Starting phenix.real_space_refine on Sat Sep 28 15:20:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/09_2024/3jbt_6480.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/09_2024/3jbt_6480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/09_2024/3jbt_6480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/09_2024/3jbt_6480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/09_2024/3jbt_6480.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbt_6480/09_2024/3jbt_6480.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Fe 7 7.16 5 P 21 5.49 5 Mg 7 5.21 5 S 455 5.16 5 C 44499 2.51 5 N 12054 2.21 5 O 13209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 161 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 70252 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "B" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, E, G, I, K, M, D, F, H, J, L, N Time building chain proxies: 24.56, per 1000 atoms: 0.35 Number of scatterers: 70252 At special positions: 0 Unit cell: (306.24, 306.24, 87.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 7 26.01 S 455 16.00 P 21 15.00 Mg 7 11.99 O 13209 8.00 N 12054 7.00 C 44499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 663 " distance=2.20 Simple disulfide: pdb=" SG CYS A 675 " - pdb=" SG CYS A 705 " distance=2.02 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS A 749 " distance=1.89 Simple disulfide: pdb=" SG CYS A 761 " - pdb=" SG CYS A 804 " distance=2.05 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 846 " distance=2.09 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.09 Conformation dependent library (CDL) restraints added in 7.3 seconds 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16464 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 133 sheets defined 30.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.69 Creating SS restraints... Processing helix chain 'A' and resid 107 through 118 removed outlier: 3.556A pdb=" N ARG A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 removed outlier: 4.126A pdb=" N LEU A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.562A pdb=" N VAL A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.939A pdb=" N LEU A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.627A pdb=" N MET A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 247 through 255 removed outlier: 4.032A pdb=" N LEU A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 307 through 318 removed outlier: 4.358A pdb=" N HIS A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 334 removed outlier: 3.831A pdb=" N ASP A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 4.118A pdb=" N TYR A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.531A pdb=" N MET A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 386 removed outlier: 3.713A pdb=" N ASP A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 407 through 421 removed outlier: 4.149A pdb=" N ASP A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 467 removed outlier: 7.002A pdb=" N SER A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A 461 " --> pdb=" O HIS A 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.818A pdb=" N ALA A 488 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR A 489 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.538A pdb=" N GLU A 528 " --> pdb=" O HIS A 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 550 removed outlier: 3.666A pdb=" N VAL A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 555 removed outlier: 4.769A pdb=" N LEU A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 575 through 591 removed outlier: 3.554A pdb=" N LEU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 589 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 911 through 916 removed outlier: 4.140A pdb=" N CYS A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 916' Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 49 through 55 Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.523A pdb=" N GLU B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'C' and resid 107 through 118 removed outlier: 3.556A pdb=" N ARG C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 143 removed outlier: 4.126A pdb=" N LEU C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.562A pdb=" N VAL C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.939A pdb=" N LEU C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 207 removed outlier: 3.627A pdb=" N MET C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 233 Processing helix chain 'C' and resid 247 through 255 removed outlier: 4.033A pdb=" N LEU C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 300 Processing helix chain 'C' and resid 307 through 318 removed outlier: 4.357A pdb=" N HIS C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS C 315 " --> pdb=" O HIS C 311 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 334 removed outlier: 3.831A pdb=" N ASP C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 removed outlier: 4.118A pdb=" N TYR C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 342 " --> pdb=" O TRP C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.531A pdb=" N MET C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 370 " --> pdb=" O GLU C 366 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 removed outlier: 3.712A pdb=" N ASP C 381 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR C 382 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 407 through 421 removed outlier: 4.149A pdb=" N ASP C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 414 " --> pdb=" O GLU C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 467 removed outlier: 7.003A pdb=" N SER C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN C 452 " --> pdb=" O LYS C 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN C 454 " --> pdb=" O CYS C 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP C 455 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE C 461 " --> pdb=" O HIS C 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 495 removed outlier: 3.818A pdb=" N ALA C 488 " --> pdb=" O TYR C 484 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR C 489 " --> pdb=" O ASN C 485 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 492 " --> pdb=" O ALA C 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 493 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 504 Processing helix chain 'C' and resid 506 through 517 Processing helix chain 'C' and resid 520 through 533 removed outlier: 3.537A pdb=" N GLU C 528 " --> pdb=" O HIS C 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 550 removed outlier: 3.666A pdb=" N VAL C 540 " --> pdb=" O LYS C 536 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 555 removed outlier: 4.769A pdb=" N LEU C 554 " --> pdb=" O LEU C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 575 through 591 removed outlier: 3.554A pdb=" N LEU C 582 " --> pdb=" O GLN C 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP C 589 " --> pdb=" O LYS C 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN C 590 " --> pdb=" O GLN C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 850 through 852 No H-bonds generated for 'chain 'C' and resid 850 through 852' Processing helix chain 'C' and resid 911 through 916 removed outlier: 4.140A pdb=" N CYS C 915 " --> pdb=" O THR C 911 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 916 " --> pdb=" O LYS C 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 916' Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 49 through 55 Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.523A pdb=" N GLU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.557A pdb=" N ARG E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 143 removed outlier: 4.126A pdb=" N LEU E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 170 removed outlier: 3.562A pdb=" N VAL E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 178 removed outlier: 3.940A pdb=" N LEU E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 207 removed outlier: 3.627A pdb=" N MET E 197 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 233 Processing helix chain 'E' and resid 247 through 255 removed outlier: 4.032A pdb=" N LEU E 251 " --> pdb=" O ASP E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 307 through 318 removed outlier: 4.358A pdb=" N HIS E 311 " --> pdb=" O PRO E 307 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS E 315 " --> pdb=" O HIS E 311 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 334 removed outlier: 3.831A pdb=" N ASP E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 removed outlier: 4.119A pdb=" N TYR E 341 " --> pdb=" O ARG E 337 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU E 342 " --> pdb=" O TRP E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 374 removed outlier: 3.531A pdb=" N MET E 368 " --> pdb=" O LEU E 364 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE E 370 " --> pdb=" O GLU E 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU E 373 " --> pdb=" O SER E 369 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET E 374 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 386 removed outlier: 3.712A pdb=" N ASP E 381 " --> pdb=" O GLU E 377 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR E 382 " --> pdb=" O ASP E 378 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 405 Processing helix chain 'E' and resid 407 through 421 removed outlier: 4.149A pdb=" N ASP E 413 " --> pdb=" O GLU E 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 414 " --> pdb=" O GLU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 467 removed outlier: 7.002A pdb=" N SER E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN E 452 " --> pdb=" O LYS E 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN E 454 " --> pdb=" O CYS E 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP E 455 " --> pdb=" O SER E 451 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS E 458 " --> pdb=" O GLN E 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE E 461 " --> pdb=" O HIS E 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 495 removed outlier: 3.818A pdb=" N ALA E 488 " --> pdb=" O TYR E 484 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR E 489 " --> pdb=" O ASN E 485 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET E 491 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA E 492 " --> pdb=" O ALA E 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER E 493 " --> pdb=" O TYR E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 504 Processing helix chain 'E' and resid 506 through 517 Processing helix chain 'E' and resid 520 through 533 removed outlier: 3.537A pdb=" N GLU E 528 " --> pdb=" O HIS E 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS E 531 " --> pdb=" O VAL E 527 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE E 532 " --> pdb=" O GLU E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 550 removed outlier: 3.666A pdb=" N VAL E 540 " --> pdb=" O LYS E 536 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 555 removed outlier: 4.770A pdb=" N LEU E 554 " --> pdb=" O LEU E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 567 Processing helix chain 'E' and resid 575 through 591 removed outlier: 3.554A pdb=" N LEU E 582 " --> pdb=" O GLN E 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP E 589 " --> pdb=" O LYS E 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN E 590 " --> pdb=" O GLN E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'E' and resid 850 through 852 No H-bonds generated for 'chain 'E' and resid 850 through 852' Processing helix chain 'E' and resid 911 through 916 removed outlier: 4.140A pdb=" N CYS E 915 " --> pdb=" O THR E 911 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS E 916 " --> pdb=" O LYS E 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 911 through 916' Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 49 through 55 Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.523A pdb=" N GLU F 69 " --> pdb=" O MET F 65 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 75 Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'G' and resid 107 through 118 removed outlier: 3.557A pdb=" N ARG G 111 " --> pdb=" O THR G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 143 removed outlier: 4.127A pdb=" N LEU G 143 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 170 removed outlier: 3.562A pdb=" N VAL G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP G 170 " --> pdb=" O GLU G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 178 removed outlier: 3.940A pdb=" N LEU G 174 " --> pdb=" O ASP G 170 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 207 removed outlier: 3.627A pdb=" N MET G 197 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS G 198 " --> pdb=" O GLY G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 233 Processing helix chain 'G' and resid 247 through 255 removed outlier: 4.032A pdb=" N LEU G 251 " --> pdb=" O ASP G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 300 Processing helix chain 'G' and resid 307 through 318 removed outlier: 4.357A pdb=" N HIS G 311 " --> pdb=" O PRO G 307 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER G 312 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS G 315 " --> pdb=" O HIS G 311 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU G 316 " --> pdb=" O SER G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 334 removed outlier: 3.831A pdb=" N ASP G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 348 removed outlier: 4.119A pdb=" N TYR G 341 " --> pdb=" O ARG G 337 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU G 342 " --> pdb=" O TRP G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 374 removed outlier: 3.531A pdb=" N MET G 368 " --> pdb=" O LEU G 364 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE G 370 " --> pdb=" O GLU G 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU G 373 " --> pdb=" O SER G 369 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET G 374 " --> pdb=" O ILE G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 386 removed outlier: 3.712A pdb=" N ASP G 381 " --> pdb=" O GLU G 377 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR G 382 " --> pdb=" O ASP G 378 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR G 384 " --> pdb=" O LYS G 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP G 385 " --> pdb=" O ASP G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 405 Processing helix chain 'G' and resid 407 through 421 removed outlier: 4.149A pdb=" N ASP G 413 " --> pdb=" O GLU G 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE G 414 " --> pdb=" O GLU G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 467 removed outlier: 7.003A pdb=" N SER G 451 " --> pdb=" O GLU G 447 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN G 452 " --> pdb=" O LYS G 448 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN G 454 " --> pdb=" O CYS G 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP G 455 " --> pdb=" O SER G 451 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS G 458 " --> pdb=" O GLN G 454 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE G 461 " --> pdb=" O HIS G 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR G 462 " --> pdb=" O LYS G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 479 through 495 removed outlier: 3.819A pdb=" N ALA G 488 " --> pdb=" O TYR G 484 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR G 489 " --> pdb=" O ASN G 485 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET G 491 " --> pdb=" O LEU G 487 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA G 492 " --> pdb=" O ALA G 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER G 493 " --> pdb=" O TYR G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 504 Processing helix chain 'G' and resid 506 through 517 Processing helix chain 'G' and resid 520 through 533 removed outlier: 3.538A pdb=" N GLU G 528 " --> pdb=" O HIS G 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS G 531 " --> pdb=" O VAL G 527 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 532 " --> pdb=" O GLU G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 550 removed outlier: 3.666A pdb=" N VAL G 540 " --> pdb=" O LYS G 536 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU G 550 " --> pdb=" O GLU G 546 " (cutoff:3.500A) Processing helix chain 'G' and resid 550 through 555 removed outlier: 4.769A pdb=" N LEU G 554 " --> pdb=" O LEU G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 567 Processing helix chain 'G' and resid 575 through 591 removed outlier: 3.553A pdb=" N LEU G 582 " --> pdb=" O GLN G 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP G 589 " --> pdb=" O LYS G 585 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN G 590 " --> pdb=" O GLN G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing helix chain 'G' and resid 850 through 852 No H-bonds generated for 'chain 'G' and resid 850 through 852' Processing helix chain 'G' and resid 911 through 916 removed outlier: 4.140A pdb=" N CYS G 915 " --> pdb=" O THR G 911 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS G 916 " --> pdb=" O LYS G 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 911 through 916' Processing helix chain 'H' and resid 2 through 14 Processing helix chain 'H' and resid 49 through 55 Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.523A pdb=" N GLU H 69 " --> pdb=" O MET H 65 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 75 Processing helix chain 'H' and resid 87 through 102 Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.558A pdb=" N ARG I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 143 removed outlier: 4.126A pdb=" N LEU I 143 " --> pdb=" O LYS I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 170 removed outlier: 3.562A pdb=" N VAL I 168 " --> pdb=" O ALA I 164 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP I 170 " --> pdb=" O GLU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 178 removed outlier: 3.939A pdb=" N LEU I 174 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 207 removed outlier: 3.627A pdb=" N MET I 197 " --> pdb=" O SER I 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS I 198 " --> pdb=" O GLY I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 233 Processing helix chain 'I' and resid 247 through 255 removed outlier: 4.033A pdb=" N LEU I 251 " --> pdb=" O ASP I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 300 Processing helix chain 'I' and resid 307 through 318 removed outlier: 4.357A pdb=" N HIS I 311 " --> pdb=" O PRO I 307 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER I 312 " --> pdb=" O GLU I 308 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE I 313 " --> pdb=" O GLN I 309 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE I 314 " --> pdb=" O ALA I 310 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS I 315 " --> pdb=" O HIS I 311 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU I 316 " --> pdb=" O SER I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 334 removed outlier: 3.831A pdb=" N ASP I 333 " --> pdb=" O ALA I 329 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE I 334 " --> pdb=" O LEU I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 348 removed outlier: 4.119A pdb=" N TYR I 341 " --> pdb=" O ARG I 337 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU I 342 " --> pdb=" O TRP I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 374 removed outlier: 3.532A pdb=" N MET I 368 " --> pdb=" O LEU I 364 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE I 370 " --> pdb=" O GLU I 366 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU I 373 " --> pdb=" O SER I 369 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET I 374 " --> pdb=" O ILE I 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 386 removed outlier: 3.712A pdb=" N ASP I 381 " --> pdb=" O GLU I 377 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR I 382 " --> pdb=" O ASP I 378 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR I 384 " --> pdb=" O LYS I 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP I 385 " --> pdb=" O ASP I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 405 Processing helix chain 'I' and resid 407 through 421 removed outlier: 4.149A pdb=" N ASP I 413 " --> pdb=" O GLU I 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE I 414 " --> pdb=" O GLU I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 467 