0.8846 (ppp) cc_final: 0.8481 (ppp) REVERT: B 1062 MET cc_start: 0.8577 (mpp) cc_final: 0.8076 (mpp) REVERT: B 1069 MET cc_start: 0.8830 (tmm) cc_final: 0.8575 (tmm) REVERT: C 212 MET cc_start: 0.9207 (mtp) cc_final: 0.8778 (mtp) REVERT: E 94 MET cc_start: 0.8505 (tpt) cc_final: 0.7951 (tpp) REVERT: E 121 MET cc_start: 0.8285 (mpp) cc_final: 0.8006 (mpp) REVERT: G 157 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7171 (m-10) REVERT: H 37 MET cc_start: 0.9172 (mmm) cc_final: 0.8716 (mmm) REVERT: K 28 GLU cc_start: 0.8490 (mp0) cc_final: 0.8233 (mp0) REVERT: K 29 MET cc_start: 0.8261 (tmm) cc_final: 0.7788 (tmm) REVERT: K 60 MET cc_start: 0.9179 (tpp) cc_final: 0.8907 (tpp) REVERT: K 97 GLN cc_start: 0.8906 (pp30) cc_final: 0.8458 (pp30) REVERT: L 25 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7990 (mm-30) REVERT: M 60 MET cc_start: 0.7781 (pmm) cc_final: 0.7486 (pmm) REVERT: O 333 MET cc_start: 0.7476 (tmm) cc_final: 0.7060 (tmm) REVERT: O 404 MET cc_start: 0.6681 (tpt) cc_final: 0.6045 (tpt) REVERT: O 531 MET cc_start: 0.7541 (tpp) cc_final: 0.6844 (tpp) REVERT: P 310 MET cc_start: 0.8904 (mmt) cc_final: 0.8687 (mmt) REVERT: U 202 MET cc_start: 0.9303 (mmm) cc_final: 0.8723 (tmm) outliers start: 30 outliers final: 10 residues processed: 260 average time/residue: 0.5327 time to fit residues: 244.5777 Evaluate side-chains 235 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 223 time to evaluate : 4.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 334 CYS Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain H residue 45 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 341 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 511 optimal weight: 9.9990 chunk 418 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 615 optimal weight: 10.0000 chunk 665 optimal weight: 10.0000 chunk 548 optimal weight: 5.9990 chunk 610 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 494 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 268 ASN 4 438 GLN A 296 HIS ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 HIS B 42 GLN B 144 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 201 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 108 GLN ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 339 HIS U 327 ASN W 339 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 58585 Z= 0.255 Angle : 0.721 28.275 79791 Z= 0.341 Chirality : 0.079 2.079 8889 Planarity : 0.004 0.069 9690 Dihedral : 15.538 168.399 9194 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 0.76 % Allowed : 9.36 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.10), residues: 6657 helix: 1.04 (0.10), residues: 2702 sheet: -0.70 (0.18), residues: 747 loop : -0.91 (0.11), residues: 3208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 4 263 HIS 0.010 0.001 HIS O 415 PHE 0.019 0.001 PHE Q 38 TYR 0.019 0.001 TYR A1151 ARG 0.009 0.000 ARG G 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 4.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 108 LEU cc_start: 0.5289 (mt) cc_final: 0.5000 (tp) REVERT: 1 140 MET cc_start: 0.7079 (ptp) cc_final: 0.6781 (ttt) REVERT: 3 47 PHE cc_start: -0.2421 (OUTLIER) cc_final: -0.3132 (m-80) REVERT: 3 51 TRP cc_start: -0.0801 (OUTLIER) cc_final: -0.1090 (t60) REVERT: 3 386 MET cc_start: 0.2651 (pp-130) cc_final: 0.2188 (ptt) REVERT: 4 385 MET cc_start: -0.0197 (tmm) cc_final: -0.2064 (tpt) REVERT: 4 424 TRP cc_start: 0.2379 (m100) cc_final: 0.1857 (m100) REVERT: 4 499 MET cc_start: 0.1779 (ptp) cc_final: 0.0687 (tpp) REVERT: A 116 MET cc_start: 0.6545 (tmm) cc_final: 0.6291 (mtp) REVERT: A 523 MET cc_start: 0.8983 (mtm) cc_final: 0.8780 (mtm) REVERT: A 1048 MET cc_start: 0.7264 (ttp) cc_final: 0.6924 (tpp) REVERT: A 1275 MET cc_start: 0.8813 (mmm) cc_final: 0.8460 (mmm) REVERT: A 1317 MET cc_start: 0.8397 (tmm) cc_final: 0.8169 (tmm) REVERT: B 262 MET cc_start: 0.9372 (mpp) cc_final: 0.9158 (mpp) REVERT: B 870 MET cc_start: 0.8837 (ppp) cc_final: 0.8351 (ppp) REVERT: B 929 MET cc_start: 0.8439 (ttt) cc_final: 0.7974 (ttm) REVERT: B 1062 MET cc_start: 0.8749 (mpp) cc_final: 0.8173 (mpp) REVERT: E 110 MET cc_start: 0.8080 (tpp) cc_final: 0.7407 (tpp) REVERT: H 37 MET cc_start: 0.9147 (mmm) cc_final: 0.8727 (mmm) REVERT: K 29 MET cc_start: 0.8314 (tmm) cc_final: 0.7730 (tmm) REVERT: K 31 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7231 (pp30) REVERT: K 97 GLN cc_start: 0.8930 (pp30) cc_final: 0.8503 (pp30) REVERT: L 25 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7989 (mm-30) REVERT: M 286 MET cc_start: 0.9632 (mmm) cc_final: 0.9016 (mmm) REVERT: M 292 MET cc_start: 0.8581 (tmm) cc_final: 0.7822 (tmm) REVERT: O 404 MET cc_start: 0.6706 (tpt) cc_final: 0.6123 (tpt) REVERT: O 531 MET cc_start: 0.7964 (tpp) cc_final: 0.7247 (tpp) REVERT: P 310 MET cc_start: 0.8838 (mmt) cc_final: 0.8583 (mmm) REVERT: Q 57 MET cc_start: 0.7785 (tpp) cc_final: 0.7491 (mmm) REVERT: Q 68 MET cc_start: 0.7774 (ptp) cc_final: 0.7565 (ptp) REVERT: W 310 MET cc_start: 0.7111 (ttt) cc_final: 0.6909 (ttm) outliers start: 45 outliers final: 18 residues processed: 271 average time/residue: 0.5194 time to fit residues: 246.8788 Evaluate side-chains 244 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 5.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 334 CYS Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain P residue 214 HIS Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 608 optimal weight: 6.9990 chunk 463 optimal weight: 7.9990 chunk 319 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 293 optimal weight: 1.9990 chunk 413 optimal weight: 1.9990 chunk 618 optimal weight: 20.0000 chunk 654 optimal weight: 9.9990 chunk 322 optimal weight: 4.9990 chunk 585 optimal weight: 0.9980 chunk 176 optimal weight: 0.0670 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 247 GLN A 872 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN M 29 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 58585 Z= 0.165 Angle : 0.681 27.379 79791 Z= 0.316 Chirality : 0.079 2.091 8889 Planarity : 0.004 0.067 9690 Dihedral : 15.481 157.090 9194 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 0.67 % Allowed : 10.22 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -0.01 (0.10), residues: 6657 helix: 1.16 (0.10), residues: 2710 sheet: -0.57 (0.18), residues: 746 loop : -0.86 (0.11), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 4 476 HIS 0.006 0.001 HIS 3 241 PHE 0.016 0.001 PHE Q 38 TYR 0.017 0.001 TYR 3 247 ARG 0.009 0.000 ARG W 285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 5.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 108 LEU cc_start: 0.5263 (mt) cc_final: 0.4980 (tp) REVERT: 1 140 MET cc_start: 0.6972 (ptp) cc_final: 0.6602 (ttt) REVERT: 3 47 PHE cc_start: -0.2386 (OUTLIER) cc_final: -0.2869 (m-80) REVERT: 3 386 MET cc_start: 0.2515 (pp-130) cc_final: 0.2007 (ptt) REVERT: 4 385 MET cc_start: -0.0163 (tmm) cc_final: -0.2064 (tpt) REVERT: 4 499 MET cc_start: 0.2335 (ptp) cc_final: 0.1292 (tpt) REVERT: A 107 MET cc_start: 0.8264 (mmm) cc_final: 0.8054 (mmm) REVERT: A 680 MET cc_start: 0.8827 (mmt) cc_final: 0.8311 (mmm) REVERT: A 1048 MET cc_start: 0.7422 (ttp) cc_final: 0.7204 (tpp) REVERT: A 1317 MET cc_start: 0.8398 (tmm) cc_final: 0.8159 (tmm) REVERT: B 431 MET cc_start: 0.8177 (tmm) cc_final: 0.7746 (tmm) REVERT: B 870 MET cc_start: 0.8849 (ppp) cc_final: 0.8488 (ppp) REVERT: B 929 MET cc_start: 0.8425 (ttt) cc_final: 0.7975 (ttm) REVERT: B 1062 MET cc_start: 0.8618 (mpp) cc_final: 0.8020 (mpp) REVERT: E 72 MET cc_start: 0.7703 (tpp) cc_final: 0.6668 (tpt) REVERT: E 94 MET cc_start: 0.8475 (tpt) cc_final: 0.7920 (tpt) REVERT: E 110 MET cc_start: 0.8220 (tpp) cc_final: 0.7833 (tpp) REVERT: H 37 MET cc_start: 0.9142 (mmm) cc_final: 0.8672 (mmm) REVERT: K 28 GLU cc_start: 0.8527 (mp0) cc_final: 0.8293 (mp0) REVERT: K 29 MET cc_start: 0.8291 (tmm) cc_final: 0.7807 (tmm) REVERT: K 97 GLN cc_start: 0.8882 (pp30) cc_final: 0.8444 (pp30) REVERT: L 16 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8977 (mp) REVERT: L 25 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7802 (mm-30) REVERT: M 60 MET cc_start: 0.7571 (ptp) cc_final: 0.7095 (pmm) REVERT: M 270 MET cc_start: 0.8342 (mmm) cc_final: 0.7380 (tpp) REVERT: M 292 MET cc_start: 0.8405 (tmm) cc_final: 0.7276 (tmm) REVERT: O 404 MET cc_start: 0.6731 (tpt) cc_final: 0.6032 (tpt) REVERT: O 531 MET cc_start: 0.8057 (tpp) cc_final: 0.7380 (tpp) REVERT: P 310 MET cc_start: 0.8822 (mmt) cc_final: 0.8585 (mmm) REVERT: Q 68 MET cc_start: 0.7786 (ptp) cc_final: 0.7470 (mtm) REVERT: U 202 MET cc_start: 0.9369 (mmm) cc_final: 0.8713 (tmm) outliers start: 40 outliers final: 15 residues processed: 267 average time/residue: 0.5172 time to fit residues: 243.5793 Evaluate side-chains 240 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 334 CYS Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain P residue 214 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 545 optimal weight: 0.0470 chunk 371 optimal weight: 10.0000 chunk 9 optimal weight: 50.0000 chunk 487 optimal weight: 8.9990 chunk 270 optimal weight: 8.9990 chunk 558 optimal weight: 0.8980 chunk 452 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 334 optimal weight: 0.8980 chunk 587 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 overall best weight: 2.