Starting phenix.real_space_refine on Fri Sep 27 05:01:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/09_2024/8i9u_35284.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/09_2024/8i9u_35284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/09_2024/8i9u_35284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/09_2024/8i9u_35284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/09_2024/8i9u_35284.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9u_35284/09_2024/8i9u_35284.cif" } resolution = 3.1 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= 0.004 sd= 0.165 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: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 402 5.16 5 C 40830 2.51 5 N 11326 2.21 5 O 12563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 196 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 65141 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3956 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 12, 'TRANS': 508} Chain: "B" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3755 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 8, 'TRANS': 490} Chain: "C" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3940 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 16, 'TRANS': 490} Chain: "D" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3880 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 14, 'TRANS': 499} Chain: "E" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3940 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 17, 'TRANS': 495} Chain: "F" Number of atoms: 3958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3958 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 13, 'TRANS': 502} Chain: "G" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3936 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 14, 'TRANS': 497} Chain: "H" Number of atoms: 3942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3942 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 13, 'TRANS': 503} Chain: "I" Number of atoms: 3956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3956 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 12, 'TRANS': 508} Chain: "J" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3755 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 8, 'TRANS': 490} Chain: "K" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3940 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 16, 'TRANS': 490} Chain: "L" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3880 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 14, 'TRANS': 499} Chain: "M" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3940 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 17, 'TRANS': 495} Chain: "N" Number of atoms: 3958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3958 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 13, 'TRANS': 502} Chain: "O" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3936 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 14, 'TRANS': 497} Chain: "P" Number of atoms: 3942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3942 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 13, 'TRANS': 503} Chain: "Q" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1133 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "R" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1124 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 30.75, per 1000 atoms: 0.47 Number of scatterers: 65141 At special positions: 0 Unit cell: (187.58, 200.01, 195.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 402 16.00 P 20 15.00 O 12563 8.00 N 11326 7.00 C 40830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.28 Conformation dependent library (CDL) restraints added in 6.5 seconds 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15814 Finding SS restraints... Secondary structure from input PDB file: 294 helices and 77 sheets defined 49.5% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'A' and resid 14 through 30 removed outlier: 3.949A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.740A pdb=" N SER A 35 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 36 " --> pdb=" O LYS A 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 36' Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 69 through 86 removed outlier: 3.835A pdb=" N GLU A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 110 removed outlier: 3.802A pdb=" N ILE A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 133 removed outlier: 3.604A pdb=" N VAL A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.719A pdb=" N ILE A 149 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 178 removed outlier: 3.816A pdb=" N PHE A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 removed outlier: 3.657A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 262 through 280 removed outlier: 4.550A pdb=" N GLU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 4.025A pdb=" N LEU A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.644A pdb=" N CYS A 385 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 402 removed outlier: 3.995A pdb=" N SER A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 3.598A pdb=" N GLY A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 444 Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.906A pdb=" N ASN A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.710A pdb=" N GLU A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.598A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.902A pdb=" N LEU B 43 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 73 removed outlier: 3.741A pdb=" N ILE B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 99 through 119 Processing helix chain 'B' and resid 122 through 144 removed outlier: 3.578A pdb=" N ILE B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.500A pdb=" N PHE B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 removed outlier: 3.585A pdb=" N ARG B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 285 removed outlier: 3.976A pdb=" N GLU B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'B' and resid 382 through 400 Processing helix chain 'B' and resid 412 through 425 Processing helix chain 'B' and resid 432 through 444 Processing helix chain 'B' and resid 445 through 455 removed outlier: 3.599A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 removed outlier: 3.560A pdb=" N LEU B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 4.008A pdb=" N LEU B 491 " --> pdb=" O ASP B 487 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 492' Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.761A pdb=" N ARG B 501 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 74 through 91 Processing helix chain 'C' and resid 96 through 110 removed outlier: 3.892A pdb=" N ILE C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 139 removed outlier: 4.023A pdb=" N SER C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 161 Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.550A pdb=" N ALA C 172 " --> pdb=" O TRP C 168 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 283 removed outlier: 3.844A pdb=" N LEU C 268 " --> pdb=" O PHE C 264 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN C 269 " --> pdb=" O THR C 265 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE C 283 " --> pdb=" O CYS C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 307 Processing helix chain 'C' and resid 316 through 326 Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.728A pdb=" N LEU C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 430 removed outlier: 3.538A pdb=" N ALA C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 442 removed outlier: 3.653A pdb=" N TYR C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 456 Processing helix chain 'C' and resid 460 through 470 Processing helix chain 'C' and resid 490 through 494 removed outlier: 3.572A pdb=" N GLY C 494 " --> pdb=" O MET C 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 490 through 494' Processing helix chain 'C' and resid 499 through 518 Processing helix chain 'D' and resid 27 through 48 removed outlier: 4.217A pdb=" N ILE D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.547A pdb=" N ILE D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 107 through 127 removed outlier: 3.831A pdb=" N ILE D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 176 through 191 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 270 through 281 Processing helix chain 'D' and resid 282 through 291 removed outlier: 3.717A pdb=" N LEU D 286 " --> pdb=" O TYR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 318 removed outlier: 3.790A pdb=" N LEU D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 Processing helix chain 'D' and resid 397 through 418 removed outlier: 3.965A pdb=" N LYS D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 443 Processing helix chain 'D' and resid 446 through 456 removed outlier: 4.353A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 470 Processing helix chain 'D' and resid 472 through 488 Processing helix chain 'D' and resid 512 through 532 removed outlier: 4.042A pdb=" N ALA D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 51 removed outlier: 4.025A pdb=" N THR E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 80 removed outlier: 3.597A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 98 removed outlier: 3.601A pdb=" N GLN E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 125 removed outlier: 3.662A pdb=" N VAL E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 removed outlier: 3.949A pdb=" N ILE E 133 " --> pdb=" O HIS E 129 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN E 139 " --> pdb=" O ASP E 135 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 173 Processing helix chain 'E' and resid 183 through 198 removed outlier: 4.169A pdb=" N VAL E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 272 through 296 Processing helix chain 'E' and resid 307 through 317 removed outlier: 3.628A pdb=" N ASN E 311 " --> pdb=" O ASP E 307 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN E 317 " --> pdb=" O LEU E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 392 through 415 removed outlier: 3.557A pdb=" N GLU E 396 " --> pdb=" O LYS E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 438 removed outlier: 4.045A pdb=" N ILE E 427 " --> pdb=" O GLY E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 454 removed outlier: 3.661A pdb=" N ALA E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 465 Processing helix chain 'E' and resid 469 through 484 removed outlier: 3.604A pdb=" N GLU E 484 " --> pdb=" O ARG E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 530 Processing helix chain 'F' and resid 17 through 34 Processing helix chain 'F' and resid 60 through 66 Processing helix chain 'F' and resid 71 through 84 removed outlier: 3.608A pdb=" N GLN F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 113 Processing helix chain 'F' and resid 115 through 138 Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 166 through 180 removed outlier: 4.197A pdb=" N GLU F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 282 removed outlier: 4.340A pdb=" N ARG F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 309 removed outlier: 3.640A pdb=" N ALA F 304 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 328 Processing helix chain 'F' and resid 382 through 404 removed outlier: 3.859A pdb=" N GLN