removed outlier: 7.003A pdb=" N SER I 451 " --> pdb=" O GLU I 447 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN I 452 " --> pdb=" O LYS I 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN I 454 " --> pdb=" O CYS I 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP I 455 " --> pdb=" O SER I 451 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS I 458 " --> pdb=" O GLN I 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS I 459 " --> pdb=" O ASP I 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE I 461 " --> pdb=" O HIS I 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR I 462 " --> pdb=" O LYS I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 479 through 495 removed outlier: 3.819A pdb=" N ALA I 488 " --> pdb=" O TYR I 484 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR I 489 " --> pdb=" O ASN I 485 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET I 491 " --> pdb=" O LEU I 487 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA I 492 " --> pdb=" O ALA I 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER I 493 " --> pdb=" O TYR I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 504 Processing helix chain 'I' and resid 506 through 517 Processing helix chain 'I' and resid 520 through 533 removed outlier: 3.538A pdb=" N GLU I 528 " --> pdb=" O HIS I 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS I 531 " --> pdb=" O VAL I 527 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE I 532 " --> pdb=" O GLU I 528 " (cutoff:3.500A) Processing helix chain 'I' and resid 534 through 550 removed outlier: 3.666A pdb=" N VAL I 540 " --> pdb=" O LYS I 536 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU I 550 " --> pdb=" O GLU I 546 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 555 removed outlier: 4.769A pdb=" N LEU I 554 " --> pdb=" O LEU I 550 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 567 Processing helix chain 'I' and resid 575 through 591 removed outlier: 3.553A pdb=" N LEU I 582 " --> pdb=" O GLN I 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP I 589 " --> pdb=" O LYS I 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN I 590 " --> pdb=" O GLN I 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 603 Processing helix chain 'I' and resid 850 through 852 No H-bonds generated for 'chain 'I' and resid 850 through 852' Processing helix chain 'I' and resid 911 through 916 removed outlier: 4.140A pdb=" N CYS I 915 " --> pdb=" O THR I 911 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS I 916 " --> pdb=" O LYS I 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 911 through 916' Processing helix chain 'J' and resid 2 through 14 Processing helix chain 'J' and resid 49 through 55 Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.523A pdb=" N GLU J 69 " --> pdb=" O MET J 65 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN J 70 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 75 Processing helix chain 'J' and resid 87 through 102 Processing helix chain 'K' and resid 107 through 118 removed outlier: 3.558A pdb=" N ARG K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 143 removed outlier: 4.126A pdb=" N LEU K 143 " --> pdb=" O LYS K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 170 removed outlier: 3.562A pdb=" N VAL K 168 " --> pdb=" O ALA K 164 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP K 170 " --> pdb=" O GLU K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 178 removed outlier: 3.940A pdb=" N LEU K 174 " --> pdb=" O ASP K 170 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 207 removed outlier: 3.627A pdb=" N MET K 197 " --> pdb=" O SER K 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS K 198 " --> pdb=" O GLY K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 233 Processing helix chain 'K' and resid 247 through 255 removed outlier: 4.033A pdb=" N LEU K 251 " --> pdb=" O ASP K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 300 Processing helix chain 'K' and resid 307 through 318 removed outlier: 4.357A pdb=" N HIS K 311 " --> pdb=" O PRO K 307 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER K 312 " --> pdb=" O GLU K 308 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE K 313 " --> pdb=" O GLN K 309 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE K 314 " --> pdb=" O ALA K 310 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS K 315 " --> pdb=" O HIS K 311 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU K 316 " --> pdb=" O SER K 312 " (cutoff:3.500A) Processing helix chain 'K' and resid 320 through 334 removed outlier: 3.831A pdb=" N ASP K 333 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE K 334 " --> pdb=" O LEU K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 337 through 348 removed outlier: 4.119A pdb=" N TYR K 341 " --> pdb=" O ARG K 337 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU K 342 " --> pdb=" O TRP K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 374 removed outlier: 3.532A pdb=" N MET K 368 " --> pdb=" O LEU K 364 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE K 370 " --> pdb=" O GLU K 366 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU K 373 " --> pdb=" O SER K 369 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET K 374 " --> pdb=" O ILE K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 376 through 386 removed outlier: 3.712A pdb=" N ASP K 381 " --> pdb=" O GLU K 377 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR K 382 " --> pdb=" O ASP K 378 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR K 384 " --> pdb=" O LYS K 380 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP K 385 " --> pdb=" O ASP K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 405 Processing helix chain 'K' and resid 407 through 421 removed outlier: 4.149A pdb=" N ASP K 413 " --> pdb=" O GLU K 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE K 414 " --> pdb=" O GLU K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 438 through 467 removed outlier: 7.003A pdb=" N SER K 451 " --> pdb=" O GLU K 447 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN K 452 " --> pdb=" O LYS K 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN K 454 " --> pdb=" O CYS K 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP K 455 " --> pdb=" O SER K 451 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS K 458 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS K 459 " --> pdb=" O ASP K 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE K 461 " --> pdb=" O HIS K 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR K 462 " --> pdb=" O LYS K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 495 removed outlier: 3.818A pdb=" N ALA K 488 " --> pdb=" O TYR K 484 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR K 489 " --> pdb=" O ASN K 485 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET K 491 " --> pdb=" O LEU K 487 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA K 492 " --> pdb=" O ALA K 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER K 493 " --> pdb=" O TYR K 489 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 504 Processing helix chain 'K' and resid 506 through 517 Processing helix chain 'K' and resid 520 through 533 removed outlier: 3.538A pdb=" N GLU K 528 " --> pdb=" O HIS K 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS K 531 " --> pdb=" O VAL K 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE K 532 " --> pdb=" O GLU K 528 " (cutoff:3.500A) Processing helix chain 'K' and resid 534 through 550 removed outlier: 3.667A pdb=" N VAL K 540 " --> pdb=" O LYS K 536 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU K 550 " --> pdb=" O GLU K 546 " (cutoff:3.500A) Processing helix chain 'K' and resid 550 through 555 removed outlier: 4.770A pdb=" N LEU K 554 " --> pdb=" O LEU K 550 " (cutoff:3.500A) Processing helix chain 'K' and resid 562 through 567 Processing helix chain 'K' and resid 575 through 591 removed outlier: 3.552A pdb=" N LEU K 582 " --> pdb=" O GLN K 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP K 589 " --> pdb=" O LYS K 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN K 590 " --> pdb=" O GLN K 586 " (cutoff:3.500A) Processing helix chain 'K' and resid 599 through 603 Processing helix chain 'K' and resid 850 through 852 No H-bonds generated for 'chain 'K' and resid 850 through 852' Processing helix chain 'K' and resid 911 through 916 removed outlier: 4.140A pdb=" N CYS K 915 " --> pdb=" O THR K 911 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS K 916 " --> pdb=" O LYS K 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 911 through 916' Processing helix chain 'L' and resid 2 through 14 Processing helix chain 'L' and resid 49 through 55 Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.523A pdb=" N GLU L 69 " --> pdb=" O MET L 65 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN L 70 " --> pdb=" O GLU L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 75 Processing helix chain 'L' and resid 87 through 102 Processing helix chain 'M' and resid 107 through 118 removed outlier: 3.558A pdb=" N ARG M 111 " --> pdb=" O THR M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 143 removed outlier: 4.126A pdb=" N LEU M 143 " --> pdb=" O LYS M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 170 removed outlier: 3.562A pdb=" N VAL M 168 " --> pdb=" O ALA M 164 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP M 170 " --> pdb=" O GLU M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 178 removed outlier: 3.939A pdb=" N LEU M 174 " --> pdb=" O ASP M 170 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY M 176 " --> pdb=" O SER M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 207 removed outlier: 3.627A pdb=" N MET M 197 " --> pdb=" O SER M 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS M 198 " --> pdb=" O GLY M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 219 through 233 Processing helix chain 'M' and resid 247 through 255 removed outlier: 4.033A pdb=" N LEU M 251 " --> pdb=" O ASP M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 300 Processing helix chain 'M' and resid 307 through 318 removed outlier: 4.357A pdb=" N HIS M 311 " --> pdb=" O PRO M 307 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE M 313 " --> pdb=" O GLN M 309 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE M 314 " --> pdb=" O ALA M 310 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS M 315 " --> pdb=" O HIS M 311 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU M 316 " --> pdb=" O SER M 312 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 334 removed outlier: 3.831A pdb=" N ASP M 333 " --> pdb=" O ALA M 329 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE M 334 " --> pdb=" O LEU M 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 337 through 348 removed outlier: 4.119A pdb=" N TYR M 341 " --> pdb=" O ARG M 337 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU M 342 " --> pdb=" O TRP M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 374 removed outlier: 3.531A pdb=" N MET M 368 " --> pdb=" O LEU M 364 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE M 370 " --> pdb=" O GLU M 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU M 373 " --> pdb=" O SER M 369 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 386 removed outlier: 3.713A pdb=" N ASP M 381 " --> pdb=" O GLU M 377 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR M 382 " --> pdb=" O ASP M 378 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR M 384 " --> pdb=" O LYS M 380 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP M 385 " --> pdb=" O ASP M 381 " (cutoff:3.500A) Processing helix chain 'M' and resid 397 through 405 Processing helix chain 'M' and resid 407 through 421 removed outlier: 4.150A pdb=" N ASP M 413 " --> pdb=" O GLU M 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE M 414 " --> pdb=" O GLU M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 467 removed outlier: 7.003A pdb=" N SER M 451 " --> pdb=" O GLU M 447 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN M 452 " --> pdb=" O LYS M 448 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN M 454 " --> pdb=" O CYS M 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP M 455 " --> pdb=" O SER M 451 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS M 458 " --> pdb=" O GLN M 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS M 459 " --> pdb=" O ASP M 455 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE M 461 " --> pdb=" O HIS M 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR M 462 " --> pdb=" O LYS M 458 " (cutoff:3.500A) Processing helix chain 'M' and resid 479 through 495 removed outlier: 3.819A pdb=" N ALA M 488 " --> pdb=" O TYR M 484 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR M 489 " --> pdb=" O ASN M 485 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET M 491 " --> pdb=" O LEU M 487 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA M 492 " --> pdb=" O ALA M 488 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER M 493 " --> pdb=" O TYR M 489 " (cutoff:3.500A) Processing helix chain 'M' and resid 496 through 504 Processing helix chain 'M' and resid 506 through 517 Processing helix chain 'M' and resid 520 through 533 removed outlier: 3.538A pdb=" N GLU M 528 " --> pdb=" O HIS M 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS M 531 " --> pdb=" O VAL M 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE M 532 " --> pdb=" O GLU M 528 " (cutoff:3.500A) Processing helix chain 'M' and resid 534 through 550 removed outlier: 3.667A pdb=" N VAL M 540 " --> pdb=" O LYS M 536 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU M 550 " --> pdb=" O GLU M 546 " (cutoff:3.500A) Processing helix chain 'M' and resid 550 through 555 removed outlier: 4.770A pdb=" N LEU M 554 " --> pdb=" O LEU M 550 " (cutoff:3.500A) Processing helix chain 'M' and resid 562 through 567 Processing helix chain 'M' and resid 575 through 591 removed outlier: 3.553A pdb=" N LEU M 582 " --> pdb=" O GLN M 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP M 589 " --> pdb=" O LYS M 585 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN M 590 " --> pdb=" O GLN M 586 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 603 Processing helix chain 'M' and resid 850 through 852 No H-bonds generated for 'chain 'M' and resid 850 through 852' Processing helix chain 'M' and resid 911 through 916 removed outlier: 4.140A pdb=" N CYS M 915 " --> pdb=" O THR M 911 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS M 916 " --> pdb=" O LYS M 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 911 through 916' Processing helix chain 'N' and resid 2 through 14 Processing helix chain 'N' and resid 49 through 55 Processing helix chain 'N' and resid 60 through 70 removed outlier: 3.522A pdb=" N GLU N 69 " --> pdb=" O MET N 65 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN N 70 " --> pdb=" O GLU N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 75 Processing helix chain 'N' and resid 87 through 102 Processing sheet with id=A, first strand: chain 'A' and resid 182 through 188 removed outlier: 3.522A pdb=" N VAL A 187 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A 240 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR A 263 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 242 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL A 150 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR A 264 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE A 152 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 395 through 396 removed outlier: 3.772A pdb=" N VAL A 395 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 435 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=B Processing sheet with id=C, first strand: chain 'A' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU A 609 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.486A pdb=" N VAL A 641 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 650 " --> pdb=" O VAL A 641 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS A 643 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 648 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 660 through 665 removed outlier: 3.786A pdb=" N CYS A 662 " --> pdb=" O CYS A 675 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASN A 685 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU A 691 " --> pdb=" O ASN A 685 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY A 719 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS A 705 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA A 717 " --> pdb=" O CYS A 705 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE A 707 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 715 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP A 729 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS A 735 " --> pdb=" O ASP A 729 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'A' and resid 746 through 749 removed outlier: 3.846A pdb=" N HIS A 748 " --> pdb=" O CYS A 761 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP A 771 " --> pdb=" O GLU A 777 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU A 777 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'A' and resid 804 through 806 removed outlier: 5.750A pdb=" N LEU A 823 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'A' and resid 854 through 858 removed outlier: 6.864A pdb=" N LEU A 866 " --> pdb=" O VAL A 875 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'A' and resid 928 through 930 removed outlier: 3.791A pdb=" N MET A 936 " --> pdb=" O VAL A 929 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL A 937 " --> pdb=" O ILE A 949 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE A 949 " --> pdb=" O VAL A 937 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'A' and resid 946 through 947 removed outlier: 3.932A pdb=" N LEU A 946 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'A' and resid 967 through 969 Processing sheet with id=M, first strand: chain 'A' and resid 985 through 986 Processing sheet with id=N, first strand: chain 'A' and resid 1009 through 1011 Processing sheet with id=O, first strand: chain 'A' and resid 1049 through 1052 Processing sheet with id=P, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 3.515A pdb=" N SER A1090 " --> pdb=" O SER A1104 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'A' and resid 1132 through 1135 Processing sheet with id=R, first strand: chain 'A' and resid 1182 through 1185 removed outlier: 4.001A pdb=" N ASP A1182 " --> pdb=" O ALA A1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A1195 " --> pdb=" O ASP A1182 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'A' and resid 1233 through 1235 Processing sheet with id=T, first strand: chain 'C' and resid 182 through 188 removed outlier: 3.522A pdb=" N VAL C 187 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 240 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR C 263 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU C 242 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL C 150 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR C 264 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE C 152 " --> pdb=" O THR C 264 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'C' and resid 395 through 396 removed outlier: 3.772A pdb=" N VAL C 395 " --> pdb=" O TYR C 435 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR C 435 " --> pdb=" O VAL C 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=U Processing sheet with id=V, first strand: chain 'C' and resid 609 through 611 removed outlier: 3.901A pdb=" N LEU C 609 " --> pdb=" O LEU C 908 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'C' and resid 621 through 623 removed outlier: 6.485A pdb=" N VAL C 641 " --> pdb=" O LEU C 650 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 650 " --> pdb=" O VAL C 641 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS C 643 " --> pdb=" O GLU C 648 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 648 " --> pdb=" O LYS C 643 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'C' and resid 660 through 665 removed outlier: 3.786A pdb=" N CYS C 662 " --> pdb=" O CYS C 675 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASN C 685 " --> pdb=" O LEU C 691 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU C 691 " --> pdb=" O ASN C 685 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'C' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY C 719 " --> pdb=" O ASN C 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS C 705 " --> pdb=" O ALA C 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA C 717 " --> pdb=" O CYS C 705 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE C 707 " --> pdb=" O LEU C 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 715 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP C 729 " --> pdb=" O CYS C 735 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N CYS C 735 " --> pdb=" O ASP C 729 " (cutoff:3.500A) Processing sheet with id=Z, first strand: chain 'C' and resid 746 through 749 removed outlier: 3.846A pdb=" N HIS C 748 " --> pdb=" O CYS C 761 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP C 771 " --> pdb=" O GLU C 777 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU C 777 " --> pdb=" O ASP C 771 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'C' and resid 804 through 806 removed outlier: 5.751A pdb=" N LEU C 823 " --> pdb=" O LEU C 832 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'C' and resid 854 through 858 removed outlier: 6.864A pdb=" N LEU C 866 " --> pdb=" O VAL C 875 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'C' and resid 928 through 930 removed outlier: 3.791A pdb=" N MET C 936 " --> pdb=" O VAL C 929 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL C 937 " --> pdb=" O ILE C 949 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE C 949 " --> pdb=" O VAL C 937 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'C' and resid 946 through 947 removed outlier: 3.932A pdb=" N LEU C 946 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'C' and resid 967 through 969 Processing sheet with id=AF, first strand: chain 'C' and resid 985 through 986 Processing sheet with id=AG, first strand: chain 'C' and resid 1009 through 1011 Processing sheet with id=AH, first strand: chain 'C' and resid 1049 through 1052 Processing sheet with id=AI, first strand: chain 'C' and resid 1090 through 1093 removed outlier: 3.515A pdb=" N SER C1090 " --> pdb=" O SER C1104 " (cutoff:3.500A) Processing sheet with id=AJ, first strand: chain 'C' and resid 1132 through 1135 Processing sheet with id=AK, first strand: chain 'C' and resid 1182 through 1185 removed outlier: 4.002A pdb=" N ASP C1182 " --> pdb=" O ALA C1195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C1195 " --> pdb=" O ASP C1182 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'C' and resid 1233 through 1235 Processing sheet with id=AM, first strand: chain 'E' and resid 182 through 188 removed outlier: 3.522A pdb=" N VAL E 187 " --> pdb=" O ASP E 243 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU E 240 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR E 263 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU E 242 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL E 150 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR E 264 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE E 152 " --> pdb=" O THR E 264 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'E' and resid 395 through 396 removed outlier: 3.771A pdb=" N VAL E 395 " --> pdb=" O TYR E 435 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR E 435 " --> pdb=" O VAL E 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN Processing sheet with id=AO, first strand: chain 'E' and resid 609 through 611 removed outlier: 3.901A pdb=" N LEU E 609 " --> pdb=" O LEU E 908 " (cutoff:3.500A) Processing sheet with id=AP, first strand: chain 'E' and resid 621 through 623 removed outlier: 6.485A pdb=" N VAL E 641 " --> pdb=" O LEU E 650 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 650 " --> pdb=" O VAL E 641 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS E 643 " --> pdb=" O GLU E 648 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU E 648 " --> pdb=" O LYS E 643 " (cutoff:3.500A) Processing sheet with id=AQ, first strand: chain 'E' and resid 660 through 665 removed outlier: 3.786A pdb=" N CYS E 662 " --> pdb=" O CYS E 675 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASN E 685 " --> pdb=" O LEU E 691 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU E 691 " --> pdb=" O ASN E 685 " (cutoff:3.500A) Processing sheet with id=AR, first strand: chain 'E' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY E 719 " --> pdb=" O ASN E 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS E 705 " --> pdb=" O ALA E 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA E 717 " --> pdb=" O CYS E 705 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE E 707 " --> pdb=" O LEU E 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU E 715 " --> pdb=" O PHE E 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP E 729 " --> pdb=" O CYS E 735 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N CYS E 735 " --> pdb=" O ASP E 729 " (cutoff:3.500A) Processing sheet with id=AS, first strand: chain 'E' and resid 746 through 749 removed outlier: 3.846A pdb=" N HIS E 748 " --> pdb=" O CYS E 761 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP E 771 " --> pdb=" O GLU E 777 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU E 777 " --> pdb=" O ASP E 771 " (cutoff:3.500A) Processing sheet with id=AT, first strand: chain 'E' and resid 804 through 806 removed outlier: 5.751A pdb=" N LEU E 823 " --> pdb=" O LEU E 832 " (cutoff:3.500A) Processing sheet with id=AU, first strand: chain 'E' and resid 854 through 858 removed outlier: 6.865A pdb=" N LEU E 866 " --> pdb=" O VAL E 875 " (cutoff:3.500A) Processing sheet with id=AV, first strand: chain 'E' and resid 928 through 930 removed outlier: 3.791A pdb=" N MET E 936 " --> pdb=" O VAL E 929 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL E 937 " --> pdb=" O ILE E 949 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE E 949 " --> pdb=" O VAL E 937 " (cutoff:3.500A) Processing sheet with id=AW, first strand: chain 'E' and resid 946 through 947 removed outlier: 3.932A pdb=" N LEU E 946 " --> pdb=" O LEU E 959 " (cutoff:3.500A) Processing sheet with id=AX, first strand: chain 'E' and resid 967 through 969 Processing sheet with id=AY, first strand: chain 'E' and resid 985 through 986 Processing sheet with id=AZ, first strand: chain 'E' and resid 1009 through 1011 Processing sheet with id=BA, first strand: chain 'E' and resid 1049 through 1052 Processing sheet with id=BB, first strand: chain 'E' and resid 1090 through 1093 removed outlier: 3.516A pdb=" N SER E1090 " --> pdb=" O SER E1104 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'E' and resid 1132 through 1135 Processing sheet with id=BD, first strand: chain 'E' and resid 1182 through 1185 removed outlier: 4.001A pdb=" N ASP E1182 " --> pdb=" O ALA E1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E1195 " --> pdb=" O ASP E1182 " (cutoff:3.500A) Processing sheet with id=BE, first strand: chain 'E' and resid 1233 through 1235 Processing sheet with id=BF, first strand: chain 'G' and resid 182 through 188 removed outlier: 3.522A pdb=" N VAL G 187 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU G 240 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR G 263 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU G 242 " --> pdb=" O THR G 263 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL G 150 " --> pdb=" O LEU G 262 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR G 264 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE G 152 " --> pdb=" O THR G 264 " (cutoff:3.500A) Processing sheet with id=BG, first strand: chain 'G' and resid 395 through 396 removed outlier: 3.772A pdb=" N VAL G 395 " --> pdb=" O TYR G 435 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR G 435 " --> pdb=" O VAL G 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=BG Processing sheet with id=BH, first strand: chain 'G' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU G 609 " --> pdb=" O LEU G 908 " (cutoff:3.500A) Processing sheet with id=BI, first strand: chain 'G' and resid 621 through 623 removed outlier: 6.485A pdb=" N VAL G 641 " --> pdb=" O LEU G 650 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU G 650 " --> pdb=" O VAL G 641 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS G 643 " --> pdb=" O GLU G 648 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU G 648 " --> pdb=" O LYS G 643 " (cutoff:3.500A) Processing sheet with id=BJ, first strand: chain 'G' and resid 660 through 665 removed outlier: 3.786A pdb=" N CYS G 662 " --> pdb=" O CYS G 675 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASN G 685 " --> pdb=" O LEU G 691 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU G 691 " --> pdb=" O ASN G 685 " (cutoff:3.500A) Processing sheet with id=BK, first strand: chain 'G' and resid 702 through 707 removed outlier: 6.216A pdb=" N GLY G 719 " --> pdb=" O ASN G 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS G 705 " --> pdb=" O ALA G 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA G 717 " --> pdb=" O CYS G 705 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE G 707 " --> pdb=" O LEU G 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU G 715 " --> pdb=" O PHE G 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP G 729 " --> pdb=" O CYS G 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS G 735 " --> pdb=" O ASP G 729 " (cutoff:3.500A) Processing sheet with id=BL, first strand: chain 'G' and resid 746 through 749 removed outlier: 3.846A pdb=" N HIS G 748 " --> pdb=" O CYS G 761 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP G 771 " --> pdb=" O GLU G 777 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU G 777 " --> pdb=" O ASP G 771 " (cutoff:3.500A) Processing sheet with id=BM, first strand: chain 'G' and resid 804 through 806 removed outlier: 5.751A pdb=" N LEU G 823 " --> pdb=" O LEU G 832 " (cutoff:3.500A) Processing sheet with id=BN, first strand: chain 'G' and resid 854 through 858 removed outlier: 6.865A pdb=" N LEU G 866 " --> pdb=" O VAL G 875 " (cutoff:3.500A) Processing sheet with id=BO, first strand: chain 'G' and resid 928 through 930 removed outlier: 3.791A pdb=" N MET G 936 " --> pdb=" O VAL G 929 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL G 937 " --> pdb=" O ILE G 949 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE G 949 " --> pdb=" O VAL G 937 " (cutoff:3.500A) Processing sheet with id=BP, first strand: chain 'G' and resid 946 through 947 removed outlier: 3.932A pdb=" N LEU G 946 " --> pdb=" O LEU G 959 " (cutoff:3.500A) Processing sheet with id=BQ, first strand: chain 'G' and resid 967 through 969 Processing sheet with id=BR, first strand: chain 'G' and resid 985 through 986 Processing sheet with id=BS, first strand: chain 'G' and resid 1009 through 1011 Processing sheet with id=BT, first strand: chain 'G' and resid 1049 through 1052 Processing sheet with id=BU, first strand: chain 'G' and resid 1090 through 1093 removed outlier: 3.516A pdb=" N SER G1090 " --> pdb=" O SER G1104 " (cutoff:3.500A) Processing sheet with id=BV, first strand: chain 'G' and resid 1132 through 1135 Processing sheet with id=BW, first strand: chain 'G' and resid 1182 through 1185 removed outlier: 4.001A pdb=" N ASP G1182 " --> pdb=" O ALA G1195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G1195 " --> pdb=" O ASP G1182 " (cutoff:3.500A) Processing sheet with id=BX, first strand: chain 'G' and resid 1233 through 1235 Processing sheet with id=BY, first strand: chain 'I' and resid 182 through 188 removed outlier: 3.522A pdb=" N VAL I 187 " --> pdb=" O ASP I 243 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU I 240 " --> pdb=" O LEU I 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR I 263 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU I 242 " --> pdb=" O THR I 263 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL I 150 " --> pdb=" O LEU I 262 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR I 264 " --> pdb=" O VAL I 150 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE I 152 " --> pdb=" O THR I 264 " (cutoff:3.500A) Processing sheet with id=BZ, first strand: chain 'I' and resid 395 through 396 removed outlier: 3.771A pdb=" N VAL I 395 " --> pdb=" O TYR I 435 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR I 435 " --> pdb=" O VAL I 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=BZ Processing sheet with id=CA, first strand: chain 'I' and resid 609 through 611 removed outlier: 3.901A pdb=" N LEU I 609 " --> pdb=" O LEU I 908 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'I' and resid 621 through 623 removed outlier: 6.486A pdb=" N VAL I 641 " --> pdb=" O LEU I 650 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU I 650 " --> pdb=" O VAL I 641 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS I 643 " --> pdb=" O GLU I 648 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU I 648 " --> pdb=" O LYS I 643 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'I' and resid 660 through 665 removed outlier: 3.786A pdb=" N CYS I 662 " --> pdb=" O CYS I 675 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASN I 685 " --> pdb=" O LEU I 691 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU I 691 " --> pdb=" O ASN I 685 " (cutoff:3.500A) Processing sheet with id=CD, first strand: chain 'I' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY I 719 " --> pdb=" O ASN I 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS I 705 " --> pdb=" O ALA I 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA I 717 " --> pdb=" O CYS I 705 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE I 707 " --> pdb=" O LEU I 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU I 715 " --> pdb=" O PHE I 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP I 729 " --> pdb=" O CYS I 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS I 735 " --> pdb=" O ASP I 729 " (cutoff:3.500A) Processing sheet with id=CE, first strand: chain 'I' and resid 746 through 749 removed outlier: 3.846A pdb=" N HIS I 748 " --> pdb=" O CYS I 761 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP I 771 " --> pdb=" O GLU I 777 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU I 777 " --> pdb=" O ASP I 771 " (cutoff:3.500A) Processing sheet with id=CF, first strand: chain 'I' and resid 804 through 806 removed outlier: 5.750A pdb=" N LEU I 823 " --> pdb=" O LEU I 832 " (cutoff:3.500A) Processing sheet with id=CG, first strand: chain 'I' and resid 854 through 858 removed outlier: 6.864A pdb=" N LEU I 866 " --> pdb=" O VAL I 875 " (cutoff:3.500A) Processing sheet with id=CH, first strand: chain 'I' and resid 928 through 930 removed outlier: 3.792A pdb=" N MET I 936 " --> pdb=" O VAL I 929 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL I 937 " --> pdb=" O ILE I 949 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE I 949 " --> pdb=" O VAL I 937 " (cutoff:3.500A) Processing sheet with id=CI, first strand: chain 'I' and resid 946 through 947 removed outlier: 3.932A pdb=" N LEU I 946 " --> pdb=" O LEU I 959 " (cutoff:3.500A) Processing sheet with id=CJ, first strand: chain 'I' and resid 967 through 969 Processing sheet with id=CK, first strand: chain 'I' and resid 985 through 986 Processing sheet with id=CL, first strand: chain 'I' and resid 1009 through 1011 Processing sheet with id=CM, first strand: chain 'I' and resid 1049 through 1052 Processing sheet with id=CN, first strand: chain 'I' and resid 1090 through 1093 removed outlier: 3.516A pdb=" N SER I1090 " --> pdb=" O SER I1104 " (cutoff:3.500A) Processing sheet with id=CO, first strand: chain 'I' and resid 1132 through 1135 Processing sheet with id=CP, first strand: chain 'I' and resid 1182 through 1185 removed outlier: 4.001A pdb=" N ASP I1182 " --> pdb=" O ALA I1195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA I1195 " --> pdb=" O ASP I1182 " (cutoff:3.500A) Processing sheet with id=CQ, first strand: chain 'I' and resid 1233 through 1235 Processing sheet with id=CR, first strand: chain 'K' and resid 182 through 188 removed outlier: 3.522A pdb=" N VAL K 187 " --> pdb=" O ASP K 243 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU K 240 " --> pdb=" O LEU K 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR K 263 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU K 242 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL K 150 " --> pdb=" O LEU K 262 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR K 264 " --> pdb=" O VAL K 150 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE K 152 " --> pdb=" O THR K 264 " (cutoff:3.500A) Processing sheet with id=CS, first strand: chain 'K' and resid 395 through 396 removed outlier: 3.772A pdb=" N VAL K 395 " --> pdb=" O TYR K 435 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR K 435 " --> pdb=" O VAL K 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=CS Processing sheet with id=CT, first strand: chain 'K' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU K 609 " --> pdb=" O LEU K 908 " (cutoff:3.500A) Processing sheet with id=CU, first strand: chain 'K' and resid 621 through 623 removed outlier: 6.486A pdb=" N VAL K 641 " --> pdb=" O LEU K 650 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU K 650 " --> pdb=" O VAL K 641 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS K 643 " --> pdb=" O GLU K 648 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU K 648 " --> pdb=" O LYS K 643 " (cutoff:3.500A) Processing sheet with id=CV, first strand: chain 'K' and resid 660 through 665 removed outlier: 3.786A pdb=" N CYS K 662 " --> pdb=" O CYS K 675 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASN K 685 " --> pdb=" O LEU K 691 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU K 691 " --> pdb=" O ASN K 685 " (cutoff:3.500A) Processing sheet with id=CW, first strand: chain 'K' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY K 719 " --> pdb=" O ASN K 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS K 705 " --> pdb=" O ALA K 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA K 717 " --> pdb=" O CYS K 705 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE K 707 " --> pdb=" O LEU K 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU K 715 " --> pdb=" O PHE K 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP K 729 " --> pdb=" O CYS K 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS K 735 " --> pdb=" O ASP K 729 " (cutoff:3.500A) Processing sheet with id=CX, first strand: chain 'K' and resid 746 through 749 removed outlier: 3.846A pdb=" N HIS K 748 " --> pdb=" O CYS K 761 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP K 771 " --> pdb=" O GLU K 777 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU K 777 " --> pdb=" O ASP K 771 " (cutoff:3.500A) Processing sheet with id=CY, first strand: chain 'K' and resid 804 through 806 removed outlier: 5.750A pdb=" N LEU K 823 " --> pdb=" O LEU K 832 " (cutoff:3.500A) Processing sheet with id=CZ, first strand: chain 'K' and resid 854 through 858 removed outlier: 6.864A pdb=" N LEU K 866 " --> pdb=" O VAL K 875 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'K' and resid 928 through 930 removed outlier: 3.792A pdb=" N MET K 936 " --> pdb=" O VAL K 929 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL K 937 " --> pdb=" O ILE K 949 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE K 949 " --> pdb=" O VAL K 937 " (cutoff:3.500A) Processing sheet with id=DB, first strand: chain 'K' and resid 946 through 947 removed outlier: 3.932A pdb=" N LEU K 946 " --> pdb=" O LEU K 959 " (cutoff:3.500A) Processing sheet with id=DC, first strand: chain 'K' and resid 967 through 969 Processing sheet with id=DD, first strand: chain 'K' and resid 985 through 986 Processing sheet with id=DE, first strand: chain 'K' and resid 1009 through 1011 Processing sheet with id=DF, first strand: chain 'K' and resid 1049 through 1052 Processing sheet with id=DG, first strand: chain 'K' and resid 1090 through 1093 removed outlier: 3.516A pdb=" N SER K1090 " --> pdb=" O SER K1104 " (cutoff:3.500A) Processing sheet with id=DH, first strand: chain 'K' and resid 1132 through 1135 Processing sheet with id=DI, first strand: chain 'K' and resid 1182 through 1185 removed outlier: 4.001A pdb=" N ASP K1182 " --> pdb=" O ALA K1195 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA K1195 " --> pdb=" O ASP K1182 " (cutoff:3.500A) Processing sheet with id=DJ, first strand: chain 'K' and resid 1233 through 1235 Processing sheet with id=DK, first strand: chain 'M' and resid 182 through 188 removed outlier: 3.521A pdb=" N VAL M 187 " --> pdb=" O ASP M 243 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU M 240 " --> pdb=" O LEU M 261 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR M 263 " --> pdb=" O LEU M 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU M 242 " --> pdb=" O THR M 263 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL M 150 " --> pdb=" O LEU M 262 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR M 264 " --> pdb=" O VAL M 150 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE M 152 " --> pdb=" O THR M 264 " (cutoff:3.500A) Processing sheet with id=DL, first strand: chain 'M' and resid 395 through 396 removed outlier: 3.771A pdb=" N VAL M 395 " --> pdb=" O TYR M 435 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR M 435 " --> pdb=" O VAL M 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=DL Processing sheet with id=DM, first strand: chain 'M' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU M 609 " --> pdb=" O LEU M 908 " (cutoff:3.500A) Processing sheet with id=DN, first strand: chain 'M' and resid 621 through 623 removed outlier: 6.486A pdb=" N VAL M 641 " --> pdb=" O LEU M 650 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU M 650 " --> pdb=" O VAL M 641 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS M 643 " --> pdb=" O GLU M 648 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU M 648 " --> pdb=" O LYS M 643 " (cutoff:3.500A) Processing sheet with id=DO, first strand: chain 'M' and resid 660 through 665 removed outlier: 3.786A pdb=" N CYS M 662 " --> pdb=" O CYS M 675 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASN M 685 " --> pdb=" O LEU M 691 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU M 691 " --> pdb=" O ASN M 685 " (cutoff:3.500A) Processing sheet with id=DP, first strand: chain 'M' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY M 719 " --> pdb=" O ASN M 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS M 705 " --> pdb=" O ALA M 717 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA M 717 " --> pdb=" O CYS M 705 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE M 707 " --> pdb=" O LEU M 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU M 715 " --> pdb=" O PHE M 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP M 729 " --> pdb=" O CYS M 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS M 735 " --> pdb=" O ASP M 729 " (cutoff:3.500A) Processing sheet with id=DQ, first strand: chain 'M' and resid 746 through 749 removed outlier: 3.846A pdb=" N HIS M 748 " --> pdb=" O CYS M 761 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP M 771 " --> pdb=" O GLU M 777 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU M 777 " --> pdb=" O ASP M 771 " (cutoff:3.500A) Processing sheet with id=DR, first strand: chain 'M' and resid 804 through 806 removed outlier: 5.751A pdb=" N LEU M 823 " --> pdb=" O LEU M 832 " (cutoff:3.500A) Processing sheet with id=DS, first strand: chain 'M' and resid 854 through 858 removed outlier: 6.865A pdb=" N LEU M 866 " --> pdb=" O VAL M 875 " (cutoff:3.500A) Processing sheet with id=DT, first strand: chain 'M' and resid 928 through 930 removed outlier: 3.791A pdb=" N MET M 936 " --> pdb=" O VAL M 929 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL M 937 " --> pdb=" O ILE M 949 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE M 949 " --> pdb=" O VAL M 937 " (cutoff:3.500A) Processing sheet with id=DU, first strand: chain 'M' and resid 946 through 947 removed outlier: 3.931A pdb=" N LEU M 946 " --> pdb=" O LEU M 959 " (cutoff:3.500A) Processing sheet with id=DV, first strand: chain 'M' and resid 967 through 969 Processing sheet with id=DW, first strand: chain 'M' and resid 985 through 986 Processing sheet with id=DX, first strand: chain 'M' and resid 1009 through 1011 Processing sheet with id=DY, first strand: chain 'M' and resid 1049 through 1052 Processing sheet with id=DZ, first strand: chain 'M' and resid 1090 through 1093 removed outlier: 3.516A pdb=" N SER M1090 " --> pdb=" O SER M1104 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'M' and resid 1132 through 1135 Processing sheet with id=EB, first strand: chain 'M' and resid 1182 through 1185 removed outlier: 4.001A pdb=" N ASP M1182 " --> pdb=" O ALA M1195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA M1195 " --> pdb=" O ASP M1182 " (cutoff:3.500A) Processing sheet with id=EC, first strand: chain 'M' and resid 1233 through 1235 2282 hydrogen bonds defined for protein. 6363 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: 42.70 Time building geometry restraints manager: 16.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 23823 1.37 - 1.55: 47172 1.55 - 1.74: 167 1.74 - 1.92: 623 1.92 - 2.10: 21 Bond restraints: 71806 Sorted by residual: bond pdb=" C4 DTP G1301 " pdb=" C5 DTP G1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C4 DTP I1301 " pdb=" C5 DTP I1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C4 DTP E1301 " pdb=" C5 DTP E1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C4 DTP A1301 " pdb=" C5 DTP A1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.82e+01 bond pdb=" C4 DTP K1301 " pdb=" C5 DTP K1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.81e+01 ... (remaining 71801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 95416 3.87 - 7.75: 1653 7.75 - 11.62: 98 11.62 - 15.50: 28 15.50 - 19.37: 21 Bond angle restraints: 97216 Sorted by residual: angle pdb=" PB DTP E1301 " pdb=" O3B DTP E1301 " pdb=" PG DTP E1301 " ideal model delta sigma weight residual 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB DTP C1301 " pdb=" O3B DTP C1301 " pdb=" PG DTP C1301 " ideal model delta sigma weight residual 139.87 120.51 19.36 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB DTP A1301 " pdb=" O3B DTP A1301 " pdb=" PG DTP A1301 " ideal model delta sigma weight residual 139.87 120.52 19.35 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB DTP I1301 " pdb=" O3B DTP I1301 " pdb=" PG DTP I1301 " ideal model delta sigma weight residual 139.87 120.54 19.33 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB DTP G1301 " pdb=" O3B DTP G1301 " pdb=" PG DTP G1301 " ideal model delta sigma weight residual 139.87 120.54 19.33 1.00e+00 1.00e+00 3.74e+02 ... (remaining 97211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.23: 38811 26.23 - 52.45: 3167 52.45 - 78.68: 848 78.68 - 104.90: 99 104.90 - 131.13: 7 Dihedral angle restraints: 42932 sinusoidal: 17529 harmonic: 25403 Sorted by residual: dihedral pdb=" CB CYS A 761 " pdb=" SG CYS A 761 " pdb=" SG CYS A 804 " pdb=" CB CYS A 804 " ideal model delta sinusoidal sigma weight residual 93.00 174.12 -81.12 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS A 704 " pdb=" SG CYS A 704 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual 93.00 150.58 -57.58 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CB CYS A 675 " pdb=" SG CYS A 675 " pdb=" SG CYS A 705 " pdb=" CB CYS A 705 " ideal model delta sinusoidal sigma weight residual 93.00 148.61 -55.61 1 1.00e+01 1.00e-02 4.18e+01 ... (remaining 42929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 9238 0.096 - 0.192: 1207 0.192 - 0.289: 241 0.289 - 0.385: 31 0.385 - 0.481: 14 Chirality restraints: 10731 Sorted by residual: chirality pdb=" CA HIS A 153 " pdb=" N HIS A 153 " pdb=" C HIS A 153 " pdb=" CB HIS A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CA HIS E 153 " pdb=" N HIS E 153 " pdb=" C HIS E 153 " pdb=" CB HIS E 153 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA HIS C 153 " pdb=" N HIS C 153 " pdb=" C HIS C 153 " pdb=" CB HIS C 153 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 10728 not shown) Planarity restraints: 12306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 280 " -0.100 5.00e-02 4.00e+02 1.58e-01 3.98e+01 pdb=" N PRO A 281 " 0.273 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 280 " -0.100 5.00e-02 4.00e+02 1.58e-01 3.97e+01 pdb=" N PRO C 281 " 0.273 5.00e-02 4.00e+02 pdb=" CA PRO C 281 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO C 281 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 280 " -0.100 5.00e-02 4.00e+02 1.57e-01 3.97e+01 pdb=" N PRO E 281 " 0.273 5.00e-02 4.00e+02 pdb=" CA PRO E 281 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO E 281 " -0.082 5.00e-02 4.00e+02 ... (remaining 12303 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 1098 2.50 - 3.10: 55855 3.10 - 3.70: 107755 3.70 - 4.30: 158651 4.30 - 4.90: 247442 Nonbonded interactions: 570801 Sorted by model distance: nonbonded pdb=" SG CYS G 704 " pdb=" SG CYS G 749 " model vdw 1.894 3.760 nonbonded pdb=" SG CYS E 704 " pdb=" SG CYS E 749 " model vdw 1.894 3.760 nonbonded pdb=" SG CYS C 704 " pdb=" SG CYS C 749 " model vdw 1.894 3.760 nonbonded pdb=" SG CYS I 704 " pdb=" SG CYS I 749 " model vdw 1.894 3.760 nonbonded pdb=" SG CYS M 704 " pdb=" SG CYS M 749 " model vdw 1.895 3.760 ... (remaining 570796 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 2.200 Check model and map are aligned: 0.430 Set scattering table: 0.540 Process input model: 136.420 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.370 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4905 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 : 0.008 0.215 71806 Z= 0.503 Angle : 1.314 19.369 97216 Z= 0.923 Chirality : 0.071 0.481 10731 Planarity : 0.010 0.158 12306 Dihedral : 19.732 131.128 26453 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 70.66 Ramachandran Plot: Outliers : 3.64 % Allowed : 8.02 % Favored : 88.34 % Rotamer: Outliers : 18.24 % Allowed : 11.14 % Favored : 70.62 % Cbeta Deviations : 0.09 % 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: -0.65 (0.09), residues: 8708 helix: 0.52 (0.10), residues: 2317 sheet: -1.68 (0.16), residues: 1134 loop : -0.52 (0.09), residues: 5257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 249 HIS 0.013 0.001 HIS D 33 PHE 0.019 0.002 PHE L 82 TYR 0.038 0.003 TYR J 67 ARG 0.007 0.001 ARG N 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3247 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1421 poor density : 1826 time to evaluate : 7.184 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7265 (ptt180) REVERT: A 206 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7552 (tt) REVERT: A 261 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7040 (tt) REVERT: A 265 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7719 (mtt180) REVERT: A 267 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8327 (tttt) REVERT: A 311 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.7057 (t-90) REVERT: A 325 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8932 (t) REVERT: A 403 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7167 (tp) REVERT: A 457 HIS cc_start: 0.6287 (OUTLIER) cc_final: 0.5743 (m-70) REVERT: A 486 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: A 528 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6747 (tt0) REVERT: A 531 HIS cc_start: 0.5231 (OUTLIER) cc_final: 0.4830 (m-70) REVERT: A 576 VAL cc_start: 0.3485 (OUTLIER) cc_final: 0.3083 (t) REVERT: A 918 SER cc_start: -0.2905 (OUTLIER) cc_final: -0.3651 (m) REVERT: A 1220 LEU cc_start: 0.4105 (OUTLIER) cc_final: 0.2705 (tp) REVERT: A 1248 GLU cc_start: 0.4410 (OUTLIER) cc_final: 0.3586 (pt0) REVERT: B 33 HIS cc_start: 0.4336 (t70) cc_final: 0.4007 (t70) REVERT: B 80 MET cc_start: 0.4811 (ttt) cc_final: 0.4044 (ttt) REVERT: C 126 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5740 (p90) REVERT: C 129 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8510 (mtt180) REVERT: C 206 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7274 (tt) REVERT: C 259 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: C 267 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8277 (ttpt) REVERT: C 301 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7329 (ptp) REVERT: C 345 LEU cc_start: 0.7675 (mp) cc_final: 0.7138 (mt) REVERT: C 403 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7307 (tp) REVERT: C 457 HIS cc_start: 0.6037 (OUTLIER) cc_final: 0.5826 (m-70) REVERT: C 486 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: C 528 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6544 (tt0) REVERT: C 531 HIS cc_start: 0.5776 (OUTLIER) cc_final: 0.5440 (m-70) REVERT: C 918 SER cc_start: -0.3873 (OUTLIER) cc_final: -0.4210 (m) REVERT: C 1220 LEU cc_start: 0.3881 (OUTLIER) cc_final: 0.2791 (tp) REVERT: C 1248 GLU cc_start: 0.4617 (OUTLIER) cc_final: 0.3829 (pm20) REVERT: D 80 MET cc_start: 0.4172 (ttt) cc_final: 0.3185 (ttt) REVERT: E 114 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8429 (mt) REVERT: E 127 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7922 (m) REVERT: E 206 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7264 (tt) REVERT: E 240 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8082 (mp) REVERT: E 265 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7169 (mtt180) REVERT: E 267 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8460 (ttpt) REVERT: E 311 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.7027 (t-90) REVERT: E 528 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6393 (tt0) REVERT: E 918 SER cc_start: -0.2318 (OUTLIER) cc_final: -0.2525 (m) REVERT: E 1220 LEU cc_start: 0.4115 (OUTLIER) cc_final: 0.3253 (tp) REVERT: E 1248 GLU cc_start: 0.4795 (OUTLIER) cc_final: 0.4115 (pt0) REVERT: G 146 GLU cc_start: 0.6256 (mm-30) cc_final: 0.6025 (mm-30) REVERT: G 206 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7609 (tt) REVERT: G 259 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: G 265 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7260 (mtt180) REVERT: G 293 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: G 386 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8789 (tp) REVERT: G 403 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7064 (tp) REVERT: G 450 CYS cc_start: 0.6445 (OUTLIER) cc_final: 0.6025 (p) REVERT: G 473 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8107 (tp) REVERT: G 528 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6530 (tt0) REVERT: G 881 HIS cc_start: -0.2517 (OUTLIER) cc_final: -0.2894 (m-70) REVERT: G 918 SER cc_start: -0.3046 (OUTLIER) cc_final: -0.3443 (m) REVERT: G 1220 LEU cc_start: 0.4259 (OUTLIER) cc_final: 0.3624 (tp) REVERT: I 155 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7612 (ptm) REVERT: I 206 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7249 (tt) REVERT: I 239 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8321 (tp) REVERT: I 267 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8284 (ttpt) REVERT: I 301 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7328 (ptp) REVERT: I 457 HIS cc_start: 0.6185 (OUTLIER) cc_final: 0.5983 (m-70) REVERT: I 528 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6671 (tt0) REVERT: I 1248 GLU cc_start: 0.3997 (OUTLIER) cc_final: 0.2695 (pt0) REVERT: J 33 HIS cc_start: 0.3818 (t70) cc_final: 0.3523 (t70) REVERT: J 80 MET cc_start: 0.4610 (ttt) cc_final: 0.3799 (ttt) REVERT: K 139 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8805 (ttmm) REVERT: K 206 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7203 (tt) REVERT: K 234 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.6926 (mmtm) REVERT: K 265 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7487 (mtt180) REVERT: K 267 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8178 (ttpp) REVERT: K 403 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7039 (tp) REVERT: K 528 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6355 (tt0) REVERT: K 918 SER cc_start: -0.2871 (OUTLIER) cc_final: -0.3121 (m) REVERT: K 1193 ILE cc_start: 0.6993 (mt) cc_final: 0.6414 (mt) REVERT: K 1220 LEU cc_start: 0.4354 (OUTLIER) cc_final: 0.3684 (tp) REVERT: K 1248 GLU cc_start: 0.4689 (OUTLIER) cc_final: 0.3668 (pm20) REVERT: M 146 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6499 (mm-30) REVERT: M 240 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8223 (mp) REVERT: M 259 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: M 260 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7941 (pt) REVERT: M 261 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7055 (tt) REVERT: M 265 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7600 (mtm180) REVERT: M 267 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8272 (ttpt) REVERT: M 301 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7490 (mtm) REVERT: M 345 LEU cc_start: 0.7496 (mp) cc_final: 0.7287 (mt) REVERT: M 374 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6696 (mmt) REVERT: M 403 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7109 (tp) REVERT: M 528 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6627 (tt0) REVERT: M 531 HIS cc_start: 0.5509 (OUTLIER) cc_final: 0.5035 (m-70) REVERT: M 576 VAL cc_start: 0.3883 (OUTLIER) cc_final: 0.3075 (t) REVERT: M 918 SER cc_start: -0.2005 (OUTLIER) cc_final: -0.2494 (m) REVERT: M 1193 ILE cc_start: 0.7077 (mt) cc_final: 0.6665 (mt) REVERT: M 1220 LEU cc_start: 0.3745 (OUTLIER) cc_final: 0.3019 (tp) REVERT: M 1248 GLU cc_start: 0.4797 (OUTLIER) cc_final: 0.3747 (pm20) outliers start: 1421 outliers final: 385 residues processed: 2741 average time/residue: 0.6901 time to fit residues: 3152.1947 Evaluate side-chains 1430 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 471 poor density : 959 time to evaluate : 6.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 881 HIS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 999 ARG Chi-restraints excluded: chain A residue 1179 TRP Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1224 HIS Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1248 GLU Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 303 LYS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 438 HIS Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 450 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 531 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 881 HIS Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 918 SER Chi-restraints excluded: chain C residue 999 ARG Chi-restraints excluded: chain C residue 1179 TRP Chi-restraints excluded: chain C residue 1181 THR Chi-restraints excluded: chain C residue 1211 GLN Chi-restraints excluded: chain C residue 1215 THR Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1224 HIS Chi-restraints excluded: chain C residue 1232 TYR Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain C residue 1248 GLU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 ARG Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 438 HIS Chi-restraints excluded: chain E residue 449 ASN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 486 PHE Chi-restraints excluded: chain E residue 515 GLU Chi-restraints excluded: chain E residue 528 GLU Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 592 MET Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 881 HIS Chi-restraints excluded: chain E residue 882 LEU Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 918 SER Chi-restraints excluded: chain E residue 999 ARG Chi-restraints excluded: chain E residue 1179 TRP Chi-restraints excluded: chain E residue 1181 THR Chi-restraints excluded: chain E residue 1211 GLN Chi-restraints excluded: chain E residue 1215 THR Chi-restraints excluded: chain E residue 1218 THR Chi-restraints excluded: chain E residue 1220 LEU Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain E residue 1248 GLU Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 265 ARG Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 301 MET Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 334 PHE Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 374 MET Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 439 ASP Chi-restraints excluded: chain G residue 449 ASN Chi-restraints excluded: chain G residue 450 CYS Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 528 GLU Chi-restraints excluded: chain G residue 531 HIS Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 557 ARG Chi-restraints excluded: chain G residue 573 THR Chi-restraints excluded: chain G residue 592 MET Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 882 LEU Chi-restraints excluded: chain G residue 885 VAL Chi-restraints excluded: chain G residue 907 ARG Chi-restraints excluded: chain G residue 918 SER Chi-restraints excluded: chain G residue 999 ARG Chi-restraints excluded: chain G residue 1179 TRP Chi-restraints excluded: chain G residue 1181 THR Chi-restraints excluded: chain G residue 1211 GLN Chi-restraints excluded: chain G residue 1215 THR Chi-restraints