Starting phenix.real_space_refine on Mon Dec 30 21:45:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9u_35284/12_2024/8i9u_35284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9u_35284/12_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/cci-nas-00/data/ceres_data/8i9u_35284/12_2024/8i9u_35284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9u_35284/12_2024/8i9u_35284.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9u_35284/12_2024/8i9u_35284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9u_35284/12_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-5532/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: 29.48, per 1000 atoms: 0.45 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: 11.96 Conformation dependent library (CDL) restraints added in 6.4 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: 5.16 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: 22.75 Time building geometry restraints manager: 14.05 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: 2.250 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: 0.070 Extract box with map and model: 1.930 Check model and map are aligned: 0.370 Set scattering table: 0.470 Process input model: 107.540 Find NCS groups from input model: 5.410 Set up NCS constraints: 0.550 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.160 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 126 poor density : 996 time to evaluate : 5.448 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: 0.5857 time to fit residues: 1099.6444 Evaluate side-chains 601 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 571 time to evaluate : 5.507 ------------------------------------------------------------------------------- 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 0.251 10649 Planarity : 0.003 0.074 11369 Dihedral : 5.820 136.194 9154 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.95 % Favored : 92.90 % Rotamer: Outliers : 1.73 % Allowed : 18.89 % Favored : 79.38 % 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 to be fit. rotamer outliers: 123 poor density : 581 time to evaluate : 5.529 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: 0.3272 (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: -0.4061 (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: 0.5570 time to fit residues: 662.0204 Evaluate side-chains 559 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 513 time to evaluate : 5.382 ------------------------------------------------------------------------------- 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: 2.9990 chunk 236 optimal weight: 30.0000 chunk 634 optimal weight: 6.9990 chunk 519 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 764 optimal weight: 3.9990 chunk 825 optimal weight: 4.9990 chunk 680 optimal weight: 8.9990 chunk 757 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 613 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 464 GLN C 115 GLN D 301 GLN F 68 GLN F 84 GLN F 386 GLN G 117 HIS G 171 GLN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 K 470 HIS M 72 ASN M 290 GLN M 291 GLN M 505 HIS N 503 GLN O 117 HIS O 201 GLN O 282 HIS ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 472 GLN ** P 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 65913 Z= 0.425 Angle : 0.831 14.352 88993 Z= 0.415 Chirality : 0.049 0.301 10649 Planarity : 0.005 0.079 11369 Dihedral : 6.716 178.779 9124 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.28 % Favored : 91.63 % Rotamer: Outliers : 3.57 % Allowed : 19.00 % Favored : 77.43 % 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: -1.54 (0.09), residues: 8447 helix: 1.00 (0.08), residues: 3986 sheet: -1.00 (0.23), residues: 501 loop : -3.38 (0.08), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP O 493 HIS 0.044 0.002 HIS F 65 PHE 0.036 0.002 PHE G 125 TYR 0.032 0.002 TYR A 422 ARG 0.009 0.001 ARG H 520 *********************** 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 806 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 553 time to evaluate : 5.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.3601 (OUTLIER) cc_final: 0.3329 (m) REVERT: B 359 LEU cc_start: 0.1564 (OUTLIER) cc_final: 0.1250 (mm) REVERT: C 349 LEU cc_start: 0.4938 (OUTLIER) cc_final: 0.4695 (pt) REVERT: D 323 MET cc_start: 0.2283 (ttp) cc_final: 0.1916 (ttm) REVERT: D 349 ASP cc_start: 0.0649 (OUTLIER) cc_final: 0.0030 (p0) REVERT: E 220 GLU cc_start: 0.3518 (tp30) cc_final: 0.3241 (tp30) REVERT: E 239 MET cc_start: 0.1486 (ttm) cc_final: 0.1042 (ttp) REVERT: E 371 MET cc_start: 0.3154 (ttp) cc_final: 0.2942 (ttt) REVERT: E 501 MET cc_start: 0.6873 (mmp) cc_final: 0.6169 (mmt) REVERT: G 382 MET cc_start: 0.1246 (mmp) cc_final: -0.0153 (mmt) REVERT: H 120 ARG cc_start: 0.7570 (tpp-160) cc_final: 0.7295 (ttm-80) REVERT: H 300 MET cc_start: 0.4706 (mmm) cc_final: 0.4347 (mmm) REVERT: I 306 MET cc_start: 0.3306 (mmt) cc_final: 0.1717 (ptm) REVERT: J 53 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7594 (tt) REVERT: J 275 MET cc_start: -0.2537 (ptp) cc_final: -0.3816 (tpt) REVERT: L 260 MET cc_start: 0.3139 (ptp) cc_final: 0.2653 (ptm) REVERT: L 374 LEU cc_start: 0.2475 (OUTLIER) cc_final: 0.2243 (pp) REVERT: M 60 MET cc_start: 0.5236 (ppp) cc_final: 0.4340 (ttp) REVERT: M 133 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7691 (mt) REVERT: M 239 MET cc_start: 0.3891 (ttm) cc_final: 0.3588 (ttm) REVERT: M 371 MET cc_start: 0.3070 (OUTLIER) cc_final: 0.2708 (ttt) REVERT: N 487 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7110 (ppp) REVERT: O 81 ASP cc_start: 0.7266 (m-30) cc_final: 