F 386 " --> pdb=" O HIS F 382 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP F 404 " --> pdb=" O ASN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 424 Processing helix chain 'F' and resid 430 through 443 removed outlier: 3.798A pdb=" N GLY F 436 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA F 439 " --> pdb=" O LEU F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.734A pdb=" N LYS F 449 " --> pdb=" O LEU F 445 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY F 456 " --> pdb=" O ALA F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 473 Processing helix chain 'F' and resid 498 through 514 removed outlier: 3.807A pdb=" N LYS F 502 " --> pdb=" O TYR F 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 36 removed outlier: 3.519A pdb=" N VAL G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 68 Processing helix chain 'G' and resid 73 through 90 Processing helix chain 'G' and resid 94 through 109 removed outlier: 3.688A pdb=" N THR G 98 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 120 through 140 removed outlier: 4.061A pdb=" N ALA G 124 " --> pdb=" O ILE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 164 removed outlier: 3.763A pdb=" N LEU G 155 " --> pdb=" O GLN G 151 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU G 156 " --> pdb=" O ARG G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 182 removed outlier: 3.561A pdb=" N ALA G 173 " --> pdb=" O SER G 169 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 removed outlier: 3.791A pdb=" N MET G 227 " --> pdb=" O GLY G 224 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN G 228 " --> pdb=" O PHE G 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 224 through 228' Processing helix chain 'G' and resid 260 through 283 removed outlier: 3.775A pdb=" N GLN G 264 " --> pdb=" O VAL G 260 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE G 273 " --> pdb=" O ALA G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 306 removed outlier: 4.008A pdb=" N GLN G 301 " --> pdb=" O ASP G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 327 Processing helix chain 'G' and resid 386 through 402 removed outlier: 3.777A pdb=" N HIS G 390 " --> pdb=" O GLU G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 424 removed outlier: 3.626A pdb=" N LEU G 416 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 427 No H-bonds generated for 'chain 'G' and resid 425 through 427' Processing helix chain 'G' and resid 430 through 441 removed outlier: 4.197A pdb=" N LEU G 434 " --> pdb=" O LYS G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 453 Processing helix chain 'G' and resid 457 through 468 removed outlier: 3.904A pdb=" N ASN G 462 " --> pdb=" O THR G 458 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS G 463 " --> pdb=" O ASN G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 516 removed outlier: 3.504A pdb=" N ASN G 501 " --> pdb=" O MET G 497 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL G 516 " --> pdb=" O LEU G 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 42 removed outlier: 4.214A pdb=" N CYS H 36 " --> pdb=" O ASN H 32 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR H 42 " --> pdb=" O GLU H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 76 removed outlier: 3.892A pdb=" N ILE H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 97 removed outlier: 4.237A pdb=" N ILE H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA H 89 " --> pdb=" O MET H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.693A pdb=" N LEU H 105 " --> pdb=" O THR H 101 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 143 removed outlier: 3.722A pdb=" N VAL H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 169 removed outlier: 4.064A pdb=" N LEU H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 189 removed outlier: 3.635A pdb=" N ALA H 180 " --> pdb=" O GLU H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 removed outlier: 4.026A pdb=" N SER H 214 " --> pdb=" O GLY H 211 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER H 215 " --> pdb=" O ILE H 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 211 through 215' Processing helix chain 'H' and resid 261 through 286 removed outlier: 3.589A pdb=" N LEU H 265 " --> pdb=" O THR H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 308 Processing helix chain 'H' and resid 317 through 328 Processing helix chain 'H' and resid 384 through 400 removed outlier: 3.868A pdb=" N ILE H 388 " --> pdb=" O LEU H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 428 removed outlier: 3.799A pdb=" N ILE H 417 " --> pdb=" O GLY H 413 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU H 418 " --> pdb=" O ALA H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 444 removed outlier: 3.695A pdb=" N ILE H 438 " --> pdb=" O GLU H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 455 removed outlier: 3.557A pdb=" N ALA H 451 " --> pdb=" O ALA H 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 470 Processing helix chain 'H' and resid 481 through 485 removed outlier: 3.598A pdb=" N GLU H 485 " --> pdb=" O ILE H 482 " (cutoff:3.500A) Processing helix chain 'H' and resid 500 through 521 removed outlier: 3.658A pdb=" N LYS H 504 " --> pdb=" O THR H 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 29 removed outlier: 3.921A pdb=" N ARG I 18 " --> pdb=" O GLY I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 36 removed outlier: 3.749A pdb=" N SER I 35 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU I 36 " --> pdb=" O LYS I 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 32 through 36' Processing helix chain 'I' and resid 59 through 64 Processing helix chain 'I' and resid 69 through 86 removed outlier: 3.834A pdb=" N GLU I 85 " --> pdb=" O LEU I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 110 removed outlier: 3.809A pdb=" N ILE I 95 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU I 107 " --> pdb=" O ASN I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 133 removed outlier: 3.612A pdb=" N VAL I 117 " --> pdb=" O HIS I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 149 removed outlier: 3.706A pdb=" N ILE I 149 " --> pdb=" O ASP I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 179 removed outlier: 3.778A pdb=" N PHE I 168 " --> pdb=" O ASN I 164 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE I 179 " --> pdb=" O ALA I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 280 removed outlier: 4.696A pdb=" N GLU I 273 " --> pdb=" O ASP I 269 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG I 274 " --> pdb=" O ILE I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 301 removed outlier: 4.341A pdb=" N LEU I 297 " --> pdb=" O ASP I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 323 Processing helix chain 'I' and resid 381 through 386 removed outlier: 3.684A pdb=" N CYS I 385 " --> pdb=" O ASP I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 402 removed outlier: 4.033A pdb=" N SER I 391 " --> pdb=" O GLU I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 431 removed outlier: 3.605A pdb=" N GLY I 431 " --> pdb=" O ALA I 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 444 Processing helix chain 'I' and resid 447 through 456 Processing helix chain 'I' and resid 459 through 477 removed outlier: 3.722A pdb=" N GLU I 473 " --> pdb=" O ALA I 469 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA I 474 " --> pdb=" O PHE I 470 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN I 475 " --> pdb=" O HIS I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 527 Processing helix chain 'J' and resid 26 through 35 removed outlier: 3.592A pdb=" N ILE J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 43 removed outlier: 3.988A pdb=" N LEU J 43 " --> pdb=" O LYS J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 73 removed outlier: 3.674A pdb=" N ILE J 70 " --> pdb=" O ASP J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 96 Processing helix chain 'J' and resid 98 through 119 Processing helix chain 'J' and resid 122 through 144 removed outlier: 3.570A pdb=" N ILE J 126 " --> pdb=" O HIS J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 167 removed outlier: 3.851A pdb=" N PHE J 155 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 189 removed outlier: 3.576A pdb=" N ARG J 189 " --> pdb=" O GLU J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 285 removed outlier: 3.993A pdb=" N GLU J 266 " --> pdb=" O ALA J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 308 Processing helix chain 'J' and resid 318 through 327 Processing helix chain 'J' and resid 382 through 400 Processing helix chain 'J' and resid 412 through 425 Processing helix chain 'J' and resid 432 through 444 Processing helix chain 'J' and resid 445 through 455 removed outlier: 3.593A pdb=" N ALA J 454 " --> pdb=" O ILE J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 472 removed outlier: 3.558A pdb=" N LEU J 461 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY J 472 " --> pdb=" O ALA J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 492 removed outlier: 4.008A pdb=" N LEU J 491 " --> pdb=" O ASP J 487 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY J 492 " --> pdb=" O MET J 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 487 through 492' Processing helix chain 'J' and resid 497 through 516 removed outlier: 3.775A pdb=" N ARG J 501 " --> pdb=" O PHE J 497 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 35 Processing helix chain 'K' and resid 62 through 70 removed outlier: 3.525A pdb=" N ILE K 66 " --> pdb=" O ASP K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 91 Processing helix chain 'K' and resid 96 through 110 removed outlier: 3.877A pdb=" N ILE K 100 " --> pdb=" O THR K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 139 removed outlier: 4.023A pdb=" N SER K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 161 Processing helix chain 'K' and resid 168 through 184 removed outlier: 3.553A pdb=" N ALA K 172 " --> pdb=" O TRP K 168 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN K 184 " --> pdb=" O VAL K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 280 removed outlier: 3.813A pdb=" N THR K 265 " --> pdb=" O GLU K 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU K 268 " --> pdb=" O PHE K 264 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU K 278 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU K 280 " --> pdb=" O GLN K 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 307 Processing helix chain 'K' and resid 316 through 326 Processing helix chain 'K' and resid 380 through 403 removed outlier: 3.728A pdb=" N LEU K 384 " --> pdb=" O SER K 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 430 removed outlier: 3.537A pdb=" N ALA K 417 " --> pdb=" O ALA K 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 442 removed outlier: 3.653A pdb=" N TYR K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 446 through 456 Processing helix chain 'K' and resid 460 through 470 Processing helix chain 'K' and resid 490 through 494 removed outlier: 3.535A pdb=" N GLY K 494 " --> pdb=" O MET K 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 490 through 494' Processing helix chain 'K' and resid 499 through 518 Processing helix chain 'L' and resid 27 through 48 removed outlier: 4.214A pdb=" N ILE L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 81 removed outlier: 3.651A pdb=" N ILE L 77 " --> pdb=" O ASP L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 