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 HIS B 289 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN E 129 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 ASN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 58585 Z= 0.200 Angle : 0.683 27.308 79791 Z= 0.317 Chirality : 0.079 2.084 8889 Planarity : 0.004 0.061 9690 Dihedral : 15.448 156.654 9190 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 0.89 % Allowed : 10.89 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.10), residues: 6657 helix: 1.25 (0.10), residues: 2710 sheet: -0.47 (0.18), residues: 735 loop : -0.84 (0.11), residues: 3212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 3 51 HIS 0.006 0.001 HIS A 415 PHE 0.038 0.001 PHE Q 38 TYR 0.014 0.001 TYR A1151 ARG 0.009 0.000 ARG W 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 4.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 108 LEU cc_start: 0.5243 (mt) cc_final: 0.4965 (tp) REVERT: 1 140 MET cc_start: 0.6985 (ptp) cc_final: 0.6705 (ttt) REVERT: 3 47 PHE cc_start: -0.2325 (OUTLIER) cc_final: -0.3066 (m-80) REVERT: 3 51 TRP cc_start: -0.0228 (OUTLIER) cc_final: -0.0664 (t60) REVERT: 3 386 MET cc_start: 0.2598 (pp-130) cc_final: 0.2089 (ptt) REVERT: 4 385 MET cc_start: -0.0140 (tmm) cc_final: -0.1976 (tpt) REVERT: A 107 MET cc_start: 0.8136 (mmm) cc_final: 0.7656 (mmm) REVERT: A 116 MET cc_start: 0.6692 (tmm) cc_final: 0.6226 (mtp) REVERT: A 680 MET cc_start: 0.8865 (mmt) cc_final: 0.8354 (mmm) REVERT: A 912 MET cc_start: 0.8325 (tpp) cc_final: 0.7772 (tpp) REVERT: A 1027 MET cc_start: 0.8560 (tpt) cc_final: 0.8335 (tpt) REVERT: A 1048 MET cc_start: 0.7542 (ttp) cc_final: 0.7306 (tpp) REVERT: A 1280 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7372 (ptp) REVERT: A 1317 MET cc_start: 0.8406 (tmm) cc_final: 0.8173 (tmm) REVERT: B 431 MET cc_start: 0.8136 (tmm) cc_final: 0.7702 (tmm) REVERT: B 870 MET cc_start: 0.8827 (ppp) cc_final: 0.8409 (ppp) REVERT: B 929 MET cc_start: 0.8451 (ttt) cc_final: 0.8004 (ttm) REVERT: B 1062 MET cc_start: 0.8617 (mpp) cc_final: 0.8018 (mpp) REVERT: E 94 MET cc_start: 0.8427 (tpt) cc_final: 0.7892 (tpt) REVERT: E 110 MET cc_start: 0.8290 (tpp) cc_final: 0.7850 (tpp) REVERT: G 157 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7344 (m-10) REVERT: H 37 MET cc_start: 0.9152 (mmm) cc_final: 0.8672 (mmm) REVERT: K 29 MET cc_start: 0.8151 (tmm) cc_final: 0.7739 (tmm) REVERT: K 97 GLN cc_start: 0.8893 (pp30) cc_final: 0.8461 (pp30) REVERT: L 16 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8978 (mp) REVERT: L 25 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7992 (mm-30) REVERT: M 60 MET cc_start: 0.7682 (ptp) cc_final: 0.7142 (pmm) REVERT: M 248 MET cc_start: 0.8713 (ptm) cc_final: 0.8342 (ptt) REVERT: M 270 MET cc_start: 0.8440 (mmm) cc_final: 0.7443 (tpp) REVERT: M 292 MET cc_start: 0.8347 (tmm) cc_final: 0.7505 (tmm) REVERT: O 404 MET cc_start: 0.6650 (tpt) cc_final: 0.5976 (tpt) REVERT: O 531 MET cc_start: 0.8024 (tpp) cc_final: 0.7763 (tpp) REVERT: P 267 MET cc_start: 0.3663 (tmm) cc_final: 0.3446 (tpt) REVERT: P 310 MET cc_start: 0.8829 (mmt) cc_final: 0.8551 (mmt) REVERT: U 202 MET cc_start: 0.9332 (mmm) cc_final: 0.8661 (tmm) outliers start: 53 outliers final: 27 residues processed: 274 average time/residue: 0.5231 time to fit residues: 254.0675 Evaluate side-chains 253 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 4.