0.7053 (m-30) REVERT: O 382 MET cc_start: 0.2321 (mmm) cc_final: 0.1906 (mmp) REVERT: O 497 MET cc_start: 0.7539 (tpp) cc_final: 0.7262 (mmm) REVERT: R 97 ILE cc_start: 0.3519 (OUTLIER) cc_final: 0.3103 (tt) outliers start: 253 outliers final: 110 residues processed: 754 average time/residue: 0.5482 time to fit residues: 730.8905 Evaluate side-chains 595 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 475 time to evaluate : 5.567 ------------------------------------------------------------------------------- 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 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 A residue 490 LEU 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 310 MET 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 D residue 84 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 57 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 85 HIS 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 191 ASN Chi-restraints excluded: chain E residue 332 LEU 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 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 477 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 311 MET 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 J residue 53 LEU 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 265 THR 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 146 GLU Chi-restraints excluded: chain L residue 176 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 323 MET Chi-restraints excluded: chain L residue 374 LEU 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 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 371 MET Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 526 MET Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 310 ILE 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 71 VAL 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 O residue 473 THR 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 142 ILE Chi-restraints excluded: chain P residue 163 LEU 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 492 MET Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain R residue 97 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 755 optimal weight: 0.9990 chunk 574 optimal weight: 7.9990 chunk 396 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 364 optimal weight: 0.7980 chunk 513 optimal weight: 6.9990 chunk 766 optimal weight: 3.9990 chunk 811 optimal weight: 0.9990 chunk 400 optimal weight: 0.2980 chunk 726 optimal weight: 0.9990 chunk 218 optimal weight: 6.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 D 482 ASN F 65 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS H 477 ASN I 20 GLN ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS M 290 GLN M 505 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 65913 Z= 0.145 Angle : 0.558 11.574 88993 Z= 0.271 Chirality : 0.040 0.220 10649 Planarity : 0.003 0.066 11369 Dihedral : 5.774 178.888 9121 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 2.06 % Allowed : 20.93 % Favored : 77.01 % 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: -0.94 (0.09), residues: 8447 helix: 1.64 (0.08), residues: 3980 sheet: -0.78 (0.24), residues: 469 loop : -3.20 (0.08), residues: 3998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 485 HIS 0.007 0.001 HIS E 403 PHE 0.014 0.001 PHE P 22 TYR 0.015 0.001 TYR H 501 ARG 0.006 0.000 ARG K 200 *********************** 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 656 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 510 time to evaluate : 5.532 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 480 MET cc_start: 0.8204 (mmm) cc_final: 0.7661 (mmp) REVERT: C 117 MET cc_start: 0.2106 (mtm) cc_final: 0.1828 (mtm) REVERT: C 336 GLU cc_start: 0.2988 (OUTLIER) cc_final: 0.2138 (tt0) REVERT: C 470 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.6140 (m-70) REVERT: D 323 MET cc_start: 0.2066 (ttp) cc_final: 0.1677 (ttm) REVERT: E 208 LEU cc_start: 0.4132 (OUTLIER) cc_final: 0.3851 (tt) REVERT: E 239 MET cc_start: 0.1293 (ttm) cc_final: 0.0899 (ttp) REVERT: E 501 MET cc_start: 0.6797 (mmp) cc_final: 0.6072 (mmt) REVERT: F 108 LEU cc_start: 0.7386 (tt) cc_final: 0.7108 (tp) REVERT: G 382 MET cc_start: 0.1479 (mmp) cc_final: -0.0228 (mmt) REVERT: H 300 MET cc_start: 0.4492 (mmm) cc_final: 0.4206 (mmm) REVERT: I 105 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7011 (t0) REVERT: I 145 ARG cc_start: 0.3041 (mmt180) cc_final: 0.1853 (ttt-90) REVERT: I 306 MET cc_start: 0.3121 (mmt) cc_final: 0.1580 (ptm) REVERT: J 275 MET cc_start: -0.2730 (ptp) cc_final: -0.4133 (tpt) REVERT: J 436 MET cc_start: 0.7737 (mtt) cc_final: 0.7530 (mtm) REVERT: K 105 MET cc_start: 0.8279 (mtt) cc_final: 0.7869 (mtt) REVERT: L 260 MET cc_start: 0.2835 (ptp) cc_final: 0.2442 (ptm) REVERT: L 323 MET cc_start: 0.0961 (OUTLIER) cc_final: 0.0342 (mmm) REVERT: M 60 MET cc_start: 0.5283 (ppp) cc_final: 0.4827 (ptm) REVERT: M 239 MET cc_start: 0.3854 (ttm) cc_final: 0.3464 (mtp) REVERT: M 342 VAL cc_start: 0.1419 (OUTLIER) cc_final: 0.1216 (t) REVERT: O 394 MET cc_start: 0.6108 (mpp) cc_final: 0.5898 (mpp) REVERT: O 497 MET cc_start: 0.7263 (tpp) cc_final: 0.7035 (mmm) REVERT: P 14 MET cc_start: 0.5351 (ppp) cc_final: 0.5048 (ppp) REVERT: P 344 MET cc_start: 0.1805 (mpp) cc_final: 0.1325 (mtm) REVERT: P 492 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7010 (mtt) outliers start: 146 outliers final: 80 residues processed: 619 average time/residue: 0.5425 time to fit residues: 594.2266 Evaluate side-chains 549 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 462 time to evaluate : 5.336 ------------------------------------------------------------------------------- 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 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 372 CYS Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 429 MET 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 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 92 THR Chi-restraints excluded: chain F residue 137 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 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 171 GLN 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 492 VAL Chi-restraints excluded: chain H residue 14 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 117 VAL 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 144 VAL Chi-restraints excluded: chain K residue 426 SER Chi-restraints excluded: chain K residue 470 HIS 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 323 MET Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain L residue 514 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 85 HIS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain M residue 435 GLN Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 184 MET Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 127 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 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 676 optimal weight: 2.9990 chunk 460 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 604 optimal weight: 10.0000 chunk 335 optimal weight: 0.6980 chunk 692 optimal weight: 0.0770 chunk 561 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 414 optimal weight: 1.9990 chunk 728 optimal weight: 8.9990 chunk 204 optimal weight: 0.8980 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 470 HIS ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS ** M 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 505 HIS P 471 HIS P 477 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 65913 Z= 0.157 Angle : 0.541 9.546 88993 Z= 0.262 Chirality : 0.040 0.196 10649 Planarity : 0.003 0.065 11369 Dihedral : 5.398 168.318 9118 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 2.41 % Allowed : 20.61 % Favored : 76.98 % 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: -0.71 (0.09), residues: 8447 helix: 1.84 (0.08), residues: 3994 sheet: -0.70 (0.24), residues: 477 loop : -3.11 (0.08), residues: 3976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 485 HIS 0.023 0.001 HIS C 470 PHE 0.019 0.001 PHE G 175 TYR 0.013 0.001 TYR H 501 ARG 0.007 0.000 ARG I 443 *********************** 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 645 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 474 time to evaluate : 6.108 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 480 MET cc_start: 0.8193 (mmm) cc_final: 0.7631 (mmp) REVERT: C 117 MET cc_start: 0.1789 (mtm) cc_final: 0.1507 (mtm) REVERT: C 470 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.5842 (m-70) REVERT: D 323 MET cc_start: 0.1959 (ttp) cc_final: 0.1596 (ttm) REVERT: E 208 LEU cc_start: 0.4130 (OUTLIER) cc_final: 0.3839 (tt) REVERT: E 239 MET cc_start: 0.1378 (ttm) cc_final: 0.0298 (tpt) REVERT: E 501 MET cc_start: 0.6946 (mmp) cc_final: 0.6371 (mmt) REVERT: G 382 MET cc_start: 0.1164 (mmp) cc_final: -0.0458 (mmt) REVERT: H 300 MET cc_start: 0.4513 (mmm) cc_final: 0.4212 (mmm) REVERT: I 105 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.6972 (t0) REVERT: I 145 ARG cc_start: 0.3075 (mmt180) cc_final: 0.1909 (ttt-90) REVERT: I 306 MET cc_start: 0.3286 (mmt) cc_final: 0.1714 (ptm) REVERT: J 275 MET cc_start: -0.2733 (ptp) cc_final: -0.4157 (tpt) REVERT: J 436 MET cc_start: 0.7827 (mtt) cc_final: 0.7525 (mtm) REVERT: K 105 MET cc_start: 0.8298 (mtt) cc_final: 0.7909 (mtt) REVERT: L 260 MET cc_start: 0.2905 (ptp) cc_final: 0.2526 (ptm) REVERT: L 323 MET cc_start: 0.1168 (OUTLIER) cc_final: 0.0517 (mmm) REVERT: M 60 MET cc_start: 0.5316 (ppp) cc_final: 0.4914 (ptm) REVERT: M 239 MET cc_start: 0.3898 (ttm) cc_final: 0.3326 (mtp) REVERT: O 394 MET cc_start: 0.6204 (mpp) cc_final: 0.5996 (mpp) REVERT: O 497 MET cc_start: 0.7344 (tpp) cc_final: 0.7109 (mmm) REVERT: P 14 MET cc_start: 0.5208 (ppp) cc_final: 0.4920 (ppp) REVERT: P 344 MET cc_start: 0.1844 (mpp) cc_final: 0.1472 (mtm) outliers start: 171 outliers final: 104 residues processed: 604 average time/residue: 0.5538 time to fit residues: 594.5941 Evaluate side-chains 567 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 459 time to evaluate : 5.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 57 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 372 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 320 MET Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 102 ILE 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 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 492 VAL Chi-restraints excluded: chain H residue 324 LEU 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 117 VAL Chi-restraints excluded: chain I residue 171 MET 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 89 GLU Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 263 ASP 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 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 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 82 ASP Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 177 VAL 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 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 290 VAL Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 414 VAL Chi-restraints excluded: chain O residue 57 THR 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 405 VAL Chi-restraints excluded: chain O residue 417 SER 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 P residue 516 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain R residue 103 VAL 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: 7.9990 chunk 731 optimal weight: 0.0570 chunk 160 optimal weight: 0.9980 chunk 476 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 812 optimal weight: 0.0170 chunk 674 optimal weight: 2.9990 chunk 376 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 268 optimal weight: 0.9990 chunk 426 optimal weight: 9.