102 Processing helix chain 'L' and resid 107 through 127 removed outlier: 3.833A pdb=" N ILE L 111 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS L 122 " --> pdb=" O ASP L 118 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY L 127 " --> pdb=" O LEU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 152 Processing helix chain 'L' and resid 160 through 171 Processing helix chain 'L' and resid 176 through 181 removed outlier: 3.625A pdb=" N SER L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 191 Processing helix chain 'L' and resid 270 through 281 Processing helix chain 'L' and resid 282 through 291 removed outlier: 3.725A pdb=" N LEU L 286 " --> pdb=" O TYR L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 317 removed outlier: 3.896A pdb=" N LEU L 314 " --> pdb=" O SER L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 340 Processing helix chain 'L' and resid 397 through 418 removed outlier: 3.963A pdb=" N LYS L 418 " --> pdb=" O CYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 443 Processing helix chain 'L' and resid 445 through 456 removed outlier: 4.261A pdb=" N TYR L 449 " --> pdb=" O GLY L 445 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N CYS L 450 " --> pdb=" O MET L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 470 Processing helix chain 'L' and resid 472 through 488 Processing helix chain 'L' and resid 512 through 532 removed outlier: 4.043A pdb=" N ALA L 518 " --> pdb=" O VAL L 514 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 51 removed outlier: 4.019A pdb=" N THR M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR M 50 " --> pdb=" O ASN M 46 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER M 51 " --> pdb=" O THR M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 80 removed outlier: 3.627A pdb=" N MET M 80 " --> pdb=" O THR M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 98 removed outlier: 3.532A pdb=" N LYS M 89 " --> pdb=" O HIS M 85 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU M 90 " --> pdb=" O GLN M 86 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN M 98 " --> pdb=" O LEU M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.645A pdb=" N VAL M 111 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP M 125 " --> pdb=" O GLU M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 151 removed outlier: 3.944A pdb=" N ILE M 133 " --> pdb=" O HIS M 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS M 150 " --> pdb=" O GLU M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 173 Processing helix chain 'M' and resid 183 through 198 removed outlier: 4.169A pdb=" N VAL M 196 " --> pdb=" O ALA M 192 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP M 198 " --> pdb=" O LEU M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 201 No H-bonds generated for 'chain 'M' and resid 199 through 201' Processing helix chain 'M' and resid 271 through 296 removed outlier: 4.316A pdb=" N LYS M 275 " --> pdb=" O VAL M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 318 removed outlier: 3.846A pdb=" N ASN M 311 " --> pdb=" O ASP M 307 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN M 318 " --> pdb=" O LEU M 314 " (cutoff:3.500A) Processing helix chain 'M' and resid 329 through 334 Processing helix chain 'M' and resid 392 through 415 removed outlier: 3.559A pdb=" N GLU M 396 " --> pdb=" O LYS M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 423 through 436 removed outlier: 3.875A pdb=" N ILE M 427 " --> pdb=" O GLY M 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 443 through 453 removed outlier: 3.706A pdb=" N ASP M 453 " --> pdb=" O ARG M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 454 through 456 No H-bonds generated for 'chain 'M' and resid 454 through 456' Processing helix chain 'M' and resid 457 through 465 Processing helix chain 'M' and resid 469 through 484 removed outlier: 3.645A pdb=" N GLU M 484 " --> pdb=" O ARG M 480 " (cutoff:3.500A) Processing helix chain 'M' and resid 510 through 530 Processing helix chain 'N' and resid 17 through 34 Processing helix chain 'N' and resid 60 through 66 Processing helix chain 'N' and resid 71 through 83 Processing helix chain 'N' and resid 95 through 113 Processing helix chain 'N' and resid 115 through 138 Processing helix chain 'N' and resid 145 through 158 Processing helix chain 'N' and resid 166 through 180 Processing helix chain 'N' and resid 252 through 282 removed outlier: 4.345A pdb=" N ARG N 256 " --> pdb=" O SER N 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 307 removed outlier: 3.632A pdb=" N ALA N 304 " --> pdb=" O PHE N 300 " (cutoff:3.500A) Processing helix chain 'N' and resid 317 through 328 Processing helix chain 'N' and resid 340 through 344 removed outlier: 3.990A pdb=" N CYS N 343 " --> pdb=" O SER N 340 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 340 through 344' Processing helix chain 'N' and resid 382 through 404 removed outlier: 3.859A pdb=" N GLN N 386 " --> pdb=" O HIS N 382 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP N 404 " --> pdb=" O ASN N 400 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 424 Processing helix chain 'N' and resid 430 through 443 removed outlier: 3.800A pdb=" N GLY N 436 " --> pdb=" O ARG N 432 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA N 439 " --> pdb=" O LEU N 435 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 456 removed outlier: 3.810A pdb=" N LYS N 449 " --> pdb=" O LEU N 445 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL N 450 " --> pdb=" O ILE N 446 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY N 456 " --> pdb=" O ALA N 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 473 Processing helix chain 'N' and resid 498 through 514 removed outlier: 3.797A pdb=" N LYS N 502 " --> pdb=" O TYR N 498 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 36 removed outlier: 3.519A pdb=" N VAL O 31 " --> pdb=" O SER O 27 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL O 36 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 68 Processing helix chain 'O' and resid 73 through 90 Processing helix chain 'O' and resid 94 through 109 removed outlier: 3.691A pdb=" N THR O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 119 No H-bonds generated for 'chain 'O' and resid 117 through 119' Processing helix chain 'O' and resid 120 through 140 removed outlier: 4.066A pdb=" N ALA O 124 " --> pdb=" O ILE O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 164 removed outlier: 3.978A pdb=" N LEU O 154 " --> pdb=" O GLU O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 182 Processing helix chain 'O' and resid 224 through 228 removed outlier: 3.760A pdb=" N MET O 227 " --> pdb=" O GLY O 224 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN O 228 " --> pdb=" O PHE O 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 224 through 228' Processing helix chain 'O' and resid 260 through 283 removed outlier: 3.822A pdb=" N ILE O 273 " --> pdb=" O ALA O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 306 removed outlier: 4.012A pdb=" N GLN O 301 " --> pdb=" O ASP O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 315 through 327 removed outlier: 3.557A pdb=" N LEU O 319 " --> pdb=" O PRO O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 386 through 402 removed outlier: 3.774A pdb=" N HIS O 390 " --> pdb=" O GLU O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 412 through 424 removed outlier: 3.625A pdb=" N LEU O 416 " --> pdb=" O ILE O 412 " (cutoff:3.500A) Processing helix chain 'O' and resid 425 through 427 No H-bonds generated for 'chain 'O' and resid 425 through 427' Processing helix chain 'O' and resid 430 through 441 removed outlier: 4.132A pdb=" N LEU O 434 " --> pdb=" O LYS O 430 " (cutoff:3.500A) Processing helix chain 'O' and resid 444 through 453 removed outlier: 3.536A pdb=" N ALA O 453 " --> pdb=" O LEU O 449 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 468 removed outlier: 3.882A pdb=" N ASN O 462 " --> pdb=" O THR O 458 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS O 463 " --> pdb=" O ASN O 459 " (cutoff:3.500A) Processing helix chain 'O' and resid 497 through 516 removed outlier: 3.511A pdb=" N ASN O 501 " --> pdb=" O MET O 497 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL O 516 " --> pdb=" O LEU O 512 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 29 removed outlier: 4.097A pdb=" N VAL P 29 " --> pdb=" O GLU P 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 26 through 29' Processing helix chain 'P' and resid 30 through 42 removed outlier: 3.743A pdb=" N ALA P 35 " --> pdb=" O ARG P 31 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N CYS P 36 " --> pdb=" O ASN P 32 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR P 42 " --> pdb=" O GLU P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 76 removed outlier: 3.889A pdb=" N ILE P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 97 removed outlier: 4.244A pdb=" N ILE P 86 " --> pdb=" O ALA P 82 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL P 87 " --> pdb=" O ALA P 83 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET P 88 " --> pdb=" O LYS P 84 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA P 89 " --> pdb=" O MET P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 122 removed outlier: 3.670A pdb=" N LEU P 105 " --> pdb=" O THR P 101 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU P 117 " --> pdb=" O GLU P 113 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU P 118 " --> pdb=" O LEU P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 143 removed outlier: 3.721A pdb=" N VAL P 128 " --> pdb=" O SER P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 169 removed outlier: 4.064A pdb=" N LEU P 163 " --> pdb=" O GLU P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 189 removed outlier: 3.635A pdb=" N ALA P 180 " --> pdb=" O GLU P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 215 removed outlier: 4.025A pdb=" N SER P 214 " --> pdb=" O GLY P 211 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER P 215 " --> pdb=" O ILE P 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 211 through 215' Processing helix chain 'P' and resid 261 through 286 removed outlier: 3.588A pdb=" N LEU P 265 " --> pdb=" O THR P 261 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 308 Processing helix chain 'P' and resid 317 through 328 Processing helix chain 'P' and resid 384 through 400 removed outlier: 3.867A pdb=" N ILE P 388 " --> pdb=" O LEU P 384 " (cutoff:3.500A) Processing helix chain 'P' and resid 413 through 428 removed outlier: 3.800A pdb=" N ILE P 417 " --> pdb=" O GLY P 413 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU P 418 " --> pdb=" O ALA P 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 434 through 444 removed outlier: 3.647A pdb=" N ILE P 438 " --> pdb=" O GLU P 434 " (cutoff:3.500A) Processing helix chain 'P' and resid 447 through 455 removed outlier: 3.555A pdb=" N ALA P 451 " --> pdb=" O ALA P 447 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 470 Processing helix chain 'P' and resid 481 through 485 removed outlier: 3.601A pdb=" N GLU P 485 " --> pdb=" O ILE P 482 " (cutoff:3.500A) Processing helix chain 'P' and resid 500 through 521 removed outlier: 3.656A pdb=" N LYS P 504 " --> pdb=" O THR P 500 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 109 removed outlier: 3.605A pdb=" N VAL Q 103 " --> pdb=" O GLY Q 99 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL Q 106 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 141 removed outlier: 3.737A pdb=" N ALA Q 128 " --> pdb=" O ILE Q 124 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY Q 136 " --> pdb=" O GLN Q 132 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG Q 139 " --> pdb=" O SER Q 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 192 through 202 Processing helix chain 'Q' and resid 218 through 232 removed outlier: 3.633A pdb=" N SER Q 222 " --> pdb=" O ASP Q 218 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER Q 223 " --> pdb=" O VAL Q 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 109 removed outlier: 3.719A pdb=" N TYR R 102 " --> pdb=" O SER R 98 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR R 107 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA R 109 " --> pdb=" O GLU R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 139 removed outlier: 3.911A pdb=" N ALA R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG R 139 " --> pdb=" O SER R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 184 removed outlier: 3.597A pdb=" N VAL R 183 " --> pdb=" O GLY R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 199 removed outlier: 3.524A pdb=" N SER R 199 " --> pdb=" O GLU R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 232 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 55 removed outlier: 7.399A pdb=" N ASP A 42 " --> pdb=" O ASP C 521 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N VAL C 523 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET A 44 " --> pdb=" O VAL C 523 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 197 through 198 removed outlier: 4.418A pdb=" N ILE A 211 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 287 removed outlier: 7.127A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.681A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 409 Processing sheet with id=AA7, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 529 removed outlier: 5.693A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 50 through 51 removed outlier: 3.838A pdb=" N LYS B 50 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AB2, first strand: chain 'B' and resid 353 through 354 removed outlier: 3.907A pdb=" N ILE B 354 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 60 removed outlier: 7.826A pdb=" N MET C 47 " --> pdb=" O ASP F 519 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE F 521 " --> pdb=" O MET C 47 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 49 " --> pdb=" O ILE F 521 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG F 523 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU C 51 " --> pdb=" O ARG F 523 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 142 through 143 removed outlier: 3.808A pdb=" N ILE C 142 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 407 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 213 through 215 Processing sheet with id=AB7, first strand: chain 'C' and resid 478 through 480 Processing sheet with id=AB8, first strand: chain 'D' and resid 153 through 154 removed outlier: 4.004A pdb=" N ARG D 153 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 421 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 222 through 224 removed outlier: 4.277A pdb=" N GLU D 222 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 389 " --> pdb=" O GLU D 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 227 through 229 Processing sheet with id=AC2, first strand: chain 'E' and resid 59 through 62 Processing sheet with id=AC3, first strand: chain 'E' and resid 210 through 215 removed outlier: 3.764A pdb=" N ILE E 385 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU E 212 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE E 387 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS E 214 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY E 389 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 229 through 231 Processing sheet with id=AC5, first strand: chain 'E' and resid 248 through 250 removed outlier: 6.783A pdb=" N ALA E 249 " --> pdb=" O ILE E 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 418 through 419 Processing sheet with id=AC7, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'F' and resid 191 through 192 removed outlier: 7.264A pdb=" N GLU F 192 " --> pdb=" O LEU F 374 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE F 376 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 210 through 212 Processing sheet with id=AD1, first strand: chain 'F' and resid 310 through 313 removed outlier: 6.329A pdb=" N PHE F 289 " --> pdb=" O VAL F 311 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU F 313 " --> pdb=" O PHE F 289 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL F 291 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR F 229 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE F 292 " --> pdb=" O TYR F 229 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU F 231 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 477 through 478 removed outlier: 3.819A pdb=" N MET F 487 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 47 through 50 Processing sheet with id=AD4, first strand: chain 'G' and resid 141 through 142 removed outlier: 3.933A pdb=" N VAL G 141 " --> pdb=" O VAL G 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL G 405 " --> pdb=" O VAL G 141 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 209 through 211 Processing sheet with id=AD6, first strand: chain 'G' and resid 214 through 216 removed outlier: 3.547A pdb=" N GLU G 356 " --> pdb=" O ILE G 353 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=AD8, first strand: chain 'G' and resid 519 through 520 removed outlier: 3.797A pdb=" N ILE G 520 " --> pdb=" O MET H 55 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE H 64 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 202 through 208 removed outlier: 3.514A pdb=" N ILE H 375 " --> pdb=" O ARG H 203 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS H 205 " --> pdb=" O ILE H 375 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU H 377 " --> pdb=" O CYS H 205 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY H 379 " --> pdb=" O ILE H 207 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 223 through 224 removed outlier: 4.132A pdb=" N PHE H 223 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 361 " --> pdb=" O PHE H 223 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER H 349 " --> pdb=" O LYS H 364 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 52 through 55 removed outlier: 6.944A pdb=" N ASP I 42 " --> pdb=" O ILE K 519 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP K 521 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET I 44 " --> pdb=" O ASP K 521 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 197 through 198 removed outlier: 4.401A pdb=" N ILE I 211 " --> pdb=" O SER I 374 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 234 through 235 Processing sheet with id=AE5, first strand: chain 'I' and resid 286 through 287 removed outlier: 7.112A pdb=" N ILE I 286 " --> pdb=" O VAL I 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'I' and resid 350 through 352 removed outlier: 3.669A pdb=" N GLU I 350 " --> pdb=" O LYS I 365 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 355 through 356 Processing sheet with id=AE8, first strand: chain 'I' and resid 408 through 409 Processing sheet with id=AE9, first strand: chain 'I' and resid 486 through 487 removed outlier: 3.519A pdb=" N ARG I 496 " --> pdb=" O GLY I 487 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 50 through 51 removed outlier: 3.873A pdb=" N LYS J 50 " --> pdb=" O THR J 64 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 289 through 291 Processing sheet with id=AF3, first strand: chain 'J' and resid 353 through 354 removed outlier: 3.907A pdb=" N ILE J 354 " --> pdb=" O ASP J 357 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP J 357 " --> pdb=" O ILE J 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'J' and resid 477 through 478 Processing sheet with id=AF5, first strand: chain 'K' and resid 57 through 60 removed outlier: 8.198A pdb=" N MET K 47 " --> pdb=" O ASP N 519 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE N 521 " --> pdb=" O MET K 47 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET K 49 " --> pdb=" O ILE N 521 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG N 523 " --> pdb=" O MET K 49 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU K 51 " --> pdb=" O ARG N 523 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 142 through 143 removed outlier: 3.811A pdb=" N ILE K 142 " --> pdb=" O LEU K 407 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU K 407 " --> pdb=" O ILE K 142 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 213 through 215 Processing sheet with id=AF8, first strand: chain 'K' and resid 478 through 480 Processing sheet with id=AF9, first strand: chain 'L' and resid 59 through 62 Processing sheet with id=AG1, first strand: chain 'L' and resid 153 through 154 removed outlier: 4.006A pdb=" N ARG L 153 " --> pdb=" O LEU L 421 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU L 421 " --> pdb=" O ARG L 153 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 222 through 224 removed outlier: 4.259A pdb=" N GLU L 222 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL L 389 " --> pdb=" O GLU L 222 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 227 through 229 Processing sheet with id=AG4, first strand: chain 'M' and resid 59 through 62 Processing sheet with id=AG5, first strand: chain 'M' and resid 210 through 215 removed outlier: 3.764A pdb=" N ILE M 385 " --> pdb=" O LYS M 210 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU M 212 " --> pdb=" O ILE M 385 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE M 387 " --> pdb=" O GLU M 212 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS M 214 " --> pdb=" O ILE M 387 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY M 389 " --> pdb=" O LYS M 214 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 229 through 231 Processing sheet with id=AG7, first strand: chain 'M' and resid 248 through 250 removed outlier: 6.790A pdb=" N ALA M 249 " --> pdb=" O ILE M 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'M' and resid 418 through 419 Processing sheet with id=AG9, first strand: chain 'N' and resid 55 through 57 removed outlier: 3.970A pdb=" N THR N 57 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS N 45 " --> pdb=" O THR N 57 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N MET N 46 " --> pdb=" O MET P 526 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 191 through 192 removed outlier: 7.258A pdb=" N GLU N 192 " --> pdb=" O LEU N 374 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE N 376 " --> pdb=" O GLU N 192 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP N 203 " --> pdb=" O LYS N 377 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 210 through 212 Processing sheet with id=AH3, first strand: chain 'N' and resid 310 through 313 removed outlier: 6.083A pdb=" N PHE N 289 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU N 313 " --> pdb=" O PHE N 289 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL N 291 " --> pdb=" O LEU N 313 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU N 231 " --> pdb=" O VAL N 290 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE N 