excluded: chain G residue 1218 THR Chi-restraints excluded: chain G residue 1220 LEU Chi-restraints excluded: chain G residue 1224 HIS Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1248 GLU Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 122 ARG Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 237 ARG Chi-restraints excluded: chain I residue 239 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 248 SER Chi-restraints excluded: chain I residue 259 GLN Chi-restraints excluded: chain I residue 260 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 265 ARG Chi-restraints excluded: chain I residue 267 LYS Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 277 LYS Chi-restraints excluded: chain I residue 278 TYR Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 308 GLU Chi-restraints excluded: chain I residue 317 CYS Chi-restraints excluded: chain I residue 318 LYS Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain I residue 334 PHE Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 384 THR Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 449 ASN Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 457 HIS Chi-restraints excluded: chain I residue 528 GLU Chi-restraints excluded: chain I residue 531 HIS Chi-restraints excluded: chain I residue 573 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 881 HIS Chi-restraints excluded: chain I residue 882 LEU Chi-restraints excluded: chain I residue 999 ARG Chi-restraints excluded: chain I residue 1179 TRP Chi-restraints excluded: chain I residue 1181 THR Chi-restraints excluded: chain I residue 1211 GLN Chi-restraints excluded: chain I residue 1218 THR Chi-restraints excluded: chain I residue 1224 HIS Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain I residue 1248 GLU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 138 GLN Chi-restraints excluded: chain K residue 139 LYS Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 155 MET Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain K residue 234 LYS Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 259 GLN Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 265 ARG Chi-restraints excluded: chain K residue 267 LYS Chi-restraints excluded: chain K residue 277 LYS Chi-restraints excluded: chain K residue 278 TYR Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 295 LEU Chi-restraints excluded: chain K residue 301 MET Chi-restraints excluded: chain K residue 303 LYS Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain K residue 311 HIS Chi-restraints excluded: chain K residue 317 CYS Chi-restraints excluded: chain K residue 318 LYS Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 334 PHE Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 358 SER Chi-restraints excluded: chain K residue 374 MET Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 403 LEU Chi-restraints excluded: chain K residue 429 ASN Chi-restraints excluded: chain K residue 449 ASN Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 473 LEU Chi-restraints excluded: chain K residue 485 ASN Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain K residue 528 GLU Chi-restraints excluded: chain K residue 531 HIS Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 557 ARG Chi-restraints excluded: chain K residue 573 THR Chi-restraints excluded: chain K residue 603 ILE Chi-restraints excluded: chain K residue 881 HIS Chi-restraints excluded: chain K residue 882 LEU Chi-restraints excluded: chain K residue 918 SER Chi-restraints excluded: chain K residue 999 ARG Chi-restraints excluded: chain K residue 1170 GLU Chi-restraints excluded: chain K residue 1179 TRP Chi-restraints excluded: chain K residue 1181 THR Chi-restraints excluded: chain K residue 1211 GLN Chi-restraints excluded: chain K residue 1215 THR Chi-restraints excluded: chain K residue 1218 THR Chi-restraints excluded: chain K residue 1220 LEU Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain K residue 1248 GLU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 155 MET Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 189 LYS Chi-restraints excluded: chain M residue 231 MET Chi-restraints excluded: chain M residue 237 ARG Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 241 ILE Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 259 GLN Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 265 ARG Chi-restraints excluded: chain M residue 267 LYS Chi-restraints excluded: chain M residue 277 LYS Chi-restraints excluded: chain M residue 278 TYR Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 301 MET Chi-restraints excluded: chain M residue 303 LYS Chi-restraints excluded: chain M residue 308 GLU Chi-restraints excluded: chain M residue 317 CYS Chi-restraints excluded: chain M residue 318 LYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 334 PHE Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 358 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 449 ASN Chi-restraints excluded: chain M residue 450 CYS Chi-restraints excluded: chain M residue 456 LEU Chi-restraints excluded: chain M residue 486 PHE Chi-restraints excluded: chain M residue 528 GLU Chi-restraints excluded: chain M residue 530 ARG Chi-restraints excluded: chain M residue 531 HIS Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 573 THR Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain M residue 881 HIS Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 918 SER Chi-restraints excluded: chain M residue 999 ARG Chi-restraints excluded: chain M residue 1170 GLU Chi-restraints excluded: chain M residue 1179 TRP Chi-restraints excluded: chain M residue 1181 THR Chi-restraints excluded: chain M residue 1211 GLN Chi-restraints excluded: chain M residue 1218 THR Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1232 TYR Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain M residue 1248 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 732 optimal weight: 8.9990 chunk 657 optimal weight: 3.9990 chunk 365 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 443 optimal weight: 5.9990 chunk 351 optimal weight: 30.0000 chunk 680 optimal weight: 30.0000 chunk 263 optimal weight: 0.7980 chunk 413 optimal weight: 4.9990 chunk 506 optimal weight: 0.9990 chunk 788 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 183 HIS A 201 ASN A 219 ASN A 259 GLN A 420 ASN A 438 HIS ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 HIS A 485 ASN A 583 GLN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 HIS A1224 HIS A1237 ASN B 52 ASN C 137 GLN C 183 HIS C 200 GLN C 201 ASN C 219 ASN C 420 ASN ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN C 579 GLN C 583 GLN ** C 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN C 904 GLN ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 ASN C1176 HIS C1224 HIS C1237 ASN ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 183 HIS E 200 GLN E 201 ASN E 219 ASN E 420 ASN ** E 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 457 HIS E 471 HIS E 583 GLN ** E 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 904 GLN ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1176 HIS E1224 HIS E1237 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN G 183 HIS G 200 GLN G 201 ASN G 219 ASN G 257 GLN G 259 GLN G 416 GLN G 420 ASN G 438 HIS ** G 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 HIS G 471 HIS G 583 GLN ** G 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 709 ASN G 904 GLN ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1176 HIS G1224 HIS G1237 ASN ** H 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN I 183 HIS I 200 GLN I 201 ASN I 219 ASN I 257 GLN I 259 GLN I 420 ASN I 471 HIS I 545 GLN I 583 GLN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 709 ASN I 904 GLN ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1237 ASN K 137 GLN K 183 HIS K 200 GLN K 201 ASN ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 257 GLN K 259 GLN K 420 ASN K 429 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 HIS K 471 HIS K 485 ASN K 583 GLN ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 904 GLN ** K1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1224 HIS K1237 ASN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN M 137 GLN M 183 HIS M 200 GLN ** M 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 ASN M 420 ASN ** M 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 457 HIS M 471 HIS M 583 GLN ** M 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 709 ASN ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 904 GLN ** M1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1224 HIS M1237 ASN ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN Total number of N/Q/H flips: 106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5197 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 71806 Z= 0.358 Angle : 0.872 15.451 97216 Z= 0.452 Chirality : 0.049 0.482 10731 Planarity : 0.006 0.060 12306 Dihedral : 14.218 136.873 10640 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 1.06 % Allowed : 6.97 % Favored : 91.97 % Rotamer: Outliers : 7.97 % Allowed : 16.76 % Favored : 75.27 % 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: -1.07 (0.09), residues: 8708 helix: 0.47 (0.10), residues: 2352 sheet: -1.61 (0.12), residues: 1589 loop : -0.94 (0.09), residues: 4767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 684 HIS 0.012 0.002 HIS M 457 PHE 0.033 0.003 PHE E 526 TYR 0.053 0.003 TYR A 845 ARG 0.008 0.001 ARG G 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1716 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 621 poor density : 1095 time to evaluate : 6.131 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.5348 (tt0) cc_final: 0.5140 (tt0) REVERT: A 261 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8626 (tt) REVERT: A 267 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8416 (ttpp) REVERT: A 353 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8612 (mt) REVERT: A 454 GLN cc_start: 0.6317 (tm-30) cc_final: 0.5696 (tm-30) REVERT: A 784 LYS cc_start: 0.4939 (mmtt) cc_final: 0.4492 (mmtt) REVERT: B 19 THR cc_start: 0.4374 (p) cc_final: 0.3832 (p) REVERT: C 206 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7452 (tt) REVERT: C 240 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8258 (mt) REVERT: C 259 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7623 (pt0) REVERT: C 261 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8635 (pp) REVERT: C 267 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8291 (ttpt) REVERT: C 301 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6732 (mtm) REVERT: C 353 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8499 (mt) REVERT: D 19 THR cc_start: 0.4799 (p) cc_final: 0.4229 (p) REVERT: E 137 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: E 261 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8803 (pp) REVERT: E 267 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8350 (ttpt) REVERT: E 301 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7177 (mtp) REVERT: E 522 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6787 (mt) REVERT: E 528 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6349 (pt0) REVERT: E 889 MET cc_start: 0.4287 (OUTLIER) cc_final: 0.3925 (ttm) REVERT: E 1192 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.5499 (pp) REVERT: F 19 THR cc_start: 0.4821 (p) cc_final: 0.4441 (p) REVERT: G 330 LEU cc_start: 0.8860 (tp) cc_final: 0.8567 (mt) REVERT: G 353 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8215 (mt) REVERT: G 522 LEU cc_start: 0.7057 (mp) cc_final: 0.6749 (mt) REVERT: G 882 LEU cc_start: -0.2164 (OUTLIER) cc_final: -0.2615 (mm) REVERT: H 22 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6090 (mtpt) REVERT: I 261 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8737 (pp) REVERT: I 267 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8291 (ttpt) REVERT: I 499 GLU cc_start: 0.4791 (tp30) cc_final: 0.4589 (tp30) REVERT: I 784 LYS cc_start: 0.5884 (mmtt) cc_final: 0.5157 (mmtt) REVERT: I 884 TRP cc_start: 0.2521 (m100) cc_final: 0.2087 (m100) REVERT: J 4 GLU cc_start: 0.6249 (tp30) cc_final: 0.6044 (tp30) REVERT: J 19 THR cc_start: 0.4876 (p) cc_final: 0.4448 (p) REVERT: K 139 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8530 (ttpt) REVERT: K 261 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8231 (tt) REVERT: K 267 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8391 (ttpt) REVERT: K 294 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7896 (mt) REVERT: K 301 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6753 (mtm) REVERT: K 412 GLU cc_start: 0.7664 (tt0) cc_final: 0.7259 (tt0) REVERT: K 439 ASP cc_start: 0.4573 (t0) cc_final: 0.4355 (t0) REVERT: K 516 LEU cc_start: 0.7276 (pt) cc_final: 0.6990 (pt) REVERT: K 528 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6408 (pt0) REVERT: L 19 THR cc_start: 0.5065 (p) cc_final: 0.4587 (p) REVERT: M 239 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8326 (tp) REVERT: M 240 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8248 (mt) REVERT: M 261 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8856 (pp) REVERT: M 267 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8118 (ttpt) REVERT: M 301 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7058 (mtp) REVERT: M 327 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8904 (mm) REVERT: M 353 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8284 (mt) outliers start: 621 outliers final: 284 residues processed: 1587 average time/residue: 0.6338 time to fit residues: 1745.0929 Evaluate side-chains 1099 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 779 time to evaluate : 6.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 1179 TRP Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 438 HIS Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 889 MET Chi-restraints excluded: chain C residue 1179 TRP Chi-restraints excluded: chain C residue 1181 THR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain C residue 1232 TYR Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 438 HIS Chi-restraints excluded: chain E residue 449 ASN Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 522 LEU Chi-restraints excluded: chain E residue 524 HIS Chi-restraints excluded: chain E residue 528 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 658 ASP Chi-restraints excluded: chain E residue 884 TRP Chi-restraints excluded: chain E residue 889 MET Chi-restraints excluded: chain E residue 1179 TRP Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 318 LYS Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 384 THR Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 449 ASN Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 491 MET Chi-restraints excluded: chain G residue 493 SER Chi-restraints excluded: chain G residue 524 HIS Chi-restraints excluded: chain G residue 528 GLU Chi-restraints excluded: chain G residue 531 HIS Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 658 ASP Chi-restraints excluded: chain G residue 882 LEU Chi-restraints excluded: chain G residue 889 MET Chi-restraints excluded: chain G residue 1179 TRP Chi-restraints excluded: chain G residue 1181 THR Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1248 GLU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 248 SER Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 265 ARG Chi-restraints excluded: chain I residue 267 LYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 370 ILE Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 449 ASN Chi-restraints excluded: chain I residue 450 CYS Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 531 HIS Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 557 ARG Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 639 LEU Chi-restraints excluded: chain I residue 847 ASP Chi-restraints excluded: chain I residue 882 LEU Chi-restraints excluded: chain I residue 889 MET Chi-restraints excluded: chain I residue 918 SER Chi-restraints excluded: chain I residue 1179 TRP Chi-restraints excluded: chain I residue 1181 THR Chi-restraints excluded: chain I residue 1224 HIS Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain K residue 138 GLN Chi-restraints excluded: chain K residue 139 LYS Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 259 GLN Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 267 LYS Chi-restraints excluded: chain K residue 274 MET Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 301 MET Chi-restraints excluded: chain K residue 303 LYS Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 358 SER Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 449 ASN Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 524 HIS Chi-restraints excluded: chain K residue 528 GLU Chi-restraints excluded: chain K residue 531 HIS Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 576 VAL Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 658 ASP Chi-restraints excluded: chain K residue 882 LEU Chi-restraints excluded: chain K residue 889 MET Chi-restraints excluded: chain K residue 918 SER Chi-restraints excluded: chain K residue 1055 ASN Chi-restraints excluded: chain K residue 1153 ILE Chi-restraints excluded: chain K residue 1179 TRP Chi-restraints excluded: chain K residue 1181 THR Chi-restraints excluded: chain K residue 1199 ILE Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 259 GLN Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 267 LYS Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 301 MET Chi-restraints excluded: chain M residue 303 LYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 358 SER Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 449 ASN Chi-restraints excluded: chain M residue 450 CYS Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 528 GLU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 847 ASP Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 918 SER Chi-restraints excluded: chain M residue 1153 ILE Chi-restraints excluded: chain M residue 1179 TRP Chi-restraints excluded: chain M residue 1199 ILE Chi-restraints excluded: chain M residue 1229 PHE Chi-restraints excluded: chain M residue 1232 TYR Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 58 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 438 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 656 optimal weight: 7.9990 chunk 536 optimal weight: 5.9990 chunk 217 optimal weight: 0.0980 chunk 789 optimal weight: 0.0000 chunk 853 optimal weight: 7.9990 chunk 703 optimal weight: 10.0000 chunk 783 optimal weight: 0.5980 chunk 269 optimal weight: 0.9980 chunk 633 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN A 449 ASN A 471 HIS A 562 ASN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 GLN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 HIS C 449 ASN C 477 GLN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 449 ASN E 562 ASN ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 ASN G 471 HIS G 485 ASN ** G 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1237 ASN I 449 ASN I 471 HIS ** I 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1001 GLN ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1237 ASN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 449 ASN K 471 HIS ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1176 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 ASN M 449 ASN M 545 GLN M 562 ASN ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1176 HIS M1237 ASN ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5141 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 71806 Z= 0.210 Angle : 0.755 14.264 97216 Z= 0.384 Chirality : 0.045 0.260 10731 Planarity : 0.004 0.102 12306 Dihedral : 11.165 121.004 9975 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.05 % Favored : 92.13 % Rotamer: Outliers : 5.49 % Allowed : 18.38 % Favored : 76.13 % 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: -1.16 (0.09), residues: 8708 helix: 0.46 (0.10), residues: 2345 sheet: -1.53 (0.12), residues: 1659 loop : -1.08 (0.09), residues: 4704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP K1202 HIS 0.010 0.001 HIS G 471 PHE 0.028 0.002 PHE K 897 TYR 0.046 0.002 TYR N 97 ARG 0.015 0.001 ARG E 999 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 428 poor density : 921 time to evaluate : 6.049 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 CYS cc_start: 0.6870 (m) cc_final: 0.6604 (m) REVERT: A 261 