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 470 HIS ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN K 470 HIS M 290 GLN M 505 HIS N 68 GLN ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 172 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 65913 Z= 0.129 Angle : 0.520 10.255 88993 Z= 0.250 Chirality : 0.040 0.239 10649 Planarity : 0.003 0.068 11369 Dihedral : 5.066 152.763 9117 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.61 % Favored : 94.33 % Rotamer: Outliers : 2.17 % Allowed : 20.92 % Favored : 76.91 % 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: -0.48 (0.09), residues: 8447 helix: 2.04 (0.08), residues: 3990 sheet: -0.51 (0.24), residues: 483 loop : -3.01 (0.08), residues: 3974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 485 HIS 0.028 0.001 HIS C 470 PHE 0.018 0.001 PHE G 175 TYR 0.014 0.001 TYR F 229 ARG 0.007 0.000 ARG I 145 *********************** 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 634 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 480 time to evaluate : 5.407 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: B 480 MET cc_start: 0.8201 (mmm) cc_final: 0.7630 (mmp) REVERT: C 336 GLU cc_start: 0.3187 (OUTLIER) cc_final: 0.2215 (tt0) REVERT: C 470 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6562 (m-70) REVERT: D 323 MET cc_start: 0.1909 (ttp) cc_final: 0.1557 (ttm) REVERT: E 208 LEU cc_start: 0.4067 (OUTLIER) cc_final: 0.3863 (tt) REVERT: E 239 MET cc_start: 0.1746 (ttm) cc_final: 0.0551 (tpt) REVERT: E 501 MET cc_start: 0.6946 (mmp) cc_final: 0.6335 (mmt) REVERT: G 185 MET cc_start: 0.4753 (OUTLIER) cc_final: 0.4531 (ptm) REVERT: G 323 MET cc_start: 0.3338 (tmm) cc_final: 0.2940 (ppp) REVERT: G 382 MET cc_start: 0.1180 (mmp) cc_final: -0.0555 (mmt) REVERT: H 300 MET cc_start: 0.4476 (mmm) cc_final: 0.4233 (mmm) REVERT: I 145 ARG cc_start: 0.3306 (mmt180) cc_final: 0.1953 (ttt-90) REVERT: I 189 ARG cc_start: 0.5107 (ttt-90) cc_final: 0.4566 (tmt170) REVERT: J 244 MET cc_start: 0.3951 (mmm) cc_final: 0.3441 (mpp) REVERT: J 275 MET cc_start: -0.2792 (ptp) cc_final: -0.4241 (tpt) REVERT: J 436 MET cc_start: 0.7727 (mtt) cc_final: 0.7447 (mtm) REVERT: K 105 MET cc_start: 0.8243 (mtt) cc_final: 0.7894 (mtt) REVERT: L 260 MET cc_start: 0.2977 (ptp) cc_final: 0.2635 (ptm) REVERT: L 323 MET cc_start: 0.1185 (OUTLIER) cc_final: 0.0497 (mmm) REVERT: M 239 MET cc_start: 0.3904 (ttm) cc_final: 0.3340 (mtp) REVERT: O 394 MET cc_start: 0.6295 (mpp) cc_final: 0.5733 (mpp) REVERT: O 497 MET cc_start: 0.7331 (tpp) cc_final: 0.7106 (mmm) REVERT: P 14 MET cc_start: 0.5160 (ppp) cc_final: 0.4850 (ppp) REVERT: P 140 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.7634 (m-70) REVERT: P 344 MET cc_start: 0.1897 (mpp) cc_final: 0.1487 (mtm) REVERT: P 492 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.6984 (mtt) outliers start: 154 outliers final: 104 residues processed: 593 average time/residue: 0.5402 time to fit residues: 569.9052 Evaluate side-chains 578 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 467 time to evaluate : 5.309 ------------------------------------------------------------------------------- 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 B residue 30 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 77 ASP 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 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 372 CYS Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 429 MET 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 320 MET Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 208 LEU 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 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 190 MET Chi-restraints excluded: chain F residue 196 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 154 LEU 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 169 MET Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 337 THR 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 171 MET 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 144 VAL Chi-restraints excluded: chain K residue 263 ASP 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 488 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 233 VAL 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 82 ASP 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 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 92 THR Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 290 VAL 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 108 VAL Chi-restraints excluded: chain O residue 267 VAL 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 140 HIS Chi-restraints excluded: chain P residue 191 PHE 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 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: 10.0000 chunk 91 optimal weight: 3.9990 chunk 463 optimal weight: 0.0670 chunk 593 optimal weight: 30.0000 chunk 459 optimal weight: 1.9990 chunk 684 optimal weight: 5.9990 chunk 453 optimal weight: 7.9990 chunk 809 optimal weight: 4.9990 chunk 506 optimal weight: 0.8980 chunk 493 optimal weight: 20.0000 chunk 373 optimal weight: 5.