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 334 CYS Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain P residue 214 HIS Chi-restraints excluded: chain P residue 302 ILE Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 220 optimal weight: 20.0000 chunk 589 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 655 optimal weight: 10.0000 chunk 543 optimal weight: 9.9990 chunk 303 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 343 optimal weight: 0.7980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 73 GLN ** 3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 339 GLN 4 340 HIS 4 457 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 236 GLN V 406 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 58585 Z= 0.239 Angle : 0.697 27.285 79791 Z= 0.325 Chirality : 0.079 2.082 8889 Planarity : 0.004 0.056 9690 Dihedral : 15.521 156.039 9190 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 1.01 % Allowed : 11.25 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.10), residues: 6657 helix: 1.27 (0.10), residues: 2716 sheet: -0.53 (0.18), residues: 736 loop : -0.82 (0.11), residues: 3205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 4 476 HIS 0.007 0.001 HIS A 415 PHE 0.026 0.001 PHE Q 38 TYR 0.014 0.001 TYR M 119 ARG 0.007 0.000 ARG W 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 5.173 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: 1 140 MET cc_start: 0.6949 (ptp) cc_final: 0.6611 (ttt) REVERT: 3 47 PHE cc_start: -0.2178 (OUTLIER) cc_final: -0.2545 (m-80) REVERT: 4 385 MET cc_start: 0.0283 (tmm) cc_final: -0.1525 (tpt) REVERT: 4 499 MET cc_start: 0.1059 (mtp) cc_final: -0.0523 (tpp) REVERT: A 107 MET cc_start: 0.8316 (mmm) cc_final: 0.7995 (mmm) REVERT: A 116 MET cc_start: 0.6734 (tmm) cc_final: 0.6417 (mtp) REVERT: A 680 MET cc_start: 0.8885 (mmt) cc_final: 0.8365 (mmm) REVERT: A 912 MET cc_start: 0.8310 (tpp) cc_final: 0.7838 (mmt) REVERT: A 1048 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7048 (tpp) REVERT: A 1280 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7360 (ptp) REVERT: A 1317 MET cc_start: 0.8452 (tmm) cc_final: 0.8194 (tmm) REVERT: B 243 MET cc_start: 0.8302 (tpt) cc_final: 0.7915 (tpp) REVERT: B 262 MET cc_start: 0.9469 (mpp) cc_final: 0.9244 (mpp) REVERT: B 431 MET cc_start: 0.8118 (tmm) cc_final: 0.7132 (tmm) REVERT: B 870 MET cc_start: 0.8807 (ppp) cc_final: 0.8383 (ppp) REVERT: B 929 MET cc_start: 0.8437 (ttt) cc_final: 0.7971 (ttm) REVERT: B 1062 MET cc_start: 0.8667 (mpp) cc_final: 0.8141 (mpp) REVERT: C 315 VAL cc_start: 0.9575 (OUTLIER) cc_final: 0.9291 (t) REVERT: E 110 MET cc_start: 0.8255 (tpp) cc_final: 0.7860 (tpp) REVERT: E 121 MET cc_start: 0.8254 (mpp) cc_final: 0.7394 (pmm) REVERT: G 157 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7369 (m-10) REVERT: H 37 MET cc_start: 0.9166 (mmm) cc_final: 0.8706 (mmm) REVERT: K 29 MET cc_start: 0.8180 (tmm) cc_final: 0.7632 (tmm) REVERT: K 104 MET cc_start: 0.8869 (mmm) cc_final: 0.8358 (mmm) REVERT: L 25 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8100 (mm-30) REVERT: M 270 MET cc_start: 0.8452 (mmm) cc_final: 0.7436 (tpp) REVERT: M 292 MET cc_start: 0.7988 (tmm) cc_final: 0.7297 (tmm) REVERT: O 118 MET cc_start: 0.7113 (mmm) cc_final: 0.6880 (mmm) REVERT: O 333 MET cc_start: 0.7242 (tmm) cc_final: 0.6345 (tmm) REVERT: O 404 MET cc_start: 0.7030 (tpt) cc_final: 0.6479 (tpt) REVERT: O 531 MET cc_start: 0.8163 (tpp) cc_final: 0.7879 (tpp) REVERT: P 310 MET cc_start: 0.8819 (mmt) cc_final: 0.8529 (mmm) outliers start: 60 outliers final: 33 residues processed: 282 average time/residue: 0.5274 time to fit residues: 263.8049 Evaluate side-chains 260 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 4.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 334 CYS Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain 4 residue 438 GLN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain P residue 214 HIS Chi-restraints excluded: chain P residue 302 ILE Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 631 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 373 optimal weight: 8.9990 chunk 478 optimal weight: 4.9990 chunk 370 optimal weight: 0.3980 chunk 551 optimal weight: 20.0000 chunk 365 optimal weight: 4.9990 chunk 652 optimal weight: 0.7980 chunk 408 optimal weight: 2.9990 chunk 397 optimal weight: 1.9990 chunk 301 optimal weight: 8.