292 " --> pdb=" O LEU N 231 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 477 through 478 removed outlier: 3.804A pdb=" N MET N 487 " --> pdb=" O GLY N 478 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 47 through 50 Processing sheet with id=AH6, first strand: chain 'O' and resid 141 through 142 removed outlier: 3.926A pdb=" N VAL O 141 " --> pdb=" O VAL O 405 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL O 405 " --> pdb=" O VAL O 141 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 208 through 211 Processing sheet with id=AH8, first strand: chain 'O' and resid 237 through 238 Processing sheet with id=AH9, first strand: chain 'O' and resid 347 through 353 removed outlier: 3.513A pdb=" N GLU O 356 " --> pdb=" O ILE O 353 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 519 through 520 removed outlier: 3.874A pdb=" N PHE P 64 " --> pdb=" O VAL P 56 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P' and resid 202 through 208 removed outlier: 3.512A pdb=" N ILE P 375 " --> pdb=" O ARG P 203 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS P 205 " --> pdb=" O ILE P 375 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU P 377 " --> pdb=" O CYS P 205 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY P 379 " --> pdb=" O ILE P 207 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'P' and resid 223 through 224 removed outlier: 4.131A pdb=" N PHE P 223 " --> pdb=" O VAL P 361 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL P 361 " --> pdb=" O PHE P 223 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER P 349 " --> pdb=" O LYS P 364 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 145 through 150 removed outlier: 6.314A pdb=" N ILE Q 116 " --> pdb=" O ILE Q 147 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ALA Q 149 " --> pdb=" O ILE Q 116 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N HIS Q 118 " --> pdb=" O ALA Q 149 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'R' and resid 145 through 148 removed outlier: 6.471A pdb=" N ILE R 116 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE R 166 " --> pdb=" O PHE R 178 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE R 178 " --> pdb=" O ILE R 166 " (cutoff:3.500A) 2993 hydrogen bonds defined for protein. 8772 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.72 Time building geometry restraints manager: 14.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 21969 1.34 - 1.46: 12064 1.46 - 1.58: 31186 1.58 - 1.70: 30 1.70 - 1.81: 664 Bond restraints: 65913 Sorted by residual: bond pdb=" CA ASP K 281 " pdb=" C ASP K 281 " ideal model delta sigma weight residual 1.533 1.524 0.009 5.60e-03 3.19e+04 2.85e+00 bond pdb=" CA LEU C 241 " pdb=" C LEU C 241 " ideal model delta sigma weight residual 1.531 1.523 0.007 5.40e-03 3.43e+04 1.73e+00 bond pdb=" N LEU E 443 " pdb=" CA LEU E 443 " ideal model delta sigma weight residual 1.458 1.468 -0.010 9.00e-03 1.23e+04 1.18e+00 bond pdb=" C SER K 380 " pdb=" O SER K 380 " ideal model delta sigma weight residual 1.234 1.244 -0.010 1.00e-02 1.00e+04 1.09e+00 bond pdb=" C SER C 380 " pdb=" O SER C 380 " ideal model delta sigma weight residual 1.234 1.244 -0.010 1.00e-02 1.00e+04 1.04e+00 ... (remaining 65908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 87328 1.31 - 2.63: 1264 2.63 - 3.94: 258 3.94 - 5.26: 79 5.26 - 6.57: 64 Bond angle restraints: 88993 Sorted by residual: angle pdb=" N ILE I 149 " pdb=" CA ILE I 149 " pdb=" C ILE I 149 " ideal model delta sigma weight residual 113.71 109.30 4.41 9.50e-01 1.11e+00 2.15e+01 angle pdb=" C ASP K 281 " pdb=" CA ASP K 281 " pdb=" CB ASP K 281 " ideal model delta sigma weight residual 117.07 110.55 6.52 1.44e+00 4.82e-01 2.05e+01 angle pdb=" CA ASP K 281 " pdb=" C ASP K 281 " pdb=" O ASP K 281 " ideal model delta sigma weight residual 117.94 120.50 -2.56 5.80e-01 2.97e+00 1.94e+01 angle pdb=" N VAL E 271 " pdb=" CA VAL E 271 " pdb=" C VAL E 271 " ideal model delta sigma weight residual 113.53 109.31 4.22 9.80e-01 1.04e+00 1.85e+01 angle pdb=" C LEU C 241 " pdb=" CA LEU C 241 " pdb=" CB LEU C 241 " ideal model delta sigma weight residual 116.53 110.37 6.16 1.47e+00 4.63e-01 1.76e+01 ... (remaining 88988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.65: 38642 28.65 - 57.31: 2002 57.31 - 85.96: 147 85.96 - 114.61: 13 114.61 - 143.26: 15 Dihedral angle restraints: 40819 sinusoidal: 16404 harmonic: 24415 Sorted by residual: dihedral pdb=" C5' ADP L 601 " pdb=" O5' ADP L 601 " pdb=" PA ADP L 601 " pdb=" O2A ADP L 601 " ideal model delta sinusoidal sigma weight residual 300.00 156.74 143.26 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O2A ADP C 601 " pdb=" O3A ADP C 601 " pdb=" PA ADP C 601 " pdb=" PB ADP C 601 " ideal model delta sinusoidal sigma weight residual -60.00 69.36 -129.36 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" O2A ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PA ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 68.60 -128.60 1 2.00e+01 2.50e-03 3.90e+01 ... (remaining 40816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 6928 0.026 - 0.052: 2150 0.052 - 0.077: 814 0.077 - 0.103: 518 0.103 - 0.129: 239 Chirality restraints: 10649 Sorted by residual: chirality pdb=" CA ILE L 300 " pdb=" N ILE L 300 " pdb=" C ILE L 300 " pdb=" CB ILE L 300 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE D 300 " pdb=" N ILE D 300 " pdb=" C ILE D 300 " pdb=" CB ILE D 300 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE D 422 " pdb=" N ILE D 422 " pdb=" C ILE D 422 " pdb=" CB ILE D 422 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 10646 not shown) Planarity restraints: 11369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 256 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO E 257 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 257 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 257 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 256 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.88e+00 pdb=" N PRO M 257 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO M 257 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO M 257 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 445 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.17e+00 pdb=" N PRO G 446 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO G 446 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO G 446 " 0.015 5.00e-02 4.00e+02 ... (remaining 11366 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 12632 2.78 - 3.31: 56844 3.31 - 3.84: 99069 3.84 - 4.37: 100049 4.37 - 4.90: 186258 Nonbonded interactions: 454852 Sorted by model distance: nonbonded pdb=" O VAL H 355 " pdb=" OG1 THR H 358 " model vdw 2.250 3.040 nonbonded pdb=" O VAL P 355 " pdb=" OG1 THR P 358 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP C 132 " pdb=" OH TYR C 437 " model vdw 2.262 3.040 nonbonded pdb=" OD2 ASP K 132 " pdb=" OH TYR K 437 " model vdw 2.263 3.040 nonbonded pdb=" OE2 GLU H 17 " pdb=" OG SER H 23 " model vdw 2.265 3.040 ... (remaining 454847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = (chain 'Q' and resid 91 through 232) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 2.030 Check model and map are aligned: 0.380 Set scattering table: 0.490 Process input model: 114.700 Find NCS groups from input model: 4.810 Set up NCS constraints: 0.470 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 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 : 0.001 0.037 65913 Z= 0.093 Angle : 0.420 6.572 88993 Z= 0.239 Chirality : 0.037 0.129 10649 Planarity : 0.002 0.036 11369 Dihedral : 15.884 143.263 25005 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.75 % Allowed : 12.10 % Favored : 87.16 % Rotamer: Outliers : 1.78 % Allowed : 16.62 % Favored : 81.61 % 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: -2.67 (0.08), residues: 8447 helix: -0.04 (0.08), residues: 3968 sheet: -1.56 (0.21), residues: 533 loop : -3.83 (0.07), residues: 3946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP Q 114 HIS 0.001 0.000 HIS J 174 PHE 0.004 0.000 PHE H 64 TYR 0.005 0.000 TYR F 239 ARG 0.001 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 996 time to evaluate : 5.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ILE cc_start: 0.1741 (OUTLIER) cc_final: 0.1419 (mp) REVERT: A 225 MET cc_start: 0.1068 (mtp) cc_final: -0.1218 (mmt) REVERT: A 256 ASP cc_start: 0.3205 (OUTLIER) cc_final: 0.1546 (t0) REVERT: B 48 MET cc_start: 0.7945 (mmt) cc_final: 0.7620 (mmt) REVERT: B 452 ASP cc_start: 0.7280 (t70) cc_final: 0.7073 (m-30) REVERT: C 374 ILE cc_start: 0.6668 (tt) cc_final: 0.6301 (tt) REVERT: E 239 MET cc_start: 0.1171 (ttm) cc_final: 0.0843 (ttp) REVERT: G 487 ASN cc_start: 0.7131 (m-40) cc_final: 0.6904 (m-40) REVERT: I 145 ARG cc_start: 0.3365 (mmt180) cc_final: 0.1812 (ttt180) REVERT: I 225 MET cc_start: -0.1132 (mtp) cc_final: -0.1771 (ptm) REVERT: I 344 MET cc_start: 0.2576 (ptt) cc_final: 0.2288 (mmm) REVERT: J 205 LEU cc_start: -0.1294 (OUTLIER) cc_final: -0.1962 (mt) REVERT: J 275 MET cc_start: -0.3037 (ptp) cc_final: -0.4077 (tpt) REVERT: K 49 MET cc_start: 0.8072 (ttm) cc_final: 0.7774 (ttm) REVERT: K 105 MET cc_start: 0.7557 (mtt) cc_final: 0.7207 (mtt) REVERT: L 57 MET cc_start: 0.6347 (mmp) cc_final: 0.5293 (mmm) REVERT: L 60 MET cc_start: 0.5239 (ttm) cc_final: 0.5013 (ttp) REVERT: L 219 ASP cc_start: 0.4068 (OUTLIER) cc_final: 0.3541 (m-30) REVERT: M 239 MET cc_start: 0.3183 (ttm) cc_final: 0.2810 (ttm) REVERT: Q 119 LEU cc_start: 0.3307 (OUTLIER) cc_final: 0.2537 (tt) REVERT: R 204 ILE cc_start: 0.5228 (OUTLIER) cc_final: 0.4915 (tp) outliers start: 126 outliers final: 24 residues processed: 1108 average time/residue: 0.6048 time to fit residues: 1131.4790 Evaluate side-chains 601 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 571 time to evaluate : 5.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 508 CYS Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain I residue 409 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 394 LEU Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 508 CYS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 709 optimal weight: 1.9990 chunk 636 optimal weight: 40.0000 chunk 353 optimal weight: 7.9990 chunk 217 optimal weight: 0.0060 chunk 429 optimal weight: 0.0980 chunk 340 optimal weight: 10.0000 chunk 658 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 400 optimal weight: 0.9980 chunk 490 optimal weight: 4.9990 chunk 762 optimal weight: 0.0870 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 242 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN C 226 HIS C 320 ASN D 368 ASN D 406 HIS D 502 ASN E 46 ASN E 264 HIS E 290 GLN E 503 GLN E 516 GLN F 23 ASN F 65 HIS F 84 GLN F 161 HIS F 386 GLN G 25 ASN G 119 GLN G 241 ASN G 432 GLN G 462 ASN G 501 ASN H 58 ASN H 80 HIS H 172 GLN H 185 GLN H 201 ASN ** H 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 ASN H 365 HIS I 20 GLN ** J 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 GLN K 320 ASN K 526 HIS L 368 ASN M 46 ASN M 147 HIS M 182 HIS M 403 HIS M 503 GLN M 516 GLN N 23 ASN N 68 GLN N 467 GLN N 497 ASN O 25 ASN O 119 GLN O 241 ASN O 432 GLN O 462 ASN O 501 ASN P 309 ASN P 365 HIS R 132 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 65913 Z= 0.137 Angle : 0.518 13.144 88993 Z= 0.250 Chirality : 0.039 0.250 10649 Planarity : 0.003 0.074 11369 Dihedral : 5.820 136.193 9154 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.96 % Favored : 92.89 % Rotamer: Outliers : 1.73 % Allowed : 18.87 % Favored : 79.39 % 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: -1.42 (0.09), residues: 8447 helix: 1.26 (0.08), residues: 3990 sheet: -0.91 (0.23), residues: 525 loop : -3.52 (0.08), residues: 3932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 485 HIS 0.015 0.001 HIS H 365 PHE 0.008 0.001 PHE D 454 TYR 0.015 0.001 TYR A 190 ARG 0.006 0.000 ARG P 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 581 time to evaluate : 5.