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- 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 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 HIS M 290 GLN M 505 HIS ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.4422 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= 0.225 Angle : 0.602 10.408 88993 Z= 0.295 Chirality : 0.042 0.251 10649 Planarity : 0.004 0.067 11369 Dihedral : 5.251 150.616 9116 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.42 % Favored : 93.51 % Rotamer: Outliers : 2.54 % Allowed : 20.83 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.09), residues: 8447 helix: 1.86 (0.08), residues: 4011 sheet: -0.46 (0.23), residues: 539 loop : -3.00 (0.08), residues: 3897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 493 HIS 0.038 0.001 HIS C 470 PHE 0.022 0.001 PHE P 103 TYR 0.018 0.001 TYR C 437 ARG 0.020 0.000 ARG C 200 *********************** 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 659 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 479 time to evaluate : 5.422 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: C 336 GLU cc_start: 0.3225 (OUTLIER) cc_final: 0.2219 (tt0) REVERT: D 323 MET cc_start: 0.1958 (ttp) cc_final: 0.1610 (ttm) REVERT: E 59 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7279 (mttp) REVERT: E 208 LEU cc_start: 0.4183 (OUTLIER) cc_final: 0.3977 (tt) REVERT: E 239 MET cc_start: 0.1777 (ttm) cc_final: 0.0511 (tpt) REVERT: F 143 MET cc_start: 0.6251 (mmp) cc_final: 0.5917 (mmp) REVERT: G 382 MET cc_start: 0.1393 (mmp) cc_final: -0.0485 (mmt) REVERT: I 105 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7142 (t0) REVERT: I 145 ARG cc_start: 0.3268 (mmt180) cc_final: 0.2021 (ttt-90) REVERT: I 306 MET cc_start: 0.3150 (mmt) cc_final: 0.1567 (ttt) REVERT: J 244 MET cc_start: 0.4256 (mmm) cc_final: 0.3806 (mpp) REVERT: J 275 MET cc_start: -0.2787 (ptp) cc_final: -0.4200 (tpt) REVERT: J 436 MET cc_start: 0.7977 (mtt) cc_final: 0.7593 (mtm) REVERT: K 105 MET cc_start: 0.8330 (mtt) cc_final: 0.7951 (mtt) REVERT: K 266 ARG cc_start: 0.2871 (OUTLIER) cc_final: 0.1611 (mmp-170) REVERT: L 260 MET cc_start: 0.3020 (ptp) cc_final: 0.2739 (ptm) REVERT: L 323 MET cc_start: 0.1229 (OUTLIER) cc_final: 0.0447 (mmm) REVERT: M 59 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.6911 (mttp) REVERT: M 239 MET cc_start: 0.4170 (ttm) cc_final: 0.3612 (mtp) REVERT: M 307 ASP cc_start: 0.1108 (OUTLIER) cc_final: 0.0545 (p0) REVERT: M 448 MET cc_start: 0.7229 (mtt) cc_final: 0.6430 (mtt) REVERT: O 382 MET cc_start: 0.2111 (mmm) cc_final: 0.1586 (mmp) REVERT: O 394 MET cc_start: 0.6451 (mpp) cc_final: 0.5840 (mpp) REVERT: O 442 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8158 (mp) REVERT: O 497 MET cc_start: 0.7518 (tpp) cc_final: 0.7269 (mmm) REVERT: P 14 MET cc_start: 0.5363 (ppp) cc_final: 0.4971 (ppp) REVERT: P 85 MET cc_start: 0.8318 (mmm) cc_final: 0.8028 (mtp) REVERT: P 523 GLN cc_start: 0.6479 (mm-40) cc_final: 0.6216 (mm-40) outliers start: 180 outliers final: 125 residues processed: 613 average time/residue: 0.5391 time to fit residues: 584.3072 Evaluate side-chains 595 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 461 time to evaluate : 5.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP 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 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 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 372 CYS 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 84 LEU Chi-restraints excluded: chain D residue 320 MET 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 57 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 85 HIS 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 208 LEU 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 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 477 VAL 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 214 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 169 MET Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 324 LEU 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 105 ASP Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 171 MET 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 266 ARG 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 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 509 VAL Chi-restraints excluded: chain L residue 532 ILE 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 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 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 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 259 LEU Chi-restraints excluded: chain N residue 310 ILE 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 95 THR Chi-restraints excluded: chain O residue 108 VAL 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 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 324 LEU Chi-restraints excluded: chain P residue 486 VAL Chi-restraints excluded: chain P residue 492 MET Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 229 LEU 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: 2.9990 chunk 323 optimal weight: 40.0000 chunk 483 optimal weight: 7.9990 chunk 243 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 514 optimal weight: 0.7980 chunk 551 optimal weight: 3.9990 chunk 400 optimal weight: 0.0040 chunk 75 optimal weight: 5.9990 chunk 636 optimal weight: 9.