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 339 GLN ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 331 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 58585 Z= 0.190 Angle : 0.682 27.289 79791 Z= 0.316 Chirality : 0.079 2.084 8889 Planarity : 0.004 0.057 9690 Dihedral : 15.521 156.245 9190 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 0.99 % Allowed : 11.80 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.10), residues: 6657 helix: 1.32 (0.10), residues: 2712 sheet: -0.46 (0.19), residues: 719 loop : -0.80 (0.11), residues: 3226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 51 HIS 0.005 0.001 HIS A 415 PHE 0.022 0.001 PHE Q 38 TYR 0.014 0.001 TYR A1116 ARG 0.006 0.000 ARG W 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 224 time to evaluate : 5.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 140 MET cc_start: 0.6925 (ptp) cc_final: 0.6602 (ttt) REVERT: 3 47 PHE cc_start: -0.2167 (OUTLIER) cc_final: -0.2901 (m-80) REVERT: 3 51 TRP cc_start: -0.0178 (OUTLIER) cc_final: -0.0648 (t60) REVERT: 4 385 MET cc_start: 0.0291 (tmm) cc_final: -0.1552 (tpt) REVERT: 4 499 MET cc_start: 0.1656 (mtp) cc_final: 0.0095 (tpp) REVERT: A 107 MET cc_start: 0.8410 (mmm) cc_final: 0.8152 (mmm) REVERT: A 116 MET cc_start: 0.6847 (tmm) cc_final: 0.6313 (mtp) REVERT: A 680 MET cc_start: 0.8871 (mmt) cc_final: 0.8338 (mmm) REVERT: A 912 MET cc_start: 0.8300 (tpp) cc_final: 0.7787 (mmt) REVERT: A 1048 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7163 (tpp) REVERT: A 1317 MET cc_start: 0.8489 (tmm) cc_final: 0.8221 (tmm) REVERT: B 262 MET cc_start: 0.9424 (mpp) cc_final: 0.9126 (mpp) REVERT: B 431 MET cc_start: 0.8006 (tmm) cc_final: 0.7665 (tmm) REVERT: B 791 MET cc_start: 0.8425 (mmm) cc_final: 0.8189 (mmt) REVERT: B 870 MET cc_start: 0.8791 (ppp) cc_final: 0.8362 (ppp) REVERT: B 929 MET cc_start: 0.8433 (ttt) cc_final: 0.7993 (ttm) REVERT: B 1062 MET cc_start: 0.8633 (mpp) cc_final: 0.8005 (mpp) REVERT: C 315 VAL cc_start: 0.9565 (OUTLIER) cc_final: 0.9261 (t) REVERT: E 72 MET cc_start: 0.7801 (tpt) cc_final: 0.7567 (tpt) REVERT: E 110 MET cc_start: 0.8336 (tpp) cc_final: 0.7924 (tpp) REVERT: G 157 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7320 (m-10) REVERT: H 37 MET cc_start: 0.9142 (mmm) cc_final: 0.8678 (mmm) REVERT: K 29 MET cc_start: 0.8161 (tmm) cc_final: 0.7617 (tmm) REVERT: K 97 GLN cc_start: 0.8980 (pp30) cc_final: 0.8560 (pp30) REVERT: K 104 MET cc_start: 0.8839 (mmm) cc_final: 0.8552 (mmm) REVERT: L 25 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8061 (mm-30) REVERT: M 248 MET cc_start: 0.8692 (ptm) cc_final: 0.8284 (ptt) REVERT: M 270 MET cc_start: 0.8514 (mmm) cc_final: 0.7520 (tpp) REVERT: M 292 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7500 (tmm) REVERT: O 118 MET cc_start: 0.7196 (mmm) cc_final: 0.6970 (mmm) REVERT: O 270 MET cc_start: 0.9010 (ppp) cc_final: 0.8739 (ppp) REVERT: O 333 MET cc_start: 0.7294 (tmm) cc_final: 0.6314 (tmm) REVERT: O 404 MET cc_start: 0.7195 (tpt) cc_final: 0.6638 (tpt) REVERT: O 531 MET cc_start: 0.8170 (tpp) cc_final: 0.7847 (tpp) REVERT: P 310 MET cc_start: 0.8822 (mmt) cc_final: 0.8543 (mmm) REVERT: Q 57 MET cc_start: 0.7368 (tpp) cc_final: 0.7050 (mmm) REVERT: U 202 MET cc_start: 0.9267 (mmm) cc_final: 0.8472 (tmm) REVERT: W 285 ARG cc_start: 0.6226 (tpm170) cc_final: 0.5268 (tpt90) REVERT: W 331 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7590 (t70) outliers start: 59 outliers final: 35 residues processed: 273 average time/residue: 0.5138 time to fit residues: 247.6203 Evaluate side-chains 264 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 4.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 334 CYS Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain 4 residue 253 LEU Chi-restraints excluded: chain 4 residue 438 GLN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain P residue 302 ILE Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain W residue 331 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 403 optimal weight: 8.9990 chunk 260 optimal weight: 6.9990 chunk 389 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 414 optimal weight: 2.9990 chunk 444 optimal weight: 2.9990 chunk 322 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 512 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 386 GLN ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 58585 Z= 0.222 Angle : 0.700 27.291 79791 Z= 0.324 Chirality : 0.079 2.082 8889 Planarity : 0.004 0.053 9690 Dihedral : 15.558 156.388 9190 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 0.88 % Allowed : 12.21 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 6657 helix: 1.33 (0.10), residues: 2720 sheet: -0.47 (0.19), residues: 729 loop : -0.78 (0.11), residues: 3208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 3 51 HIS 0.029 0.001 HIS W 331 PHE 0.021 0.001 PHE Q 38 TYR 0.014 0.001 TYR A1333 ARG 0.013 0.000 ARG G 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 4.