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8361 (tt) REVERT: A 295 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8426 (mt) REVERT: A 403 LEU cc_start: 0.7038 (tt) cc_final: 0.6630 (tt) REVERT: A 417 GLU cc_start: 0.6596 (tm-30) cc_final: 0.6204 (tm-30) REVERT: A 421 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8672 (mmtp) REVERT: A 784 LYS cc_start: 0.5823 (mmtt) cc_final: 0.5048 (mmtt) REVERT: B 19 THR cc_start: 0.4144 (p) cc_final: 0.3708 (p) REVERT: C 160 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8530 (ttmt) REVERT: C 240 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8173 (mt) REVERT: C 261 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8673 (pp) REVERT: C 301 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6560 (mtm) REVERT: C 417 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6605 (tm-30) REVERT: C 421 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8469 (mmtp) REVERT: C 600 LYS cc_start: 0.4123 (OUTLIER) cc_final: 0.3887 (mttt) REVERT: D 19 THR cc_start: 0.4539 (p) cc_final: 0.4026 (p) REVERT: D 82 PHE cc_start: 0.0986 (t80) cc_final: 0.0756 (t80) REVERT: E 160 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8637 (mmmm) REVERT: E 261 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8795 (pp) REVERT: E 326 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8533 (tp) REVERT: E 481 MET cc_start: 0.6750 (mmm) cc_final: 0.6501 (mmm) REVERT: E 528 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6320 (pt0) REVERT: E 651 LEU cc_start: 0.5291 (tp) cc_final: 0.4866 (tp) REVERT: E 700 GLU cc_start: 0.3430 (mp0) cc_final: 0.3169 (mt-10) REVERT: F 19 THR cc_start: 0.4786 (p) cc_final: 0.4370 (p) REVERT: G 334 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: G 403 LEU cc_start: 0.7365 (tt) cc_final: 0.7139 (tt) REVERT: G 421 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8544 (mmtp) REVERT: G 925 GLU cc_start: 0.5438 (OUTLIER) cc_final: 0.5102 (mp0) REVERT: I 261 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8572 (pp) REVERT: I 332 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7888 (ttm-80) REVERT: I 487 LEU cc_start: 0.7125 (pp) cc_final: 0.6726 (tp) REVERT: I 784 LYS cc_start: 0.5654 (mmtt) cc_final: 0.5041 (mmtt) REVERT: I 921 MET cc_start: 0.0841 (mtt) cc_final: 0.0367 (mtt) REVERT: J 19 THR cc_start: 0.4229 (p) cc_final: 0.3857 (p) REVERT: K 126 PHE cc_start: 0.6821 (p90) cc_final: 0.5934 (p90) REVERT: K 160 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8489 (ttmt) REVERT: K 294 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7689 (mt) REVERT: K 417 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6594 (tm-30) REVERT: K 421 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8548 (mmtp) REVERT: K 439 ASP cc_start: 0.4608 (t0) cc_final: 0.4204 (t0) REVERT: K 700 GLU cc_start: 0.3419 (mp0) cc_final: 0.3162 (mt-10) REVERT: L 19 THR cc_start: 0.4810 (p) cc_final: 0.4342 (p) REVERT: M 261 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8695 (pp) REVERT: M 342 LEU cc_start: 0.8644 (tp) cc_final: 0.8427 (tt) REVERT: M 353 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8313 (mt) REVERT: M 368 MET cc_start: 0.7932 (mmm) cc_final: 0.7553 (mmt) REVERT: M 528 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6455 (pt0) outliers start: 428 outliers final: 258 residues processed: 1251 average time/residue: 0.6097 time to fit residues: 1339.6554 Evaluate side-chains 1068 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 790 time to evaluate : 6.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 889 MET Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1179 TRP Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1055 ASN Chi-restraints excluded: chain C residue 1153 ILE Chi-restraints excluded: chain C residue 1179 TRP Chi-restraints excluded: chain C residue 1181 THR Chi-restraints excluded: chain C residue 1224 HIS Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 438 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 528 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 653 ILE Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain E residue 884 TRP Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1179 TRP Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 334 PHE Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 507 LEU Chi-restraints excluded: chain G residue 524 HIS Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1179 TRP Chi-restraints excluded: chain G residue 1224 HIS Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1248 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 248 SER Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 274 MET Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 573 THR Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 847 ASP Chi-restraints excluded: chain I residue 940 VAL Chi-restraints excluded: chain I residue 1179 TRP Chi-restraints excluded: chain I residue 1181 THR Chi-restraints excluded: chain I residue 1214 TYR Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 295 LEU Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 332 ARG Chi-restraints excluded: chain K residue 358 SER Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain K residue 504 MET Chi-restraints excluded: chain K residue 506 SER Chi-restraints excluded: chain K residue 524 HIS Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 576 VAL Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 889 MET Chi-restraints excluded: chain K residue 918 SER Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1055 ASN Chi-restraints excluded: chain K residue 1179 TRP Chi-restraints excluded: chain K residue 1181 THR Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 259 GLN Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 303 LYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 358 SER Chi-restraints excluded: chain M residue 360 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 384 THR Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 450 CYS Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 528 GLU Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 847 ASP Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 918 SER Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1153 ILE Chi-restraints excluded: chain M residue 1179 TRP Chi-restraints excluded: chain M residue 1199 ILE Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1229 PHE Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 85 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 780 optimal weight: 0.3980 chunk 593 optimal weight: 7.9990 chunk 409 optimal weight: 6.9990 chunk 87 optimal weight: 50.0000 chunk 376 optimal weight: 3.9990 chunk 530 optimal weight: 5.9990 chunk 792 optimal weight: 9.9990 chunk 839 optimal weight: 30.0000 chunk 414 optimal weight: 4.9990 chunk 751 optimal weight: 5.9990 chunk 226 optimal weight: 50.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 HIS C 562 ASN C 599 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN E 171 HIS E 235 HIS E 562 ASN ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS G 235 HIS G 463 GLN ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS I 235 HIS I 562 ASN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1163 HIS I1219 ASN ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 HIS K 441 GLN K 454 GLN K 463 GLN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 709 ASN ** K1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 171 HIS M 693 HIS ** M 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 71806 Z= 0.433 Angle : 0.804 12.755 97216 Z= 0.411 Chirality : 0.046 0.232 10731 Planarity : 0.005 0.068 12306 Dihedral : 10.647 149.970 9803 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.29 % Favored : 91.95 % Rotamer: Outliers : 6.02 % Allowed : 19.36 % Favored : 74.62 % 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: -1.56 (0.09), residues: 8708 helix: 0.06 (0.10), residues: 2429 sheet: -1.77 (0.11), residues: 1757 loop : -1.28 (0.09), residues: 4522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I1202 HIS 0.008 0.001 HIS G 183 PHE 0.044 0.002 PHE C 526 TYR 0.032 0.003 TYR N 97 ARG 0.009 0.001 ARG G 999 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 469 poor density : 835 time to evaluate : 6.106 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8610 (tm) REVERT: A 146 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6597 (mm-30) REVERT: A 261 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.8927 (tt) REVERT: A 265 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8437 (mtt180) REVERT: A 298 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8957 (t80) REVERT: A 406 MET cc_start: 0.5788 (ptm) cc_final: 0.5542 (ptm) REVERT: A 417 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6572 (tm-30) REVERT: A 421 LYS cc_start: 0.9115 (mmtt) cc_final: 0.8557 (mmtp) REVERT: A 503 LEU cc_start: 0.6587 (tp) cc_final: 0.6091 (tp) REVERT: A 1213 PHE cc_start: 0.5497 (t80) cc_final: 0.4703 (m-10) REVERT: C 140 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8623 (tm) REVERT: C 259 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7824 (pt0) REVERT: C 298 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8802 (t80) REVERT: C 326 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8426 (mp) REVERT: C 332 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8213 (ttp-170) REVERT: C 406 MET cc_start: 0.6594 (ptm) cc_final: 0.6348 (ttp) REVERT: C 439 ASP cc_start: 0.4617 (t0) cc_final: 0.4367 (t0) REVERT: C 454 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5369 (tt0) REVERT: C 522 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6751 (mp) REVERT: C 548 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6171 (mm) REVERT: D 82 PHE cc_start: 0.1017 (t80) cc_final: 0.0745 (t80) REVERT: E 160 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8777 (ttmt) REVERT: E 261 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9232 (tp) REVERT: E 439 ASP cc_start: 0.5462 (t0) cc_final: 0.4524 (t0) REVERT: E 454 GLN cc_start: 0.5678 (OUTLIER) cc_final: 0.4937 (tt0) REVERT: E 481 MET cc_start: 0.7567 (mmm) cc_final: 0.7262 (mmt) REVERT: E 528 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6369 (pt0) REVERT: F 65 MET cc_start: 0.4593 (tpt) cc_final: 0.3916 (mmt) REVERT: G 421 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8884 (mmtp) REVERT: G 925 GLU cc_start: 0.5619 (OUTLIER) cc_final: 0.5129 (mp0) REVERT: I 140 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8797 (tm) REVERT: I 439 ASP cc_start: 0.4427 (t0) cc_final: 0.4212 (t0) REVERT: I 784 LYS cc_start: 0.5523 (mmtt) cc_final: 0.4806 (mmtt) REVERT: I 921 MET cc_start: 0.1167 (mtt) cc_final: 0.0847 (mtt) REVERT: K 140 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8803 (tt) REVERT: K 160 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.8459 (ttmt) REVERT: K 417 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7339 (tm-30) REVERT: K 421 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8758 (mptt) REVERT: K 439 ASP cc_start: 0.4591 (t0) cc_final: 0.4233 (t0) REVERT: K 522 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6122 (mp) REVERT: K 700 GLU cc_start: 0.4165 (mp0) cc_final: 0.3955 (mt-10) REVERT: M 115 CYS cc_start: 0.6957 (m) cc_final: 0.6568 (m) REVERT: M 353 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8240 (mt) REVERT: M 522 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6648 (mp) REVERT: M 528 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6218 (pt0) REVERT: M 687 MET cc_start: 0.4641 (tpp) cc_final: 0.4309 (tpp) REVERT: N 65 MET cc_start: 0.5100 (tpt) cc_final: 0.4777 (tpt) outliers start: 469 outliers final: 311 residues processed: 1210 average time/residue: 0.6161 time to fit residues: 1315.4513 Evaluate side-chains 1044 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 709 time to evaluate : 6.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 889 MET Chi-restraints excluded: chain A residue 916 LYS Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1018 LEU Chi-restraints excluded: chain C residue 1055 ASN Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 528 GLU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 653 ILE Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 177 CYS Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 401 CYS Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 507 LEU Chi-restraints excluded: chain G residue 524 HIS Chi-restraints excluded: chain G residue 531 HIS Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1220 LEU Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1248 GLU Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 248 SER Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 274 MET Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 317 CYS Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 370 ILE Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 471 HIS Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 572 GLU Chi-restraints excluded: chain I residue 573 THR Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 630 ILE Chi-restraints excluded: chain I residue 714 LEU Chi-restraints excluded: chain I residue 847 ASP Chi-restraints excluded: chain I residue 918 SER Chi-restraints excluded: chain I residue 940 VAL Chi-restraints excluded: chain I residue 1007 TRP Chi-restraints excluded: chain I residue 1181 THR Chi-restraints excluded: chain I residue 1214 TYR Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 274 MET Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 317 CYS Chi-restraints excluded: chain K residue 327 ILE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 454 GLN Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 504 MET Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 522 LEU Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 889 MET Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1018 LEU Chi-restraints excluded: chain K residue 1153 ILE Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 65 MET Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 259 GLN Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 313 ILE Chi-restraints excluded: chain M residue 317 CYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 358 SER Chi-restraints excluded: chain M residue 360 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 450 CYS Chi-restraints excluded: chain M residue 452 GLN Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 522 LEU Chi-restraints excluded: chain M residue 528 GLU Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 630 ILE Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 847 ASP Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1018 LEU Chi-restraints excluded: chain M residue 1193 ILE Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1229 PHE Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 85 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 698 optimal weight: 30.0000 chunk 476 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 624 optimal weight: 1.9990 chunk 346 optimal weight: 40.0000 chunk 715 optimal weight: 20.0000 chunk 579 optimal weight: 30.0000 chunk 0 optimal weight: 7.9990 chunk 428 optimal weight: 10.0000 chunk 753 optimal weight: 0.9990 chunk 211 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 153 HIS A 471 HIS A 562 ASN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN A 703 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 HIS ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN C 737 ASN ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1044 GLN ** C1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 HIS ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 827 HIS ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1237 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 827 HIS ** G1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 562 ASN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 827 HIS ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 562 ASN ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 693 HIS ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1237 ASN ** M 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5389 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 71806 Z= 0.341 Angle : 0.746 12.221 97216 Z= 0.380 Chirality : 0.045 0.262 10731 Planarity : 0.004 0.066 12306 Dihedral : 9.882 144.176 9736 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.48 % Favored : 91.77 % Rotamer: Outliers : 5.83 % Allowed : 20.31 % Favored : 73.87 % 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: -1.55 (0.09), residues: 8708 helix: 0.22 (0.11), residues: 2359 sheet: -1.88 (0.11), residues: 1729 loop : -1.31 (0.09), residues: 4620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 728 HIS 0.010 0.001 HIS A 471 PHE 0.027 0.002 PHE A 505 TYR 0.031 0.002 TYR N 97 ARG 0.007 0.000 ARG G 999 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 454 poor density : 791 time to evaluate : 6.203 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8202 (tp) REVERT: A 265 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8418 (mtt180) REVERT: A 417 GLU cc_start: 0.6985 (tm-30) cc_final: 0.6502 (tm-30) REVERT: A 421 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8576 (mmtp) REVERT: A 454 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.5168 (tt0) REVERT: B 65 MET cc_start: 0.4509 (OUTLIER) cc_final: 0.4246 (tpt) REVERT: C 298 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8760 (t80) REVERT: C 330 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8914 (mt) REVERT: C 421 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8708 (mmtp) REVERT: C 439 ASP cc_start: 0.4724 (t0) cc_final: 0.4504 (t0) REVERT: C 522 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6644 (mt) REVERT: C 548 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6265 (mm) REVERT: C 797 MET cc_start: 0.2353 (mmp) cc_final: 0.0991 (mmp) REVERT: D 82 PHE cc_start: 0.1028 (t80) cc_final: 0.0787 (t80) REVERT: E 160 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8497 (ttmt) REVERT: E 332 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7932 (ttp-110) REVERT: E 439 ASP cc_start: 0.5015 (t0) cc_final: 0.4689 (t0) REVERT: E 481 MET cc_start: 0.7518 (mmm) cc_final: 0.7194 (mmt) REVERT: E 528 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5584 (pt0) REVERT: F 65 MET cc_start: 0.4577 (tpt) cc_final: 0.4150 (mmt) REVERT: G 261 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9384 (tt) REVERT: G 491 MET cc_start: 0.5243 (OUTLIER) cc_final: 0.4991 (mtt) REVERT: G 925 GLU cc_start: 0.5534 (OUTLIER) cc_final: 0.5173 (mp0) REVERT: I 267 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8441 (ttpt) REVERT: I 454 GLN cc_start: 0.6308 (OUTLIER) cc_final: 0.5969 (tp40) REVERT: I 487 LEU cc_start: 0.6217 (tp) cc_final: 0.5951 (tp) REVERT: I 921 MET cc_start: 0.0695 (mtt) cc_final: 0.0434 (mtt) REVERT: I 1018 LEU cc_start: 0.1267 (OUTLIER) cc_final: 0.0771 (tt) REVERT: K 160 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8632 (ttmt) REVERT: K 261 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9129 (pp) REVERT: K 417 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7457 (tm-30) REVERT: K 421 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8584 (mptt) REVERT: K 439 ASP cc_start: 0.4587 (t0) cc_final: 0.4138 (t0) REVERT: K 522 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6207 (mp) REVERT: M 115 CYS cc_start: 0.6851 (m) cc_final: 0.6502 (m) REVERT: M 206 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7729 (tt) REVERT: M 687 MET cc_start: 0.3938 (tpp) cc_final: 0.3613 (tpp) REVERT: M 1018 LEU cc_start: 0.1604 (OUTLIER) cc_final: 0.1339 (tt) REVERT: N 65 MET cc_start: 0.4956 (tpt) cc_final: 0.4569 (tpt) outliers start: 454 outliers final: 284 residues processed: 1140 average time/residue: 0.6219 time to fit residues: 1243.8827 Evaluate side-chains 1018 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 712 time to evaluate : 6.