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- 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 470 HIS ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 ASN H 346 HIS I 353 GLN ** 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 ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 65913 Z= 0.216 Angle : 0.593 10.918 88993 Z= 0.292 Chirality : 0.042 0.249 10649 Planarity : 0.003 0.070 11369 Dihedral : 5.290 148.961 9114 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.93 % Rotamer: Outliers : 2.51 % Allowed : 20.92 % Favored : 76.58 % 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: -0.57 (0.09), residues: 8447 helix: 1.82 (0.08), residues: 4020 sheet: -0.47 (0.23), residues: 533 loop : -2.98 (0.08), residues: 3894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 493 HIS 0.020 0.001 HIS K 470 PHE 0.019 0.001 PHE G 175 TYR 0.014 0.001 TYR C 437 ARG 0.005 0.000 ARG I 443 *********************** 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 650 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 472 time to evaluate : 5.837 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: 0.4450 (ptp) cc_final: 0.3990 (ptt) REVERT: C 229 MET cc_start: 0.1775 (mmp) cc_final: 0.1563 (mmp) REVERT: C 336 GLU cc_start: 0.3388 (OUTLIER) cc_final: 0.2313 (tt0) REVERT: C 470 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.6210 (m-70) REVERT: D 323 MET cc_start: 0.2026 (ttp) cc_final: 0.1664 (ttm) REVERT: E 59 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7313 (mttp) REVERT: E 239 MET cc_start: 0.1768 (ttm) cc_final: 0.0545 (tpt) REVERT: E 426 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: E 532 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6524 (m-30) REVERT: F 143 MET cc_start: 0.6511 (mmp) cc_final: 0.6270 (mmp) REVERT: F 221 MET cc_start: 0.3851 (OUTLIER) cc_final: 0.3110 (mpp) REVERT: G 382 MET cc_start: 0.1315 (mmp) cc_final: -0.0478 (mmt) REVERT: H 300 MET cc_start: 0.4423 (mmm) cc_final: 0.4140 (mmm) REVERT: I 145 ARG cc_start: 0.3045 (mmt180) cc_final: 0.1943 (ttt-90) REVERT: I 306 MET cc_start: 0.2891 (mmt) cc_final: 0.1333 (ttt) REVERT: J 275 MET cc_start: -0.2806 (ptp) cc_final: -0.4196 (tpt) REVERT: J 436 MET cc_start: 0.7992 (mtt) cc_final: 0.7778 (mtm) REVERT: K 266 ARG cc_start: 0.2777 (OUTLIER) cc_final: 0.1445 (mmp-170) REVERT: L 48 ILE cc_start: 0.7427 (pt) cc_final: 0.7178 (pt) REVERT: L 260 MET cc_start: 0.3243 (ptp) cc_final: 0.2978 (ptm) REVERT: L 320 MET cc_start: 0.3288 (OUTLIER) cc_final: 0.2665 (mtm) REVERT: L 323 MET cc_start: 0.1039 (OUTLIER) cc_final: 0.0270 (mmm) REVERT: M 59 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7311 (mttp) REVERT: M 239 MET cc_start: 0.4178 (ttm) cc_final: 0.3758 (mtp) REVERT: M 307 ASP cc_start: 0.1723 (OUTLIER) cc_final: 0.1227 (p0) REVERT: M 448 MET cc_start: 0.7336 (mtt) cc_final: 0.6534 (mtt) REVERT: O 382 MET cc_start: 0.2271 (mmm) cc_final: 0.1619 (mmp) REVERT: O 394 MET cc_start: 0.6530 (mpp) cc_final: 0.5926 (mpp) REVERT: P 14 MET cc_start: 0.5141 (ppp) cc_final: 0.4870 (ppp) REVERT: P 85 MET cc_start: 0.8327 (mmm) cc_final: 0.7738 (mtp) outliers start: 178 outliers final: 127 residues processed: 606 average time/residue: 0.5309 time to fit residues: 569.1010 Evaluate side-chains 598 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 460 time to evaluate : 5.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP 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 38 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 310 MET 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 121 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 372 CYS 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 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 115 SER Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 320 MET 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 57 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 526 MET Chi-restraints excluded: chain E residue 532 ASP 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 189 PHE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 221 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 214 VAL Chi-restraints excluded: chain G residue 405 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 324 LEU 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 171 MET Chi-restraints excluded: chain I residue 384 MET 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 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 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 488 VAL Chi-restraints excluded: chain K residue 501 VAL 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 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 59 LYS Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 82 ASP 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 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 M residue 526 MET 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 310 ILE 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 71 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL 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 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 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 P residue 516 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 736 optimal weight: 8.9990 chunk 775 optimal weight: 5.9990 chunk 707 optimal weight: 2.9990 chunk 754 optimal weight: 6.9990 chunk 454 optimal weight: 6.9990 chunk 328 optimal weight: 9.9990 chunk 592 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 681 optimal weight: 0.0020 chunk 713 optimal weight: 1.9990 chunk 751 optimal weight: 4.