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 140 MET cc_start: 0.6466 (ptp) cc_final: 0.6219 (ttt) REVERT: 3 47 PHE cc_start: -0.1921 (OUTLIER) cc_final: -0.2648 (m-80) REVERT: 3 51 TRP cc_start: 0.0134 (OUTLIER) cc_final: -0.0348 (t60) REVERT: 4 385 MET cc_start: 0.0287 (tmm) cc_final: -0.1645 (tpt) REVERT: 4 386 GLN cc_start: 0.6003 (OUTLIER) cc_final: 0.5248 (tt0) REVERT: 4 499 MET cc_start: 0.1682 (mtp) cc_final: -0.0896 (tmm) REVERT: A 60 MET cc_start: 0.6398 (ttt) cc_final: 0.5492 (ttt) REVERT: A 107 MET cc_start: 0.8441 (mmm) cc_final: 0.8194 (mmm) REVERT: A 116 MET cc_start: 0.6917 (tmm) cc_final: 0.6405 (mtp) REVERT: A 680 MET cc_start: 0.8887 (mmt) cc_final: 0.8344 (mmm) REVERT: A 912 MET cc_start: 0.8341 (tpp) cc_final: 0.7827 (mmt) REVERT: A 1317 MET cc_start: 0.8495 (tmm) cc_final: 0.8226 (tmm) REVERT: B 338 MET cc_start: 0.9382 (ttt) cc_final: 0.9103 (mtt) REVERT: B 607 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8915 (p) REVERT: B 791 MET cc_start: 0.8422 (mmm) cc_final: 0.8180 (mmt) REVERT: B 870 MET cc_start: 0.8790 (ppp) cc_final: 0.8352 (ppp) REVERT: B 929 MET cc_start: 0.8447 (ttt) cc_final: 0.8007 (ttm) REVERT: B 1062 MET cc_start: 0.8639 (mpp) cc_final: 0.8010 (mpp) REVERT: E 72 MET cc_start: 0.7900 (tpt) cc_final: 0.7673 (tpt) REVERT: E 110 MET cc_start: 0.8274 (tpp) cc_final: 0.7930 (tpp) REVERT: G 157 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7428 (m-10) REVERT: H 37 MET cc_start: 0.9154 (mmm) cc_final: 0.8689 (mmm) REVERT: K 29 MET cc_start: 0.8163 (tmm) cc_final: 0.7620 (tmm) REVERT: K 104 MET cc_start: 0.8836 (mmm) cc_final: 0.8537 (mmm) REVERT: L 25 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8004 (mm-30) REVERT: M 248 MET cc_start: 0.8780 (ptm) cc_final: 0.8384 (ptt) REVERT: M 270 MET cc_start: 0.8437 (mmm) cc_final: 0.7466 (tpp) REVERT: M 292 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7373 (tmm) REVERT: O 118 MET cc_start: 0.7281 (mmm) cc_final: 0.7064 (mmm) REVERT: O 333 MET cc_start: 0.7280 (tmm) cc_final: 0.6211 (tmm) REVERT: O 404 MET cc_start: 0.6837 (tpt) cc_final: 0.6332 (tpp) REVERT: O 531 MET cc_start: 0.8212 (tpp) cc_final: 0.7871 (tpp) REVERT: P 310 MET cc_start: 0.8854 (mmt) cc_final: 0.8562 (mmm) REVERT: U 202 MET cc_start: 0.9267 (mmm) cc_final: 0.8495 (tmm) REVERT: W 285 ARG cc_start: 0.6389 (tpm170) cc_final: 0.5421 (tpt90) REVERT: W 331 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7916 (t-170) outliers start: 52 outliers final: 38 residues processed: 267 average time/residue: 0.5393 time to fit residues: 255.1929 Evaluate side-chains 265 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 5.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain 4 residue 253 LEU Chi-restraints excluded: chain 4 residue 386 GLN Chi-restraints excluded: chain 4 residue 438 GLN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain M residue 149 HIS Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain P residue 302 ILE Chi-restraints excluded: chain W residue 331 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 593 optimal weight: 20.0000 chunk 625 optimal weight: 6.9990 chunk 570 optimal weight: 30.0000 chunk 608 optimal weight: 10.0000 chunk 624 optimal weight: 5.9990 chunk 365 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 477 optimal weight: 3.9990 chunk 186 optimal weight: 0.0050 chunk 549 optimal weight: 7.9990 chunk 575 optimal weight: 9.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 58585 Z= 0.230 Angle : 0.711 27.292 79791 Z= 0.329 Chirality : 0.079 2.085 8889 Planarity : 0.004 0.050 9690 Dihedral : 15.596 155.951 9190 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 0.84 % Allowed : 12.47 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 6657 helix: 1.30 (0.10), residues: 2724 sheet: -0.47 (0.19), residues: 722 loop : -0.76 (0.11), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 3 51 HIS 0.013 0.001 HIS P 214 PHE 0.020 0.001 PHE A 197 TYR 0.015 0.001 TYR A1333 ARG 0.009 0.000 ARG V 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 5.