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7537 (tppt) cc_final: 0.7271 (mmmt) REVERT: A 161 ILE cc_start: 0.1522 (OUTLIER) cc_final: 0.1273 (mp) REVERT: A 225 MET cc_start: 0.1139 (mtp) cc_final: -0.1066 (mmt) REVERT: B 48 MET cc_start: 0.7906 (mmt) cc_final: 0.7449 (mmm) REVERT: E 239 MET cc_start: 0.1403 (ttm) cc_final: 0.1019 (ttp) REVERT: G 323 MET cc_start: 0.3267 (tmm) cc_final: 0.2779 (tmm) REVERT: G 382 MET cc_start: 0.1512 (mmp) cc_final: 0.0076 (mmt) REVERT: H 300 MET cc_start: 0.4577 (mmm) cc_final: 0.4188 (mmm) REVERT: I 105 ASP cc_start: 0.6512 (m-30) cc_final: 0.6176 (m-30) REVERT: I 145 ARG cc_start: 0.3113 (mmt180) cc_final: 0.1879 (ttt-90) REVERT: I 306 MET cc_start: 0.3549 (mmt) cc_final: 0.3271 (mmm) REVERT: I 384 MET cc_start: 0.3281 (mmm) cc_final: 0.2887 (tpt) REVERT: J 275 MET cc_start: -0.2932 (ptp) cc_final: -0.4062 (tpt) REVERT: K 105 MET cc_start: 0.7572 (mtt) cc_final: 0.7174 (mtt) REVERT: L 323 MET cc_start: 0.1075 (OUTLIER) cc_final: 0.0334 (mmm) REVERT: M 60 MET cc_start: 0.4374 (ppp) cc_final: 0.2820 (ttp) REVERT: M 239 MET cc_start: 0.3154 (ttm) cc_final: 0.2828 (ttm) REVERT: M 393 MET cc_start: 0.4271 (pmm) cc_final: 0.4031 (pmm) REVERT: O 227 MET cc_start: 0.1339 (mmm) cc_final: 0.0094 (mtm) REVERT: O 394 MET cc_start: 0.5134 (mmt) cc_final: 0.4863 (mpp) outliers start: 123 outliers final: 44 residues processed: 676 average time/residue: 0.5564 time to fit residues: 662.1611 Evaluate side-chains 559 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 513 time to evaluate : 5.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 65 HIS Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 227 MET Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 173 TYR Chi-restraints excluded: chain J residue 310 MET Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 507 ILE Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 494 VAL Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 184 MET Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 468 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 423 optimal weight: 0.0060 chunk 236 optimal weight: 30.0000 chunk 634 optimal weight: 6.9990 chunk 519 optimal weight: 0.3980 chunk 210 optimal weight: 3.9990 chunk 764 optimal weight: 3.9990 chunk 825 optimal weight: 6.9990 chunk 680 optimal weight: 8.9990 chunk 757 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 613 optimal weight: 9.9990 overall best weight: 3.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 464 GLN D 301 GLN ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN F 84 GLN F 386 GLN G 117 HIS H 58 ASN H 59 HIS ** H 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN H 359 GLN H 471 HIS K 226 HIS M 72 ASN M 290 GLN M 291 GLN M 505 HIS O 117 HIS ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 472 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 65913 Z= 0.293 Angle : 0.707 12.801 88993 Z= 0.350 Chirality : 0.045 0.243 10649 Planarity : 0.005 0.078 11369 Dihedral : 6.288 160.585 9124 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.83 % Favored : 92.07 % Rotamer: Outliers : 3.02 % Allowed : 18.94 % Favored : 78.04 % 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: -1.27 (0.09), residues: 8447 helix: 1.31 (0.08), residues: 3988 sheet: -0.93 (0.24), residues: 461 loop : -3.31 (0.08), residues: 3998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP O 493 HIS 0.052 0.002 HIS F 65 PHE 0.032 0.002 PHE O 125 TYR 0.028 0.002 TYR C 437 ARG 0.007 0.001 ARG N 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 557 time to evaluate : 5.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.3578 (OUTLIER) cc_final: 0.3300 (m) REVERT: B 359 LEU cc_start: 0.1379 (OUTLIER) cc_final: 0.1076 (mm) REVERT: B 480 MET cc_start: 0.8092 (mmm) cc_final: 0.7688 (mmp) REVERT: C 117 MET cc_start: 0.2279 (mtm) cc_final: 0.2023 (mtm) REVERT: C 349 LEU cc_start: 0.4933 (OUTLIER) cc_final: 0.4710 (pt) REVERT: D 323 MET cc_start: 0.1910 (ttp) cc_final: 0.1548 (ttm) REVERT: E 239 MET cc_start: 0.1507 (ttm) cc_final: 0.1053 (ttp) REVERT: E 371 MET cc_start: 0.3256 (ttp) cc_final: 0.3026 (ttt) REVERT: E 501 MET cc_start: 0.6531 (mmp) cc_final: 0.5929 (mmp) REVERT: F 510 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8470 (p) REVERT: G 382 MET cc_start: 0.1260 (mmp) cc_final: -0.0240 (mmt) REVERT: H 120 ARG cc_start: 0.7429 (tpp-160) cc_final: 0.7200 (ttm-80) REVERT: H 300 MET cc_start: 0.4507 (mmm) cc_final: 0.4182 (mmm) REVERT: I 145 ARG cc_start: 0.3072 (mmt180) cc_final: 0.1866 (ttt-90) REVERT: I 306 MET cc_start: 0.3122 (mmt) cc_final: 0.1654 (ptm) REVERT: J 275 MET cc_start: -0.2695 (ptp) cc_final: -0.3921 (tpt) REVERT: L 260 MET cc_start: 0.3052 (ptp) cc_final: 0.2569 (ptm) REVERT: L 323 MET cc_start: 0.1242 (OUTLIER) cc_final: 0.0034 (mmm) REVERT: M 60 MET cc_start: 0.4919 (ppp) cc_final: 0.3959 (ttp) REVERT: M 239 MET cc_start: 0.3701 (ttm) cc_final: 0.3421 (ttm) REVERT: M 371 MET cc_start: 0.3268 (OUTLIER) cc_final: 0.2954 (ttt) REVERT: N 487 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.6945 (ppp) REVERT: O 382 MET cc_start: 0.2166 (mmm) cc_final: 0.1904 (mmp) REVERT: O 497 MET cc_start: 0.7370 (tpp) cc_final: 0.7106 (mmm) outliers start: 214 outliers final: 93 residues processed: 727 average time/residue: 0.5689 time to fit residues: 728.5264 Evaluate side-chains 568 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 468 time to evaluate : 5.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 404 ASP Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 526 MET Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 487 MET Chi-restraints excluded: chain N residue 494 VAL Chi-restraints excluded: chain O residue 32 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain Q residue 229 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 755 optimal weight: 3.9990 chunk 574 optimal weight: 8.9990 chunk 396 optimal weight: 0.1980 chunk 84 optimal weight: 0.8980 chunk 364 optimal weight: 0.8980 chunk 513 optimal weight: 2.9990 chunk 766 optimal weight: 3.9990 chunk 811 optimal weight: 1.9990 chunk 400 optimal weight: 4.9990 chunk 726 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 470 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN F 65 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN H 219 HIS M 290 GLN M 505 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 65913 Z= 0.166 Angle : 0.552 11.776 88993 Z= 0.269 Chirality : 0.040 0.206 10649 Planarity : 0.003 0.064 11369 Dihedral : 5.796 159.798 9121 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 2.44 % Allowed : 20.34 % Favored : 77.22 % 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: -0.85 (0.09), residues: 8447 helix: 1.74 (0.08), residues: 3978 sheet: -0.79 (0.24), residues: 469 loop : -3.18 (0.08), residues: 4000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 485 HIS 0.010 0.001 HIS D 406 PHE 0.015 0.001 PHE G 175 TYR 0.021 0.001 TYR H 505 ARG 0.007 0.000 ARG I 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 506 time to evaluate : 5.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 480 MET cc_start: 0.8128 (mmm) cc_final: 0.7625 (mmp) REVERT: C 100 ILE cc_start: 0.8160 (mm) cc_final: 0.7955 (mm) REVERT: C 117 MET cc_start: 0.2128 (mtm) cc_final: 0.1814 (mtm) REVERT: C 270 MET cc_start: 0.1714 (mmt) cc_final: 0.1508 (mmt) REVERT: D 323 MET cc_start: 0.1801 (ttp) cc_final: 0.1410 (ttm) REVERT: E 208 LEU cc_start: 0.4125 (OUTLIER) cc_final: 0.3835 (tt) REVERT: E 220 GLU cc_start: 0.3436 (tp30) cc_final: 0.3153 (tp30) REVERT: E 239 MET cc_start: 0.1248 (ttm) cc_final: 0.0865 (ttp) REVERT: F 163 GLU cc_start: 0.6288 (pt0) cc_final: 0.5899 (pt0) REVERT: G 175 PHE cc_start: 0.4402 (m-80) cc_final: 0.4190 (m-10) REVERT: G 382 MET cc_start: 0.1477 (mmp) cc_final: -0.0025 (mmt) REVERT: H 300 MET cc_start: 0.4480 (mmm) cc_final: 0.4197 (mmm) REVERT: I 145 ARG cc_start: 0.3289 (mmt180) cc_final: 0.1881 (ttt-90) REVERT: I 306 MET cc_start: 0.3273 (mmt) cc_final: 0.1797 (ptm) REVERT: J 275 MET cc_start: -0.2708 (ptp) cc_final: -0.4171 (tpt) REVERT: K 105 MET cc_start: 0.8228 (mtt) cc_final: 0.7822 (mtt) REVERT: L 260 MET cc_start: 0.3109 (ptp) cc_final: 0.2655 (ptm) REVERT: L 323 MET cc_start: 0.1091 (OUTLIER) cc_final: 0.0421 (mmm) REVERT: M 60 MET cc_start: 0.5407 (ppp) cc_final: 0.4817 (ptm) REVERT: M 239 MET cc_start: 0.3787 (ttm) cc_final: 0.3211 (mtp) REVERT: M 371 MET cc_start: 0.3119 (OUTLIER) cc_final: 0.2633 (ttt) REVERT: N 92 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8252 (t) REVERT: O 382 MET cc_start: 0.2119 (mmm) cc_final: 0.1801 (mmp) REVERT: O 394 MET cc_start: 0.6014 (mpp) cc_final: 0.5682 (mpp) REVERT: O 497 MET cc_start: 0.7170 (tpp) cc_final: 0.6957 (mmm) REVERT: R 97 ILE cc_start: 0.3478 (OUTLIER) cc_final: 0.3036 (tt) outliers start: 173 outliers final: 95 residues processed: 640 average time/residue: 0.5603 time to fit residues: 635.8201 Evaluate side-chains 567 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 467 time to evaluate : 5.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 435 GLN Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 32 ILE Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 676 optimal weight: 6.9990 chunk 460 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 604 optimal weight: 9.9990 chunk 335 optimal weight: 7.9990 chunk 692 optimal weight: 10.0000 chunk 561 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 414 optimal weight: 0.9990 chunk 728 optimal weight: 0.0980 chunk 204 optimal weight: 0.1980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN ** H 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS M 290 GLN M 505 HIS O 282 HIS ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 65913 Z= 0.218 Angle : 0.594 10.115 88993 Z= 0.290 Chirality : 0.042 0.240 10649 Planarity : 0.004 0.066 11369 Dihedral : 5.723 149.866 9121 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.11 % Rotamer: Outliers : 2.96 % Allowed : 20.44 % Favored : 76.60 % 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: -0.76 (0.09), residues: 8447 helix: 1.75 (0.08), residues: 4002 sheet: -0.69 (0.23), residues: 531 loop : -3.13 (0.08), residues: 3914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 485 HIS 0.010 0.001 HIS O 117 PHE 0.022 0.001 PHE P 103 TYR 0.018 0.001 TYR H 505 ARG 0.006 0.000 ARG K 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 481 time to evaluate : 6.