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- 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 470 HIS D 406 HIS D 482 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 GLN ** 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 ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 65913 Z= 0.266 Angle : 0.650 11.217 88993 Z= 0.321 Chirality : 0.043 0.244 10649 Planarity : 0.004 0.069 11369 Dihedral : 5.487 151.774 9114 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 2.35 % Allowed : 20.92 % Favored : 76.73 % 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: -0.70 (0.09), residues: 8447 helix: 1.66 (0.08), residues: 4024 sheet: -0.68 (0.23), residues: 521 loop : -2.95 (0.08), residues: 3902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 493 HIS 0.037 0.001 HIS C 470 PHE 0.022 0.001 PHE P 103 TYR 0.018 0.001 TYR C 437 ARG 0.006 0.000 ARG C 377 *********************** 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 634 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 467 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: A 306 MET cc_start: 0.4305 (ptp) cc_final: 0.3864 (ptt) REVERT: C 336 GLU cc_start: 0.3456 (OUTLIER) cc_final: 0.2366 (tt0) REVERT: C 470 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.6966 (m-70) REVERT: D 323 MET cc_start: 0.2122 (ttp) cc_final: 0.1758 (ttm) REVERT: E 59 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7449 (tppt) REVERT: E 239 MET cc_start: 0.1902 (ttm) cc_final: 0.0724 (tpt) REVERT: E 426 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: F 120 THR cc_start: 0.8364 (m) cc_final: 0.8080 (p) REVERT: F 143 MET cc_start: 0.6549 (mmp) cc_final: 0.6347 (mmp) REVERT: F 321 MET cc_start: 0.4243 (pmm) cc_final: 0.3985 (pmm) REVERT: G 323 MET cc_start: 0.3633 (tmm) cc_final: 0.2808 (ppp) REVERT: G 382 MET cc_start: 0.1622 (mmp) cc_final: 0.0096 (mmt) REVERT: I 145 ARG cc_start: 0.3294 (mmt180) cc_final: 0.2166 (ttt-90) REVERT: I 167 PHE cc_start: 0.4227 (OUTLIER) cc_final: 0.3888 (m-80) REVERT: I 430 MET cc_start: 0.6340 (tpp) cc_final: 0.5941 (tpp) REVERT: J 275 MET cc_start: -0.2907 (ptp) cc_final: -0.3983 (tpt) REVERT: J 436 MET cc_start: 0.8078 (mtt) cc_final: 0.7702 (mtm) REVERT: K 266 ARG cc_start: 0.2798 (OUTLIER) cc_final: 0.1447 (mmp-170) REVERT: L 320 MET cc_start: 0.3418 (OUTLIER) cc_final: 0.2841 (mtm) REVERT: L 323 MET cc_start: 0.1165 (OUTLIER) cc_final: 0.0400 (mmm) REVERT: M 59 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7512 (mttm) REVERT: M 239 MET cc_start: 0.4277 (ttm) cc_final: 0.3850 (mtp) REVERT: M 307 ASP cc_start: 0.1833 (OUTLIER) cc_final: 0.1231 (p0) REVERT: M 448 MET cc_start: 0.7415 (mtt) cc_final: 0.6613 (mtt) REVERT: M 468 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7085 (ptm) REVERT: O 382 MET cc_start: 0.2510 (mmm) cc_final: 0.1725 (mmp) REVERT: O 394 MET cc_start: 0.6647 (mpp) cc_final: 0.6007 (mpp) REVERT: P 14 MET cc_start: 0.5392 (ppp) cc_final: 0.5115 (ppp) REVERT: P 85 MET cc_start: 0.8343 (mmm) cc_final: 0.7807 (mtp) outliers start: 167 outliers final: 132 residues processed: 595 average time/residue: 0.5342 time to fit residues: 563.4844 Evaluate side-chains 591 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 448 time to evaluate : 5.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP 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 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 121 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 374 ILE 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 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 115 SER 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 57 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 491 ILE 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 189 PHE 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 361 THR 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 405 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 324 LEU Chi-restraints excluded: chain H residue 333 LEU 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 106 GLU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 384 MET 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 144 VAL Chi-restraints excluded: chain K residue 263 ASP 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 429 MET 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 61 ILE 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 94 LEU 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 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 468 MET Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 139 VAL 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 361 THR 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 71 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 108 VAL 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 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 233 SER 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 492 MET 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 Chi-restraints excluded: chain R residue 217 GLU 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: 0.2980 chunk 486 optimal weight: 8.9990 chunk 378 optimal weight: 7.9990 chunk 554 optimal weight: 3.9990 chunk 836 optimal weight: 0.9980 chunk 770 optimal weight: 0.9990 chunk 666 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 514 optimal weight: 0.9980 chunk 408 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 470 HIS ** E 191 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 ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 65913 Z= 0.139 Angle : 0.555 12.684 88993 Z= 0.271 Chirality : 0.040 0.288 10649 Planarity : 0.003 0.072 11369 Dihedral : 5.147 146.664 9114 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 1.68 % Allowed : 21.86 % 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: 1.96 (0.08), residues: 4022 sheet: -0.35 (0.23), residues: 516 loop : -2.85 (0.09), residues: 3909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 485 HIS 0.016 0.001 HIS D 406 PHE 0.019 0.001 PHE G 175 TYR 0.014 0.001 TYR F 229 ARG 0.004 0.000 ARG M 534 ********************** 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 587 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 468 time to evaluate : 5.