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 140 MET cc_start: 0.6415 (ptp) cc_final: 0.6193 (ttt) REVERT: 3 47 PHE cc_start: -0.1781 (OUTLIER) cc_final: -0.2565 (m-80) REVERT: 3 51 TRP cc_start: 0.0039 (OUTLIER) cc_final: -0.0616 (t60) REVERT: 3 293 MET cc_start: -0.4994 (tpt) cc_final: -0.5263 (tpt) REVERT: 4 385 MET cc_start: 0.0395 (tmm) cc_final: -0.1405 (tpt) REVERT: 4 499 MET cc_start: 0.1795 (mtp) cc_final: 0.0197 (tpt) REVERT: A 60 MET cc_start: 0.6474 (ttt) cc_final: 0.5518 (ttt) REVERT: A 107 MET cc_start: 0.8446 (mmm) cc_final: 0.8213 (mmm) REVERT: A 116 MET cc_start: 0.6923 (tmm) cc_final: 0.6475 (mtp) REVERT: A 680 MET cc_start: 0.8883 (mmt) cc_final: 0.8343 (mmm) REVERT: A 912 MET cc_start: 0.8380 (tpp) cc_final: 0.7943 (mmt) REVERT: A 1317 MET cc_start: 0.8501 (tmm) cc_final: 0.8233 (tmm) REVERT: B 243 MET cc_start: 0.8579 (tpp) cc_final: 0.8102 (tpp) REVERT: B 338 MET cc_start: 0.9394 (ttt) cc_final: 0.9108 (mtt) REVERT: B 431 MET cc_start: 0.8018 (tmm) cc_final: 0.7734 (tmm) REVERT: B 607 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8938 (p) REVERT: B 791 MET cc_start: 0.8386 (mmm) cc_final: 0.8153 (mmt) REVERT: B 870 MET cc_start: 0.8812 (ppp) cc_final: 0.8370 (ppp) REVERT: B 929 MET cc_start: 0.8456 (ttt) cc_final: 0.8019 (ttm) REVERT: B 1062 MET cc_start: 0.8637 (mpp) cc_final: 0.8008 (mpp) REVERT: E 72 MET cc_start: 0.7992 (tpt) cc_final: 0.7764 (tpt) REVERT: E 110 MET cc_start: 0.8300 (tpp) cc_final: 0.7941 (tpp) REVERT: G 157 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: H 37 MET cc_start: 0.9166 (mmm) cc_final: 0.8714 (mmm) REVERT: K 29 MET cc_start: 0.8153 (tmm) cc_final: 0.7612 (tmm) REVERT: K 104 MET cc_start: 0.8871 (mmm) cc_final: 0.8570 (mmm) REVERT: L 25 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7976 (mm-30) REVERT: M 248 MET cc_start: 0.8763 (ptm) cc_final: 0.8426 (ptt) REVERT: M 270 MET cc_start: 0.8453 (mmm) cc_final: 0.7485 (tpp) REVERT: M 292 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7406 (tmm) REVERT: O 118 MET cc_start: 0.7327 (mmm) cc_final: 0.7110 (mmm) REVERT: O 333 MET cc_start: 0.7267 (tmm) cc_final: 0.6178 (tmm) REVERT: O 404 MET cc_start: 0.6885 (tpt) cc_final: 0.6282 (tpt) REVERT: O 531 MET cc_start: 0.8245 (tpp) cc_final: 0.7907 (tpp) REVERT: P 310 MET cc_start: 0.8785 (mmt) cc_final: 0.8496 (mmm) REVERT: U 202 MET cc_start: 0.9259 (mmm) cc_final: 0.8484 (tmm) REVERT: W 285 ARG cc_start: 0.6619 (tpm170) cc_final: 0.5708 (tpt90) outliers start: 50 outliers final: 39 residues processed: 265 average time/residue: 0.5181 time to fit residues: 243.6921 Evaluate side-chains 261 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 4.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain 4 residue 253 LEU Chi-restraints excluded: chain 4 residue 438 GLN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain M residue 149 HIS Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain P residue 302 ILE Chi-restraints excluded: chain W residue 282 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 605 optimal weight: 10.0000 chunk 399 optimal weight: 6.9990 chunk 642 optimal weight: 5.9990 chunk 392 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 446 optimal weight: 1.9990 chunk 674 optimal weight: 9.9990 chunk 620 optimal weight: 8.9990 chunk 537 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 414 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 162 ASN ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 GLN O 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 58585 Z= 0.350 Angle : 0.787 27.351 79791 Z= 0.370 Chirality : 0.079 2.089 8889 Planarity : 0.004 0.050 9690 Dihedral : 15.776 155.658 9190 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 0.93 % Allowed : 12.47 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.10), residues: 6657 helix: 1.08 (0.10), residues: 2734 sheet: -0.69 (0.18), residues: 728 loop : -0.81 (0.11), residues: 3195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 3 51 HIS 0.010 0.001 HIS A 415 PHE 0.020 0.002 PHE Q 38 TYR 0.020 0.002 TYR 3 247 ARG 0.029 0.001 ARG Q 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 4.