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1224 HIS Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1055 ASN Chi-restraints excluded: chain C residue 1153 ILE Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 528 GLU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1220 LEU Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1236 ASP Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 491 MET Chi-restraints excluded: chain G residue 507 LEU Chi-restraints excluded: chain G residue 524 HIS Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 898 LEU Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1069 VAL Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain G residue 1248 GLU Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 267 LYS Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 317 CYS Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 365 ASP Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 572 GLU Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 847 ASP Chi-restraints excluded: chain I residue 918 SER Chi-restraints excluded: chain I residue 1007 TRP Chi-restraints excluded: chain I residue 1018 LEU Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 317 CYS Chi-restraints excluded: chain K residue 327 ILE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 506 SER Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 522 LEU Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 543 ASN Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 630 ILE Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1018 LEU Chi-restraints excluded: chain K residue 1069 VAL Chi-restraints excluded: chain K residue 1153 ILE Chi-restraints excluded: chain K residue 1220 LEU Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 177 CYS Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain M residue 209 ASP Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 259 GLN Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 317 CYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 365 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 384 THR Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 445 LEU Chi-restraints excluded: chain M residue 450 CYS Chi-restraints excluded: chain M residue 452 GLN Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 528 GLU Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 566 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 688 THR Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 714 LEU Chi-restraints excluded: chain M residue 847 ASP Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1018 LEU Chi-restraints excluded: chain M residue 1193 ILE Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 85 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 282 optimal weight: 1.9990 chunk 755 optimal weight: 0.6980 chunk 165 optimal weight: 9.9990 chunk 492 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 839 optimal weight: 20.0000 chunk 697 optimal weight: 20.0000 chunk 388 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 277 optimal weight: 4.9990 chunk 440 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS A 562 ASN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 GLN ** A1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN C 565 GLN C 693 HIS C 827 HIS ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN E 543 ASN E 562 ASN E 565 GLN ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 844 GLN ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1121 HIS ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1176 HIS I 153 HIS I 454 GLN I 562 ASN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 844 GLN ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN ** K 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1121 HIS ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 599 ASN ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 737 ASN ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1055 ASN M1121 HIS ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.6832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 71806 Z= 0.324 Angle : 0.744 12.964 97216 Z= 0.375 Chirality : 0.044 0.271 10731 Planarity : 0.004 0.064 12306 Dihedral : 9.648 147.916 9701 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.50 % Favored : 91.75 % Rotamer: Outliers : 5.35 % Allowed : 21.41 % Favored : 73.24 % 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: -1.63 (0.09), residues: 8708 helix: 0.15 (0.10), residues: 2387 sheet: -1.90 (0.11), residues: 1799 loop : -1.36 (0.09), residues: 4522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 770 HIS 0.029 0.001 HIS A 471 PHE 0.042 0.002 PHE A 526 TYR 0.054 0.002 TYR D 97 ARG 0.007 0.000 ARG G 999 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 764 time to evaluate : 6.226 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6594 (mm-30) REVERT: A 265 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8283 (mtt180) REVERT: A 298 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8613 (t80) REVERT: A 330 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8986 (mp) REVERT: A 417 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6770 (tm-30) REVERT: A 421 LYS cc_start: 0.9063 (mmtt) cc_final: 0.8629 (mmtp) REVERT: A 454 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.4981 (tt0) REVERT: A 728 TRP cc_start: 0.4444 (OUTLIER) cc_final: 0.3603 (t-100) REVERT: A 761 CYS cc_start: 0.0514 (OUTLIER) cc_final: 0.0255 (t) REVERT: A 814 MET cc_start: 0.0517 (mmm) cc_final: -0.0142 (mmm) REVERT: B 65 MET cc_start: 0.4638 (OUTLIER) cc_final: 0.4391 (tpt) REVERT: C 298 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8812 (t80) REVERT: C 330 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9050 (mt) REVERT: C 421 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8578 (mmtp) REVERT: C 522 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6552 (mp) REVERT: C 548 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6379 (mm) REVERT: C 797 MET cc_start: 0.2380 (mmp) cc_final: 0.1244 (mmp) REVERT: D 82 PHE cc_start: 0.0870 (t80) cc_final: 0.0668 (t80) REVERT: E 267 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8564 (ttpt) REVERT: E 298 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8867 (t80) REVERT: E 481 MET cc_start: 0.7496 (mmm) cc_final: 0.7268 (mmt) REVERT: E 528 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.5426 (pt0) REVERT: G 155 MET cc_start: 0.8213 (ptt) cc_final: 0.7628 (ptt) REVERT: G 461 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7816 (mm) REVERT: G 889 MET cc_start: 0.6283 (tpp) cc_final: 0.5765 (tpp) REVERT: G 925 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.5128 (mp0) REVERT: I 267 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8445 (ttpt) REVERT: I 921 MET cc_start: 0.0622 (mtt) cc_final: 0.0323 (mtt) REVERT: K 160 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8642 (ttmt) REVERT: K 417 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7563 (tm-30) REVERT: K 421 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8646 (mptt) REVERT: K 439 ASP cc_start: 0.4524 (t0) cc_final: 0.4230 (t0) REVERT: K 522 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6170 (mp) REVERT: M 115 CYS cc_start: 0.6791 (m) cc_final: 0.6561 (m) REVERT: M 206 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7722 (tt) REVERT: M 522 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6632 (mt) REVERT: M 687 MET cc_start: 0.4347 (tpp) cc_final: 0.4075 (tpp) REVERT: M 1018 LEU cc_start: 0.1577 (OUTLIER) cc_final: 0.1298 (tt) outliers start: 417 outliers final: 307 residues processed: 1090 average time/residue: 0.6201 time to fit residues: 1197.1105 Evaluate side-chains 1013 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 684 time to evaluate : 6.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 728 TRP Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1224 HIS Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 205 ARG Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 528 GLU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 623 PHE Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1220 LEU Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1236 ASP Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 177 CYS Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 365 ASP Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 712 HIS Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 898 LEU Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1069 VAL Chi-restraints excluded: chain G residue 1211 GLN Chi-restraints excluded: chain G residue 1220 LEU Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 267 LYS Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 298 PHE Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 317 CYS Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 365 ASP Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 413 ASP Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 847 ASP Chi-restraints excluded: chain I residue 940 VAL Chi-restraints excluded: chain I residue 1007 TRP Chi-restraints excluded: chain I residue 1069 VAL Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 274 MET Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 317 CYS Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 457 HIS Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 506 SER Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 522 LEU Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 577 TYR Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 934 GLU Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1018 LEU Chi-restraints excluded: chain K residue 1069 VAL Chi-restraints excluded: chain K residue 1153 ILE Chi-restraints excluded: chain K residue 1220 LEU Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 259 GLN Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 317 CYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 365 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 384 THR Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 452 GLN Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 496 MET Chi-restraints excluded: chain M residue 522 LEU Chi-restraints excluded: chain M residue 528 GLU Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 714 LEU Chi-restraints excluded: chain M residue 847 ASP Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1018 LEU Chi-restraints excluded: chain M residue 1055 ASN Chi-restraints excluded: chain M residue 1193 ILE Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 74 TYR Chi-restraints excluded: chain N residue 85 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 809 optimal weight: 30.0000 chunk 94 optimal weight: 8.9990 chunk 478 optimal weight: 0.7980 chunk 613 optimal weight: 6.9990 chunk 475 optimal weight: 40.0000 chunk 706 optimal weight: 0.9980 chunk 468 optimal weight: 30.0000 chunk 836 optimal weight: 30.0000 chunk 523 optimal weight: 1.9990 chunk 510 optimal weight: 0.9990 chunk 386 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 471 HIS A 565 GLN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN A 844 GLN ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 737 ASN ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1044 GLN ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS G 200 GLN G 416 GLN G 531 HIS G 701 GLN ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 562 ASN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 701 GLN ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 747 ASN ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN K 441 GLN ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 701 GLN K 881 HIS K1044 GLN ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 183 HIS ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1044 GLN ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5328 moved from start: 0.7071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 71806 Z= 0.195 Angle : 0.703 14.338 97216 Z= 0.350 Chirality : 0.043 0.261 10731 Planarity : 0.004 0.054 12306 Dihedral : 8.851 124.908 9669 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.32 % Favored : 92.03 % Rotamer: Outliers : 4.38 % Allowed : 22.37 % Favored : 73.25 % 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: -1.49 (0.09), residues: 8708 helix: 0.37 (0.11), residues: 2352 sheet: -1.74 (0.11), residues: 1827 loop : -1.36 (0.09), residues: 4529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP M1202 HIS 0.011 0.001 HIS G 531 PHE 0.038 0.001 PHE K 526 TYR 0.038 0.002 TYR D 97 ARG 0.008 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 810 time to evaluate : 6.211 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6502 (mm-30) REVERT: A 421 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8231 (mmtp) REVERT: A 439 ASP cc_start: 0.4596 (t0) cc_final: 0.4243 (t0) REVERT: A 454 GLN cc_start: 0.5934 (OUTLIER) cc_final: 0.4864 (tt0) REVERT: A 728 TRP cc_start: 0.4346 (OUTLIER) cc_final: 0.3601 (t-100) REVERT: A 1208 GLU cc_start: 0.1268 (OUTLIER) cc_final: -0.0499 (pm20) REVERT: B 65 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.4397 (tpt) REVERT: C 421 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8494 (mmtp) REVERT: C 522 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6454 (mt) REVERT: C 600 LYS cc_start: 0.3652 (OUTLIER) cc_final: 0.3316 (pttm) REVERT: C 669 ASP cc_start: 0.1857 (m-30) cc_final: 0.1309 (t70) REVERT: C 797 MET cc_start: 0.2382 (mmp) cc_final: 0.1244 (mmp) REVERT: C 1010 GLN cc_start: 0.5584 (OUTLIER) cc_final: 0.5203 (mp10) REVERT: C 1208 GLU cc_start: 0.1129 (OUTLIER) cc_final: -0.0390 (pm20) REVERT: E 330 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8808 (mp) REVERT: E 528 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.5302 (pt0) REVERT: G 126 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.5967 (p90) REVERT: G 143 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7923 (pp) REVERT: G 623 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.5950 (m-80) REVERT: G 925 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.5209 (mp0) REVERT: I 491 MET cc_start: 0.5789 (OUTLIER) cc_final: 0.5559 (mpp) REVERT: I 504 MET cc_start: 0.6241 (tpp) cc_final: 0.5554 (mmm) REVERT: I 921 MET cc_start: 0.0419 (mtt) cc_final: 0.0126 (mtt) REVERT: I 1018 LEU cc_start: 0.1467 (OUTLIER) cc_final: 0.1131 (tt) REVERT: J 19 THR cc_start: 0.5636 (p) cc_final: 0.5333 (p) REVERT: K 160 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8298 (ttmm) REVERT: K 417 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7269 (tm-30) REVERT: K 421 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8438 (mptt) REVERT: K 439 ASP cc_start: 0.4413 (t0) cc_final: 0.4054 (t0) REVERT: M 206 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7536 (tt) REVERT: M 326 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8820 (mp) REVERT: M 339 GLU cc_start: 0.6642 (tm-30) cc_final: 0.6363 (tm-30) REVERT: M 443 ASP cc_start: 0.5448 (t0) cc_final: 0.5178 (t0) outliers start: 341 outliers final: 246 residues processed: 1074 average time/residue: 0.6370 time to fit residues: 1216.8392 Evaluate side-chains 978 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 713 time to evaluate : 6.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 728 TRP Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1208 GLU Chi-restraints excluded: chain A residue 1224 HIS Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1153 ILE Chi-restraints excluded: chain C residue 1208 GLU Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 439 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 528 GLU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1236 ASP Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 577 TYR Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 623 PHE Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain G residue 701 GLN Chi-restraints excluded: chain G residue 712 HIS Chi-restraints excluded: chain G residue 770 TRP Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 898 LEU Chi-restraints excluded: chain G residue 925 GLU Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1069 VAL Chi-restraints excluded: chain G residue 1211 GLN Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 365 ASP Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 418 PHE Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 491 MET Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 847 ASP Chi-restraints excluded: chain I residue 918 SER Chi-restraints excluded: chain I residue 1018 LEU Chi-restraints excluded: chain I residue 1069 VAL Chi-restraints excluded: chain I residue 1231 THR Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 274 MET Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 317 CYS Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 457 HIS Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 506 SER Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain K residue 577 TYR Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1018 LEU Chi-restraints excluded: chain K residue 1069 VAL Chi-restraints excluded: chain K residue 1153 ILE Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 317 CYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 365 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 384 THR Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 445 LEU Chi-restraints excluded: chain M residue 452 GLN Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 714 LEU Chi-restraints excluded: chain M residue 847 ASP Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1193 ILE Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 85 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 517 optimal weight: 0.8980 chunk 334 optimal weight: 0.0070 chunk 499 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 531 optimal weight: 3.9990 chunk 569 optimal weight: 8.9990 chunk 413 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 657 optimal weight: 0.0670 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 HIS B 33 HIS ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN C 701 GLN C 703 ASN C 737 ASN ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 701 GLN G 703 ASN ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 562 ASN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 701 GLN ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1044 GLN ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 562 ASN ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 701 GLN K 827 HIS K 844 GLN ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 731 ASN M1055 ASN ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5304 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 71806 Z= 0.181 Angle : 0.708 12.775 97216 Z= 0.350 Chirality : 0.043 0.263 10731 Planarity : 0.004 0.070 12306 Dihedral : 8.446 115.645 9636 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.19 % Favored : 92.17 % Rotamer: Outliers : 3.79 % Allowed : 23.21 % Favored : 73.01 % 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: -1.51 (0.09), residues: 8708 helix: 0.39 (0.11), residues: 2380 sheet: -1.79 (0.11), residues: 1911 loop : -1.36 (0.09), residues: 4417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I1202 HIS 0.030 0.001 HIS A 471 PHE 0.037 0.001 PHE K 526 TYR 0.033 0.001 TYR D 97 ARG 0.004 0.000 ARG G 999 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 782 time to evaluate : 6.185 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6463 (mm-30) REVERT: A 417 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6361 (tm-30) REVERT: A 421 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8677 (mmtp) REVERT: A 454 GLN cc_start: 0.5713 (OUTLIER) cc_final: 0.4794 (tt0) REVERT: A 553 HIS cc_start: 0.3202 (p-80) cc_final: 0.2950 (p-80) REVERT: A 728 TRP cc_start: 0.4598 (OUTLIER) cc_final: 0.3817 (t-100) REVERT: A 1214 TYR cc_start: 0.4312 (t80) cc_final: 0.3944 (t80) REVERT: B 65 MET cc_start: 0.4584 (tpt) cc_final: 0.4342 (tpt) REVERT: C 330 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8944 (mt) REVERT: C 522 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6287 (mt) REVERT: C 600 LYS cc_start: 0.3941 (OUTLIER) cc_final: 0.3645 (pttm) REVERT: C 669 ASP cc_start: 0.1762 (m-30) cc_final: 0.1282 (t70) REVERT: C 797 MET cc_start: 0.2084 (mmp) cc_final: 0.0959 (mmp) REVERT: C 1010 GLN cc_start: 0.5612 (OUTLIER) cc_final: 0.5294 (mp10) REVERT: D 65 MET cc_start: 0.4289 (tpt) cc_final: 0.3495 (mmt) REVERT: E 205 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8380 (ttm170) REVERT: E 267 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8471 (ttpt) REVERT: E 330 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8934 (mp) REVERT: G 403 LEU cc_start: 0.7333 (tt) cc_final: 0.7075 (tt) REVERT: G 623 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.5888 (m-80) REVERT: I 143 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7786 (pp) REVERT: I 330 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8982 (mp) REVERT: I 491 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.5500 (mpp) REVERT: I 921 MET cc_start: 0.0579 (mtt) cc_final: 0.0341 (mtt) REVERT: I 1018 LEU cc_start: 0.1569 (OUTLIER) cc_final: 0.1214 (tt) REVERT: I 1208 GLU cc_start: 0.1597 (OUTLIER) cc_final: -0.0575 (pm20) REVERT: J 19 THR cc_start: 0.5612 (p) cc_final: 0.5280 (p) REVERT: K 126 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.6093 (p90) REVERT: K 374 MET cc_start: 0.7306 (mmm) cc_final: 0.7052 (mmp) REVERT: K 417 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7232 (tm-30) REVERT: K 421 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8396 (mptt) REVERT: K 439 ASP cc_start: 0.4303 (t0) cc_final: 0.4076 (t0) REVERT: L 65 MET cc_start: 0.3175 (tpt) cc_final: 0.2720 (tpt) REVERT: M 206 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7449 (tt) REVERT: M 339 GLU cc_start: 0.6648 (tm-30) cc_final: 0.6408 (tm-30) REVERT: M 504 MET cc_start: 0.5990 (tpp) cc_final: 0.5355 (mmm) REVERT: M 739 MET cc_start: 0.3091 (pmm) cc_final: 0.1235 (ptp) outliers start: 295 outliers final: 230 residues processed: 1010 average time/residue: 0.6325 time to fit residues: 1129.8285 Evaluate side-chains 951 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 704 time to evaluate : 6.