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.4194 (ptp) cc_final: 0.3780 (ptt) REVERT: C 336 GLU cc_start: 0.3419 (OUTLIER) cc_final: 0.2358 (tt0) REVERT: C 470 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.5918 (m-70) REVERT: D 323 MET cc_start: 0.2003 (ttp) cc_final: 0.1670 (ttm) REVERT: E 239 MET cc_start: 0.1763 (ttm) cc_final: 0.0614 (tpt) REVERT: F 108 LEU cc_start: 0.7594 (tt) cc_final: 0.7361 (tp) REVERT: F 221 MET cc_start: 0.3433 (OUTLIER) cc_final: 0.2982 (mpp) REVERT: G 323 MET cc_start: 0.3633 (tmm) cc_final: 0.2752 (ppp) REVERT: G 382 MET cc_start: 0.1817 (mmp) cc_final: 0.0264 (mmt) REVERT: I 145 ARG cc_start: 0.3035 (mmt180) cc_final: 0.1967 (ttt-90) REVERT: I 167 PHE cc_start: 0.4161 (OUTLIER) cc_final: 0.3783 (m-80) REVERT: I 189 ARG cc_start: 0.5328 (ttt-90) cc_final: 0.4850 (tmt170) REVERT: I 306 MET cc_start: 0.3077 (mmt) cc_final: 0.1465 (ttt) REVERT: I 388 MET cc_start: 0.4123 (mmm) cc_final: 0.3904 (mmt) REVERT: J 275 MET cc_start: -0.2950 (ptp) cc_final: -0.4039 (tpt) REVERT: K 266 ARG cc_start: 0.2781 (OUTLIER) cc_final: 0.1430 (mmp-170) REVERT: L 320 MET cc_start: 0.2968 (OUTLIER) cc_final: 0.2401 (mtm) REVERT: L 323 MET cc_start: 0.0921 (OUTLIER) cc_final: 0.0291 (mmm) REVERT: M 28 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5302 (mt) REVERT: M 59 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7387 (mttp) REVERT: M 239 MET cc_start: 0.4231 (ttm) cc_final: 0.3797 (mtp) REVERT: O 382 MET cc_start: 0.2166 (mmm) cc_final: 0.1574 (mmp) REVERT: O 394 MET cc_start: 0.6546 (mpp) cc_final: 0.5949 (mpp) REVERT: P 85 MET cc_start: 0.8264 (mmm) cc_final: 0.7708 (mtp) REVERT: P 492 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7640 (mtt) outliers start: 119 outliers final: 95 residues processed: 559 average time/residue: 0.5614 time to fit residues: 555.6584 Evaluate side-chains 558 residues out of total 7095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 453 time to evaluate : 5.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP 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 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 372 CYS Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 470 HIS 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 509 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 243 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 189 PHE Chi-restraints excluded: chain F residue 221 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 361 THR 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 185 MET 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 169 MET Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 333 LEU 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 167 PHE Chi-restraints excluded: chain I residue 236 CYS Chi-restraints excluded: chain I residue 384 MET Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 249 ILE 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 266 ARG 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 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 320 MET Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 386 VAL 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 166 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain N residue 92 THR 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 O residue 32 ILE 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 267 VAL Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 417 SER 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 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 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: 40.0000 chunk 709 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 614 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 185 optimal weight: 7.9990 chunk 667 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 685 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 470 HIS ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS ** 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 = 0.4744 r_free = 0.4744 target = 0.249454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.205859 restraints weight = 85339.005| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 2.70 r_work: 0.3955 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 65913 Z= 0.219 Angle : 0.611 12.432 88993 Z= 0.299 Chirality : 0.042 0.213 10649 Planarity : 0.004 0.070 11369 Dihedral : 5.269 150.576 9114 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.22 % Favored : 93.70 % Rotamer: Outliers : 1.82 % Allowed : 21.89 % Favored : 76.29 % 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: -0.46 (0.09), residues: 8447 helix: 1.87 (0.08), residues: 4024 sheet: -0.34 (0.23), residues: 516 loop : -2.86 (0.09), residues: 3907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 493 HIS 0.020 0.001 HIS K 470 PHE 0.036 0.001 PHE N 336 TYR 0.016 0.001 TYR C 437 ARG 0.004 0.000 ARG I 443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11873.88 seconds wall clock time: 210 minutes 35.84 seconds (12635.84 seconds total)