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 143 LEU cc_start: 0.5391 (OUTLIER) cc_final: 0.5095 (pp) REVERT: 3 47 PHE cc_start: -0.1550 (OUTLIER) cc_final: -0.2451 (m-80) REVERT: 3 51 TRP cc_start: -0.0186 (OUTLIER) cc_final: -0.1048 (t60) REVERT: 3 293 MET cc_start: -0.4788 (tpt) cc_final: -0.5010 (tpt) REVERT: 4 385 MET cc_start: 0.0583 (tmm) cc_final: -0.1307 (tpt) REVERT: A 60 MET cc_start: 0.6350 (ttt) cc_final: 0.5444 (ttt) REVERT: A 116 MET cc_start: 0.7011 (tmm) cc_final: 0.6754 (mtp) REVERT: A 680 MET cc_start: 0.8943 (mmt) cc_final: 0.8443 (mmm) REVERT: A 912 MET cc_start: 0.8399 (tpp) cc_final: 0.7858 (tpp) REVERT: A 1317 MET cc_start: 0.8455 (tmm) cc_final: 0.8168 (tmm) REVERT: B 139 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8308 (ttt) REVERT: B 243 MET cc_start: 0.8630 (tpp) cc_final: 0.8199 (tpp) REVERT: B 431 MET cc_start: 0.8186 (tmm) cc_final: 0.7800 (tmm) REVERT: B 607 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8975 (p) REVERT: B 791 MET cc_start: 0.8462 (mmm) cc_final: 0.8227 (mmt) REVERT: B 870 MET cc_start: 0.8822 (ppp) cc_final: 0.8404 (ppp) REVERT: B 1062 MET cc_start: 0.8704 (mpp) cc_final: 0.8145 (mpp) REVERT: E 72 MET cc_start: 0.8355 (tpt) cc_final: 0.8123 (tpt) REVERT: E 110 MET cc_start: 0.8252 (tpp) cc_final: 0.8045 (tpp) REVERT: E 121 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7765 (pmm) REVERT: G 124 GLU cc_start: 0.4497 (OUTLIER) cc_final: 0.3436 (pm20) REVERT: G 157 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7498 (m-10) REVERT: H 37 MET cc_start: 0.9215 (mmm) cc_final: 0.8727 (mmm) REVERT: K 29 MET cc_start: 0.8131 (tmm) cc_final: 0.7593 (tmm) REVERT: K 104 MET cc_start: 0.8910 (mmm) cc_final: 0.8586 (mmm) REVERT: L 15 MET cc_start: 0.8432 (tpp) cc_final: 0.8200 (tpp) REVERT: L 25 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8012 (mm-30) REVERT: L 38 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7191 (tm-30) REVERT: M 270 MET cc_start: 0.8493 (mmm) cc_final: 0.7565 (tpp) REVERT: M 292 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7522 (tmm) REVERT: M 319 MET cc_start: 0.7806 (tmm) cc_final: 0.7511 (tmm) REVERT: O 118 MET cc_start: 0.7432 (mmm) cc_final: 0.7220 (mmm) REVERT: O 333 MET cc_start: 0.7264 (tmm) cc_final: 0.6205 (tmm) REVERT: O 404 MET cc_start: 0.6961 (tpt) cc_final: 0.6418 (tpt) REVERT: O 531 MET cc_start: 0.8275 (tpp) cc_final: 0.7947 (tpp) REVERT: P 310 MET cc_start: 0.8844 (mmt) cc_final: 0.8547 (mmm) outliers start: 55 outliers final: 40 residues processed: 266 average time/residue: 0.5430 time to fit residues: 253.3582 Evaluate side-chains 266 residues out of total 5937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 4.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain 4 residue 253 LEU Chi-restraints excluded: chain 4 residue 438 GLN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain M residue 149 HIS Chi-restraints excluded: chain M residue 292 MET Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain P residue 302 ILE Chi-restraints excluded: chain Q residue 68 MET Chi-restraints excluded: chain W residue 282 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 329 optimal weight: 8.9990 chunk 426 optimal weight: 8.9990 chunk 572 optimal weight: 40.0000 chunk 164 optimal weight: 0.7980 chunk 495 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 537 optimal weight: 10.0000 chunk 225 optimal weight: 0.6980 chunk 552 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 overall best weight: 5.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 260 ASN 4 171 GLN ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 417 GLN O 534 GLN ** P 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.058187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.040352 restraints weight = 621621.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.041065 restraints weight = 303001.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.041037 restraints weight = 181888.934| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 58585 Z= 0.317 Angle : 0.757 27.417 79791 Z= 0.355 Chirality : 0.079 2.091 8889 Planarity : 0.004 0.050 9690 Dihedral : 15.854 156.022 9190 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 0.88 % Allowed : 12.61 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.10), residues: 6657 helix: 1.08 (0.10), residues: 2722 sheet: -0.66 (0.19), residues: 729 loop : -0.83 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 3 51 HIS 0.009 0.001 HIS P 214 PHE 0.019 0.002 PHE A 197 TYR 0.019 0.001 TYR 3 247 ARG 0.006 0.000 ARG W 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7447.05 seconds wall clock time: 135 minutes 27.31 seconds (8127.31 seconds total)