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 MET cc_start: 0.2260 (mtm) cc_final: 0.1940 (mtm) REVERT: C 336 GLU cc_start: 0.3152 (OUTLIER) cc_final: 0.2173 (tt0) REVERT: C 470 HIS cc_start: 0.8319 (OUTLIER) cc_final: 0.6107 (m-70) REVERT: D 323 MET cc_start: 0.1910 (ttp) cc_final: 0.1556 (ttm) REVERT: D 349 ASP cc_start: 0.0746 (OUTLIER) cc_final: 0.0020 (p0) REVERT: E 208 LEU cc_start: 0.4163 (OUTLIER) cc_final: 0.3955 (tt) REVERT: E 220 GLU cc_start: 0.3554 (tp30) cc_final: 0.3353 (tp30) REVERT: E 239 MET cc_start: 0.1757 (ttm) cc_final: 0.0480 (tpt) REVERT: G 382 MET cc_start: 0.1253 (mmp) cc_final: -0.0155 (mmt) REVERT: H 300 MET cc_start: 0.4581 (mmm) cc_final: 0.4297 (mmm) REVERT: I 105 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7032 (t0) REVERT: I 145 ARG cc_start: 0.3371 (mmt180) cc_final: 0.1988 (ttt-90) REVERT: I 306 MET cc_start: 0.3423 (mmt) cc_final: 0.1868 (ptm) REVERT: I 344 MET cc_start: 0.2883 (mtm) cc_final: 0.1547 (mmp) REVERT: J 53 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7602 (tt) REVERT: J 275 MET cc_start: -0.2610 (ptp) cc_final: -0.3774 (tpt) REVERT: K 105 MET cc_start: 0.8313 (mtt) cc_final: 0.7917 (mtt) REVERT: L 260 MET cc_start: 0.2991 (ptp) cc_final: 0.2642 (ptm) REVERT: L 323 MET cc_start: 0.1212 (OUTLIER) cc_final: 0.0497 (mmm) REVERT: M 60 MET cc_start: 0.5525 (ppp) cc_final: 0.5173 (ptm) REVERT: M 239 MET cc_start: 0.4061 (ttm) cc_final: 0.3495 (mtp) REVERT: M 371 MET cc_start: 0.3031 (OUTLIER) cc_final: 0.2562 (ttt) REVERT: N 197 LYS cc_start: 0.7367 (mppt) cc_final: 0.6835 (tppt) REVERT: O 382 MET cc_start: 0.2281 (mmm) cc_final: 0.1877 (mmp) REVERT: O 394 MET cc_start: 0.6344 (mpp) cc_final: 0.6108 (mpp) REVERT: O 497 MET cc_start: 0.7406 (tpp) cc_final: 0.7194 (mmm) REVERT: P 523 GLN cc_start: 0.6694 (mm-40) cc_final: 0.6350 (mm-40) REVERT: R 97 ILE cc_start: 0.3374 (OUTLIER) cc_final: 0.2875 (tt) outliers start: 210 outliers final: 134 residues processed: 646 average time/residue: 0.5740 time to fit residues: 659.2074 Evaluate side-chains 605 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 462 time to evaluate : 5.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 310 MET Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 429 MET Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 435 GLN Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 160 MET Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 417 SER Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 477 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain P residue 516 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 273 optimal weight: 0.7980 chunk 731 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 chunk 476 optimal weight: 20.0000 chunk 200 optimal weight: 1.9990 chunk 812 optimal weight: 0.0270 chunk 674 optimal weight: 4.9990 chunk 376 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 268 optimal weight: 0.9980 chunk 426 optimal weight: 0.2980 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS H 477 ASN K 470 HIS M 290 GLN M 505 HIS N 68 GLN O 73 HIS P 172 GLN P 471 HIS P 477 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 65913 Z= 0.127 Angle : 0.522 11.112 88993 Z= 0.252 Chirality : 0.040 0.214 10649 Planarity : 0.003 0.067 11369 Dihedral : 5.349 141.847 9117 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 2.02 % Allowed : 21.34 % Favored : 76.65 % 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: -0.47 (0.09), residues: 8447 helix: 2.05 (0.08), residues: 3986 sheet: -0.68 (0.23), residues: 511 loop : -3.00 (0.08), residues: 3950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 485 HIS 0.036 0.001 HIS K 470 PHE 0.022 0.001 PHE G 175 TYR 0.020 0.001 TYR H 505 ARG 0.007 0.000 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 495 time to evaluate : 5.664 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: B 480 MET cc_start: 0.8188 (mmm) cc_final: 0.7986 (mmm) REVERT: C 470 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.5145 (m-70) REVERT: D 323 MET cc_start: 0.1844 (ttp) cc_final: 0.1503 (ttm) REVERT: D 349 ASP cc_start: 0.0770 (OUTLIER) cc_final: 0.0005 (p0) REVERT: E 208 LEU cc_start: 0.4099 (OUTLIER) cc_final: 0.3897 (tt) REVERT: E 220 GLU cc_start: 0.3593 (tp30) cc_final: 0.3387 (tp30) REVERT: E 239 MET cc_start: 0.1740 (ttm) cc_final: 0.0470 (tpt) REVERT: G 323 MET cc_start: 0.3114 (tmm) cc_final: 0.2853 (ppp) REVERT: G 382 MET cc_start: 0.1192 (mmp) cc_final: -0.0526 (mmt) REVERT: I 105 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.7054 (t0) REVERT: I 145 ARG cc_start: 0.3322 (mmt180) cc_final: 0.2018 (ttt-90) REVERT: I 189 ARG cc_start: 0.5141 (ttt-90) cc_final: 0.4595 (tmt170) REVERT: I 306 MET cc_start: 0.3350 (mmt) cc_final: 0.1779 (ptm) REVERT: I 344 MET cc_start: 0.2741 (mtm) cc_final: 0.1386 (mmp) REVERT: J 275 MET cc_start: -0.2728 (ptp) cc_final: -0.4191 (tpt) REVERT: J 436 MET cc_start: 0.7745 (mtt) cc_final: 0.7467 (mtm) REVERT: L 260 MET cc_start: 0.3013 (ptp) cc_final: 0.2676 (ptm) REVERT: L 323 MET cc_start: 0.1158 (OUTLIER) cc_final: 0.0437 (mmm) REVERT: M 239 MET cc_start: 0.3934 (ttm) cc_final: 0.3375 (mtp) REVERT: M 371 MET cc_start: 0.3238 (OUTLIER) cc_final: 0.2718 (ttt) REVERT: M 393 MET cc_start: 0.5231 (pmm) cc_final: 0.4975 (mpp) REVERT: P 492 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7147 (mtt) outliers start: 143 outliers final: 94 residues processed: 600 average time/residue: 0.5795 time to fit residues: 610.7754 Evaluate side-chains 569 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 468 time to evaluate : 5.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 310 MET Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 488 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 160 MET Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 397 ARG Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain P residue 516 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 182 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 783 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 463 optimal weight: 5.9990 chunk 593 optimal weight: 7.9990 chunk 459 optimal weight: 2.9990 chunk 684 optimal weight: 5.9990 chunk 453 optimal weight: 4.9990 chunk 809 optimal weight: 4.9990 chunk 506 optimal weight: 0.9980 chunk 493 optimal weight: 20.0000 chunk 373 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 231 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 346 HIS H 472 GLN ** I 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS M 290 GLN ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 201 GLN P 50 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 65913 Z= 0.337 Angle : 0.722 14.378 88993 Z= 0.358 Chirality : 0.046 0.219 10649 Planarity : 0.004 0.069 11369 Dihedral : 6.086 163.568 9117 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.34 % Favored : 92.59 % Rotamer: Outliers : 2.95 % Allowed : 20.63 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.09), residues: 8447 helix: 1.51 (0.08), residues: 4010 sheet: -0.78 (0.22), residues: 557 loop : -3.07 (0.08), residues: 3880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 493 HIS 0.013 0.001 HIS O 117 PHE 0.036 0.002 PHE P 103 TYR 0.020 0.002 TYR C 437 ARG 0.006 0.001 ARG N 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 476 time to evaluate : 5.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8594 (tt) REVERT: C 336 GLU cc_start: 0.3624 (OUTLIER) cc_final: 0.2494 (tt0) REVERT: C 470 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.6444 (m-70) REVERT: D 323 MET cc_start: 0.2077 (ttp) cc_final: 0.1712 (ttm) REVERT: D 349 ASP cc_start: 0.0735 (OUTLIER) cc_final: 0.0004 (p0) REVERT: E 59 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7898 (ttmm) REVERT: E 239 MET cc_start: 0.1684 (ttm) cc_final: 0.0502 (tpt) REVERT: F 107 ASP cc_start: 0.7890 (t70) cc_final: 0.7652 (t0) REVERT: F 221 MET cc_start: 0.4160 (OUTLIER) cc_final: 0.3528 (mpp) REVERT: G 382 MET cc_start: 0.1184 (mmp) cc_final: -0.0477 (mmt) REVERT: I 306 MET cc_start: 0.3607 (mmt) cc_final: 0.1855 (ptm) REVERT: I 344 MET cc_start: 0.3259 (mtm) cc_final: 0.3053 (mtm) REVERT: I 430 MET cc_start: 0.6558 (tpp) cc_final: 0.6185 (tpp) REVERT: J 53 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7716 (tt) REVERT: J 275 MET cc_start: -0.2599 (ptp) cc_final: -0.4032 (tpt) REVERT: K 266 ARG cc_start: 0.2985 (OUTLIER) cc_final: 0.1599 (mmp-170) REVERT: L 260 MET cc_start: 0.3181 (ptp) cc_final: 0.2886 (ptm) REVERT: L 323 MET cc_start: 0.1322 (OUTLIER) cc_final: 0.0291 (mmm) REVERT: M 59 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7445 (mttm) REVERT: M 239 MET cc_start: 0.4155 (ttm) cc_final: 0.3738 (mtp) REVERT: M 307 ASP cc_start: 0.1836 (OUTLIER) cc_final: 0.1181 (p0) REVERT: M 371 MET cc_start: 0.3347 (OUTLIER) cc_final: 0.2818 (ttt) REVERT: M 393 MET cc_start: 0.5343 (pmm) cc_final: 0.5111 (mpp) REVERT: O 382 MET cc_start: 0.2413 (mmm) cc_final: 0.1678 (mmp) REVERT: O 442 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8023 (mp) REVERT: P 22 PHE cc_start: 0.4295 (OUTLIER) cc_final: 0.3828 (m-80) REVERT: P 85 MET cc_start: 0.8382 (mmm) cc_final: 0.7837 (mtp) REVERT: P 523 GLN cc_start: 0.6701 (mm-40) cc_final: 0.6466 (mm-40) REVERT: R 97 ILE cc_start: 0.3731 (OUTLIER) cc_final: 0.3123 (tt) outliers start: 209 outliers final: 136 residues processed: 637 average time/residue: 0.5556 time to fit residues: 627.6425 Evaluate side-chains 601 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 450 time to evaluate : 5.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 221 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 169 MET Chi-restraints excluded: chain H residue 351 TYR Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 236 CYS Chi-restraints excluded: chain I residue 384 MET Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 266 ARG Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 488 VAL Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 131 ILE Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 496 ASP Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 397 ARG Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 417 SER Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 477 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 50 ASN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 182 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 500 optimal weight: 0.9980 chunk 323 optimal weight: 5.9990 chunk 483 optimal weight: 20.0000 chunk 243 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 514 optimal weight: 6.9990 chunk 551 optimal weight: 1.9990 chunk 400 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 636 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 ASN ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 346 HIS ** I 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 GLN ** J 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS M 290 GLN ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 65913 Z= 0.221 Angle : 0.609 12.613 88993 Z= 0.300 Chirality : 0.042 0.203 10649 Planarity : 0.004 0.078 11369 Dihedral : 5.859 170.161 9115 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 2.42 % Allowed : 21.14 % Favored : 76.43 % 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: -0.75 (0.09), residues: 8447 helix: 1.66 (0.08), residues: 4020 sheet: -0.81 (0.23), residues: 525 loop : -3.00 (0.08), residues: 3902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 474 HIS 0.010 0.001 HIS K 470 PHE 0.014 0.001 PHE P 103 TYR 0.018 0.001 TYR P 47 ARG 0.005 0.000 ARG N 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 467 time to evaluate : 5.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 VAL cc_start: 0.7146 (m) cc_final: 0.6847 (m) REVERT: C 336 GLU cc_start: 0.3408 (OUTLIER) cc_final: 0.2321 (tt0) REVERT: C 470 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.6298 (m-70) REVERT: D 323 MET cc_start: 0.2018 (ttp) cc_final: 0.1686 (ttm) REVERT: D 349 ASP cc_start: 0.0434 (OUTLIER) cc_final: -0.0230 (p0) REVERT: E 59 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7636 (ttmm) REVERT: E 239 MET cc_start: 0.1758 (ttm) cc_final: 0.0553 (tpt) REVERT: F 120 THR cc_start: 0.8531 (m) cc_final: 0.8223 (m) REVERT: G 382 MET cc_start: 0.1541 (mmp) cc_final: -0.0074 (mmt) REVERT: I 145 ARG cc_start: 0.3139 (mmt180) cc_final: 0.2034 (ttt-90) REVERT: I 167 PHE cc_start: 0.4211 (OUTLIER) cc_final: 0.3847 (m-80) REVERT: I 306 MET cc_start: 0.3326 (mmt) cc_final: 0.1792 (ptm) REVERT: I 344 MET cc_start: 0.3240 (mtm) cc_final: 0.3010 (mtm) REVERT: J 53 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7676 (tt) REVERT: J 275 MET cc_start: -0.2635 (ptp) cc_final: -0.4000 (tpt) REVERT: K 266 ARG cc_start: 0.2810 (OUTLIER) cc_final: 0.1457 (mmp-170) REVERT: L 48 ILE cc_start: 0.7553 (pt) cc_final: 0.7286 (pt) REVERT: L 260 MET cc_start: 0.3289 (ptp) cc_final: 0.3046 (ptm) REVERT: L 320 MET cc_start: 0.3406 (OUTLIER) cc_final: 0.2818 (mtm) REVERT: L 323 MET cc_start: 0.1024 (OUTLIER) cc_final: 0.0318 (mmm) REVERT: M 59 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7696 (mttp) REVERT: M 239 MET cc_start: 0.4219 (ttm) cc_final: 0.3797 (mtp) REVERT: M 307 ASP cc_start: 0.1966 (OUTLIER) cc_final: 0.1335 (p0) REVERT: O 382 MET cc_start: 0.2543 (mmm) cc_final: 0.1817 (mmp) REVERT: P 85 MET cc_start: 0.8345 (mmm) cc_final: 0.7803 (mtp) REVERT: P 523 GLN cc_start: 0.6819 (mm-40) cc_final: 0.6504 (mm-40) REVERT: R 97 ILE cc_start: 0.3642 (OUTLIER) cc_final: 0.3038 (tt) outliers start: 172 outliers final: 130 residues processed: 595 average time/residue: 0.5690 time to fit residues: 597.7284 Evaluate side-chains 595 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 453 time to evaluate : 5.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 227 MET Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 169 MET Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 236 CYS Chi-restraints excluded: chain I residue 384 MET Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain J residue 263 LYS Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 265 THR Chi-restraints excluded: chain K residue 266 ARG Chi-restraints excluded: chain K residue 291 ILE Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 429 MET Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 488 VAL Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 336 PHE Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 477 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain P residue 219 HIS Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain P residue 500 THR Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 182 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 736 optimal weight: 6.9990 chunk 775 optimal weight: 6.9990 chunk 707 optimal weight: 6.9990 chunk 754 optimal weight: 0.8980 chunk 454 optimal weight: 2.9990 chunk 328 optimal weight: 0.9990 chunk 592 optimal weight: 30.0000 chunk 231 optimal weight: 0.1980 chunk 681 optimal weight: 0.6980 chunk 713 optimal weight: 5.9990 chunk 751 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN ** I 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 GLN K 118 HIS K 470 HIS M 290 GLN ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 65913 Z= 0.131 Angle : 0.538 10.293 88993 Z= 0.262 Chirality : 0.040 0.204 10649 Planarity : 0.003 0.070 11369 Dihedral : 5.412 167.930 9115 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 1.62 % Allowed : 21.92 % Favored : 76.46 % 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: -0.39 (0.09), residues: 8447 helix: 2.00 (0.08), residues: 4024 sheet: -0.54 (0.24), residues: 488 loop : -2.87 (0.08), residues: 3935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 485 HIS 0.065 0.001 HIS K 470 PHE 0.023 0.001 PHE I 167 TYR 0.020 0.001 TYR H 505 ARG 0.005 0.000 ARG K 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 471 time to evaluate : 5.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.4352 (ptp) cc_final: 0.3926 (ptt) REVERT: C 336 GLU cc_start: 0.3351 (OUTLIER) cc_final: 0.2326 (tt0) REVERT: C 470 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.5049 (m-70) REVERT: C 516 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7973 (mt) REVERT: D 323 MET cc_start: 0.2009 (ttp) cc_final: 0.1681 (ttm) REVERT: D 349 ASP cc_start: 0.0676 (OUTLIER) cc_final: -0.0176 (p0) REVERT: E 239 MET cc_start: 0.1870 (ttm) cc_final: 0.0683 (tpt) REVERT: E 501 MET cc_start: 0.7875 (mmt) cc_final: 0.7540 (mmt) REVERT: G 382 MET cc_start: 0.1772 (mmp) cc_final: 0.0130 (mmt) REVERT: I 145 ARG cc_start: 0.3029 (mmt180) cc_final: 0.2075 (ttt-90) REVERT: I 167 PHE cc_start: 0.4683 (OUTLIER) cc_final: 0.3499 (t80) REVERT: I 171 MET cc_start: 0.5364 (mtm) cc_final: 0.5012 (mpp) REVERT: I 189 ARG cc_start: 0.5292 (ttt-90) cc_final: 0.4725 (tmt170) REVERT: I 306 MET cc_start: 0.3177 (mmt) cc_final: 0.1585 (ptm) REVERT: I 344 MET cc_start: 0.3257 (mtm) cc_final: 0.1723 (mmp) REVERT: J 275 MET cc_start: -0.2771 (ptp) cc_final: -0.4200 (tpt) REVERT: L 320 MET cc_start: 0.2958 (OUTLIER) cc_final: 0.2403 (mtm) REVERT: L 323 MET cc_start: 0.0923 (OUTLIER) cc_final: 0.0329 (mmm) REVERT: M 59 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7293 (mttp) REVERT: M 239 MET cc_start: 0.4191 (ttm) cc_final: 0.3621 (mtp) REVERT: N 259 LEU cc_start: 0.2406 (OUTLIER) cc_final: 0.1641 (mp) REVERT: O 382 MET cc_start: 0.2035 (mmm) cc_final: 0.1459 (mmp) REVERT: P 85 MET cc_start: 0.8239 (mmm) cc_final: 0.7668 (mtp) outliers start: 115 outliers final: 88 residues processed: 553 average time/residue: 0.5551 time to fit residues: 541.7720 Evaluate side-chains 551 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 454 time to evaluate : 5.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 169 MET Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 384 MET Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 429 MET Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 477 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 182 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 495 optimal weight: 0.9990 chunk 797 optimal weight: 7.9990 chunk 486 optimal weight: 20.0000 chunk 378 optimal weight: 0.0770 chunk 554 optimal weight: 4.9990 chunk 836 optimal weight: 5.9990 chunk 770 optimal weight: 0.8980 chunk 666 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 514 optimal weight: 3.9990 chunk 408 optimal weight: 1.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS ** M 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 65913 Z= 0.171 Angle : 0.562 11.704 88993 Z= 0.274 Chirality : 0.041 0.213 10649 Planarity : 0.003 0.072 11369 Dihedral : 5.392 156.722 9115 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 1.72 % Allowed : 21.89 % Favored : 76.39 % 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: -0.35 (0.09), residues: 8447 helix: 2.02 (0.08), residues: 4022 sheet: -0.54 (0.24), residues: 493 loop : -2.82 (0.09), residues: 3932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 493 HIS 0.007 0.001 HIS K 470 PHE 0.032 0.001 PHE N 336 TYR 0.016 0.001 TYR H 505 ARG 0.004 0.000 ARG E 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16894 Ramachandran restraints generated. 8447 Oldfield, 0 Emsley, 8447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 467 time to evaluate : 5.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.4225 (ptp) cc_final: 0.3797 (ptt) REVERT: B 35 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8585 (tt) REVERT: C 202 GLU cc_start: 0.3617 (mm-30) cc_final: 0.3348 (mp0) REVERT: C 229 MET cc_start: 0.2156 (mmp) cc_final: 0.1858 (mmp) REVERT: C 336 GLU cc_start: 0.3391 (OUTLIER) cc_final: 0.2417 (tt0) REVERT: C 470 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.5867 (m-70) REVERT: D 323 MET cc_start: 0.2106 (ttp) cc_final: 0.1771 (ttm) REVERT: D 349 ASP cc_start: 0.1104 (OUTLIER) cc_final: 0.0173 (p0) REVERT: E 239 MET cc_start: 0.1784 (ttm) cc_final: 0.0631 (tpt) REVERT: E 371 MET cc_start: 0.3376 (ttp) cc_final: 0.3115 (ttt) REVERT: E 501 MET cc_start: 0.7906 (mmt) cc_final: 0.7297 (mmt) REVERT: G 382 MET cc_start: 0.1604 (mmp) cc_final: 0.0127 (mmt) REVERT: I 145 ARG cc_start: 0.3068 (mmt180) cc_final: 0.2097 (ttt-90) REVERT: I 167 PHE cc_start: 0.4500 (OUTLIER) cc_final: 0.3372 (m-80) REVERT: I 171 MET cc_start: 0.5303 (mtm) cc_final: 0.5069 (mpp) REVERT: I 189 ARG cc_start: 0.5396 (ttt-90) cc_final: 0.4892 (tmt170) REVERT: I 306 MET cc_start: 0.3213 (mmt) cc_final: 0.1607 (ptm) REVERT: I 344 MET cc_start: 0.3128 (mtm) cc_final: 0.1595 (mmp) REVERT: J 275 MET cc_start: -0.2804 (ptp) cc_final: -0.4223 (tpt) REVERT: K 266 ARG cc_start: 0.2772 (OUTLIER) cc_final: 0.1408 (mmp-170) REVERT: L 48 ILE cc_start: 0.7491 (pt) cc_final: 0.7207 (pt) REVERT: L 320 MET cc_start: 0.2958 (OUTLIER) cc_final: 0.2408 (mtm) REVERT: L 323 MET cc_start: 0.1150 (OUTLIER) cc_final: 0.0453 (mmm) REVERT: M 59 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7490 (mttp) REVERT: O 382 MET cc_start: 0.2013 (mmm) cc_final: 0.1396 (mmp) REVERT: P 85 MET cc_start: 0.8222 (mmm) cc_final: 0.7707 (mtp) REVERT: P 523 GLN cc_start: 0.6781 (mm-40) cc_final: 0.6547 (mm-40) outliers start: 122 outliers final: 100 residues processed: 563 average time/residue: 0.5508 time to fit residues: 550.4605 Evaluate side-chains 572 residues out of total 7095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 463 time to evaluate : 5.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 169 MET Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 236 CYS Chi-restraints excluded: chain I residue 384 MET Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 266 ARG Chi-restraints excluded: chain K residue 291 ILE Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 429 MET Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 488 VAL Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 310 SER Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 477 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 170 SER Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 500 THR Chi-restraints excluded: chain Q residue 216 ILE Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 182 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 529 optimal weight: 9.9990 chunk 709 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 614 optimal weight: 2.9990 chunk 98 optimal weight: 0.0970 chunk 185 optimal weight: 20.0000 chunk 667 optimal weight: 0.4980 chunk 279 optimal weight: 4.9990 chunk 685 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS H 346 HIS ** I 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS ** M 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.250467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.206009 restraints weight = 85573.868| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 2.75 r_work: 0.3957 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 65913 Z= 0.189 Angle : 0.579 11.380 88993 Z= 0.284 Chirality : 0.041 0.214 10649 Planarity : 0.003 0.071 11369 Dihedral : 5.425 149.055 9115 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 1.85 % Allowed : 21.87 % Favored : 76.28 % 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: -0.38 (0.09), residues: 8447 helix: 1.96 (0.08), residues: 4024 sheet: -0.50 (0.24), residues: 500 loop : -2.80 (0.09), residues: 3923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 493 HIS 0.036 0.001 HIS K 470 PHE 0.026 0.001 PHE N 336 TYR 0.017 0.001 TYR H 505 ARG 0.005 0.000 ARG N 432 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13152.98 seconds wall clock time: 230 minutes 11.83 seconds (13811.83 seconds total)