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 728 TRP Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 701 GLN Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1199 ILE Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 205 ARG Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 770 TRP Chi-restraints excluded: chain E residue 940 VAL Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1236 ASP Chi-restraints excluded: chain E residue 1240 ILE Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 577 TYR Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 623 PHE Chi-restraints excluded: chain G residue 701 GLN Chi-restraints excluded: chain G residue 712 HIS Chi-restraints excluded: chain G residue 770 TRP Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 940 VAL Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain G residue 1240 ILE Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 111 ARG Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 MET Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 365 ASP Chi-restraints excluded: chain I residue 370 ILE Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 418 PHE Chi-restraints excluded: chain I residue 438 HIS Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 491 MET Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 630 ILE Chi-restraints excluded: chain I residue 701 GLN Chi-restraints excluded: chain I residue 1018 LEU Chi-restraints excluded: chain I residue 1069 VAL Chi-restraints excluded: chain I residue 1208 GLU Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 274 MET Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 370 ILE Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 457 HIS Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 506 SER Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain K residue 577 TYR Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 701 GLN Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1018 LEU Chi-restraints excluded: chain K residue 1153 ILE Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain K residue 1240 ILE Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 365 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 384 THR Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 445 LEU Chi-restraints excluded: chain M residue 452 GLN Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 491 MET Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 847 ASP Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 940 VAL Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1055 ASN Chi-restraints excluded: chain M residue 1153 ILE Chi-restraints excluded: chain M residue 1193 ILE Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 74 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 761 optimal weight: 1.9990 chunk 801 optimal weight: 8.9990 chunk 731 optimal weight: 8.9990 chunk 779 optimal weight: 7.9990 chunk 469 optimal weight: 20.0000 chunk 339 optimal weight: 20.0000 chunk 612 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 704 optimal weight: 20.0000 chunk 737 optimal weight: 30.0000 chunk 776 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 171 HIS A 471 HIS ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN ** A1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 259 GLN ** C 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 997 GLN ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN G 497 HIS ** G 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 844 GLN G1044 GLN ** G1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 562 ASN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 HIS K 497 HIS ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 731 ASN ** K1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 827 HIS M 844 GLN ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1055 ASN ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.7669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.146 71806 Z= 0.537 Angle : 0.884 17.562 97216 Z= 0.445 Chirality : 0.049 0.301 10731 Planarity : 0.005 0.079 12306 Dihedral : 9.263 159.172 9629 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.69 % Favored : 90.71 % Rotamer: Outliers : 4.24 % Allowed : 23.09 % Favored : 72.67 % 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: -1.93 (0.09), residues: 8708 helix: -0.30 (0.10), residues: 2401 sheet: -1.84 (0.11), residues: 1862 loop : -1.53 (0.09), residues: 4445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP K1201 HIS 0.048 0.002 HIS A 471 PHE 0.041 0.002 PHE E 298 TYR 0.035 0.003 TYR A 383 ARG 0.013 0.001 ARG G 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 674 time to evaluate : 6.260 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7682 (tt) REVERT: A 365 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7159 (t70) REVERT: A 421 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8619 (mmtp) REVERT: A 431 LYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6330 (pttm) REVERT: A 454 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.5194 (tt0) REVERT: A 728 TRP cc_start: 0.4940 (OUTLIER) cc_final: 0.4115 (t-100) REVERT: B 65 MET cc_start: 0.4685 (OUTLIER) cc_final: 0.4470 (tpt) REVERT: B 80 MET cc_start: 0.2036 (tpt) cc_final: 0.1716 (tpt) REVERT: C 251 LEU cc_start: 0.9131 (mt) cc_final: 0.8635 (mt) REVERT: C 298 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8745 (t80) REVERT: C 522 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6091 (mp) REVERT: C 669 ASP cc_start: 0.1787 (m-30) cc_final: 0.1512 (t70) REVERT: D 65 MET cc_start: 0.4593 (tpt) cc_final: 0.3945 (tpt) REVERT: E 160 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8562 (mtmt) REVERT: E 267 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8715 (ttpt) REVERT: E 330 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9099 (mp) REVERT: E 533 LEU cc_start: 0.4805 (pt) cc_final: 0.4435 (pp) REVERT: E 1191 MET cc_start: 0.1881 (mmt) cc_final: 0.1608 (mmt) REVERT: H 80 MET cc_start: 0.1601 (tpt) cc_final: 0.1155 (tpt) REVERT: I 267 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8436 (ttpt) REVERT: I 491 MET cc_start: 0.5939 (OUTLIER) cc_final: 0.5686 (mpp) REVERT: I 921 MET cc_start: 0.1026 (mtt) cc_final: 0.0603 (mtt) REVERT: I 1018 LEU cc_start: 0.1424 (OUTLIER) cc_final: 0.0965 (tt) REVERT: K 160 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.8613 (ttmt) REVERT: K 261 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9313 (pp) REVERT: K 421 LYS cc_start: 0.9205 (mmtt) cc_final: 0.8823 (mptt) REVERT: K 1214 TYR cc_start: 0.5349 (OUTLIER) cc_final: 0.5080 (t80) REVERT: M 206 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7958 (tt) REVERT: M 443 ASP cc_start: 0.5591 (t0) cc_final: 0.5371 (t0) REVERT: M 457 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6845 (m170) REVERT: M 504 MET cc_start: 0.6727 (tpp) cc_final: 0.6040 (mmm) REVERT: M 522 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6456 (mp) REVERT: M 739 MET cc_start: 0.2981 (pmm) cc_final: 0.1030 (ptp) REVERT: N 65 MET cc_start: 0.5528 (tpt) cc_final: 0.5028 (mmt) outliers start: 330 outliers final: 240 residues processed: 933 average time/residue: 0.6387 time to fit residues: 1050.9892 Evaluate side-chains 882 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 622 time to evaluate : 6.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 728 TRP Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1224 HIS Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1153 ILE Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1229 PHE Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 770 TRP Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1220 LEU Chi-restraints excluded: chain E residue 1224 HIS Chi-restraints excluded: chain E residue 1229 PHE Chi-restraints excluded: chain E residue 1236 ASP Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 577 TYR Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 712 HIS Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 898 LEU Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1069 VAL Chi-restraints excluded: chain G residue 1229 PHE Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 248 SER Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 259 GLN Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 267 LYS Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 274 MET Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 317 CYS Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain I residue 365 ASP Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 491 MET Chi-restraints excluded: chain I residue 496 MET Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 598 ILE Chi-restraints excluded: chain I residue 1018 LEU Chi-restraints excluded: chain I residue 1069 VAL Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 256 SER Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 264 THR Chi-restraints excluded: chain K residue 274 MET Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 418 PHE Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 457 HIS Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 506 SER Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain K residue 577 TYR Chi-restraints excluded: chain K residue 598 ILE Chi-restraints excluded: chain K residue 884 TRP Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1018 LEU Chi-restraints excluded: chain K residue 1069 VAL Chi-restraints excluded: chain K residue 1214 TYR Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain K residue 1229 PHE Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain M residue 213 SER Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 298 PHE Chi-restraints excluded: chain M residue 317 CYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 365 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 445 LEU Chi-restraints excluded: chain M residue 457 HIS Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 491 MET Chi-restraints excluded: chain M residue 522 LEU Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 598 ILE Chi-restraints excluded: chain M residue 624 SER Chi-restraints excluded: chain M residue 674 THR Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 847 ASP Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1153 ILE Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1224 HIS Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 74 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 511 optimal weight: 0.7980 chunk 824 optimal weight: 1.9990 chunk 503 optimal weight: 0.2980 chunk 391 optimal weight: 0.9980 chunk 573 optimal weight: 3.9990 chunk 864 optimal weight: 7.9990 chunk 795 optimal weight: 5.9990 chunk 688 optimal weight: 0.5980 chunk 71 optimal weight: 8.9990 chunk 531 optimal weight: 0.7980 chunk 422 optimal weight: 0.0040 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN ** A1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1126 HIS E 640 GLN ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 452 GLN G 545 GLN G 565 GLN ** G 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 701 GLN ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 311 HIS ** K 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 463 GLN M 565 GLN ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5355 moved from start: 0.7792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 71806 Z= 0.192 Angle : 0.747 14.711 97216 Z= 0.367 Chirality : 0.044 0.297 10731 Planarity : 0.004 0.069 12306 Dihedral : 8.351 119.702 9613 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.12 % Favored : 92.31 % Rotamer: Outliers : 2.70 % Allowed : 24.80 % Favored : 72.51 % 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: -1.59 (0.09), residues: 8708 helix: 0.23 (0.11), residues: 2352 sheet: -1.81 (0.11), residues: 1918 loop : -1.36 (0.09), residues: 4438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP K1201 HIS 0.017 0.001 HIS A 471 PHE 0.031 0.001 PHE K 526 TYR 0.032 0.002 TYR D 97 ARG 0.016 0.001 ARG M 608 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17416 Ramachandran restraints generated. 8708 Oldfield, 0 Emsley, 8708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 733 time to evaluate : 6.219 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: 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: 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: symmetry clash REVERT: A 146 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6477 (mm-30) REVERT: A 421 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8773 (mmtp) REVERT: A 454 GLN cc_start: 0.6107 (OUTLIER) cc_final: 0.5016 (tt0) REVERT: A 728 TRP cc_start: 0.4907 (OUTLIER) cc_final: 0.4136 (t-100) REVERT: A 739 MET cc_start: 0.3326 (pmm) cc_final: 0.1504 (ptm) REVERT: B 65 MET cc_start: 0.4601 (OUTLIER) cc_final: 0.4374 (tpt) REVERT: C 298 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8412 (t80) REVERT: C 503 LEU cc_start: 0.6109 (tt) cc_final: 0.5777 (tt) REVERT: C 522 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6163 (mt) REVERT: C 1010 GLN cc_start: 0.5838 (OUTLIER) cc_final: 0.5321 (mp10) REVERT: D 65 MET cc_start: 0.4439 (tpt) cc_final: 0.3952 (tpt) REVERT: E 160 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8711 (mtmm) REVERT: E 267 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8493 (ttpt) REVERT: E 487 LEU cc_start: 0.7012 (tp) cc_final: 0.6787 (tp) REVERT: E 533 LEU cc_start: 0.4693 (pt) cc_final: 0.4332 (pp) REVERT: E 1191 MET cc_start: 0.1852 (mmt) cc_final: 0.1575 (mmt) REVERT: I 330 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8954 (mp) REVERT: I 921 MET cc_start: 0.0844 (mtt) cc_final: 0.0439 (mtt) REVERT: K 126 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.6042 (p90) REVERT: K 421 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8742 (mptt) REVERT: K 553 HIS cc_start: 0.4603 (p-80) cc_final: 0.4222 (p-80) REVERT: K 739 MET cc_start: 0.3436 (ptp) cc_final: 0.1215 (mtt) REVERT: L 65 MET cc_start: 0.3149 (tpt) cc_final: 0.2885 (tpt) REVERT: M 206 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7570 (tt) REVERT: M 443 ASP cc_start: 0.5788 (t0) cc_final: 0.5553 (t0) REVERT: M 504 MET cc_start: 0.6370 (tpp) cc_final: 0.5544 (mmm) REVERT: M 739 MET cc_start: 0.2953 (pmm) cc_final: 0.1021 (ptp) REVERT: N 65 MET cc_start: 0.5806 (tpt) cc_final: 0.5055 (mmt) outliers start: 210 outliers final: 168 residues processed: 903 average time/residue: 0.6756 time to fit residues: 1090.7960 Evaluate side-chains 854 residues out of total 7791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 675 time to evaluate : 6.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 728 TRP Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 HIS Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 712 HIS Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1153 ILE Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 418 PHE Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 HIS Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain E residue 577 TYR Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 712 HIS Chi-restraints excluded: chain E residue 770 TRP Chi-restraints excluded: chain E residue 1007 TRP Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1193 ILE Chi-restraints excluded: chain E residue 1236 ASP Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 298 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 370 ILE Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 418 PHE Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 577 TYR Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 712 HIS Chi-restraints excluded: chain G residue 770 TRP Chi-restraints excluded: chain G residue 881 HIS Chi-restraints excluded: chain G residue 898 LEU Chi-restraints excluded: chain G residue 1007 TRP Chi-restraints excluded: chain G residue 1069 VAL Chi-restraints excluded: chain H residue 14 CYS Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 330 LEU Chi-restraints excluded: chain I residue 365 ASP Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 468 HIS Chi-restraints excluded: chain I residue 491 MET Chi-restraints excluded: chain I residue 496 MET Chi-restraints excluded: chain I residue 534 ASP Chi-restraints excluded: chain I residue 847 ASP Chi-restraints excluded: chain I residue 940 VAL Chi-restraints excluded: chain I residue 1069 VAL Chi-restraints excluded: chain I residue 1234 THR Chi-restraints excluded: chain I residue 1240 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 274 MET Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 298 PHE Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 445 LEU Chi-restraints excluded: chain K residue 457 HIS Chi-restraints excluded: chain K residue 468 HIS Chi-restraints excluded: chain K residue 506 SER Chi-restraints excluded: chain K residue 533 LEU Chi-restraints excluded: chain K residue 534 ASP Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain K residue 577 TYR Chi-restraints excluded: chain K residue 1007 TRP Chi-restraints excluded: chain K residue 1018 LEU Chi-restraints excluded: chain K residue 1069 VAL Chi-restraints excluded: chain K residue 1224 HIS Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 126 PHE Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 365 ASP Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 445 LEU Chi-restraints excluded: chain M residue 468 HIS Chi-restraints excluded: chain M residue 491 MET Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 674 THR Chi-restraints excluded: chain M residue 712 HIS Chi-restraints excluded: chain M residue 847 ASP Chi-restraints excluded: chain M residue 882 LEU Chi-restraints excluded: chain M residue 908 LEU Chi-restraints excluded: chain M residue 1007 TRP Chi-restraints excluded: chain M residue 1153 ILE Chi-restraints excluded: chain M residue 1220 LEU Chi-restraints excluded: chain M residue 1240 ILE Chi-restraints excluded: chain N residue 14 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 546 optimal weight: 0.8980 chunk 733 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 634 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 689 optimal weight: 0.6980 chunk 288 optimal weight: 2.9990 chunk 708 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 GLN B 70 ASN C 562 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1044 GLN E 599 ASN ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 562 ASN ** G 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 531 HIS K 701 GLN ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.199129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.157429 restraints weight = 135290.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.159794 restraints weight = 231504.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.155700 restraints weight = 116157.276| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.7923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 71806 Z= 0.219 Angle : 0.734 13.956 97216 Z= 0.360 Chirality : 0.043 0.345 10731 Planarity : 0.004 0.072 12306 Dihedral : 8.155 125.051 9608 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.66 % Favored : 91.74 % Rotamer: Outliers : 2.82 % Allowed : 24.85 % Favored : 72.33 % 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: -1.57 (0.09), residues: 8708 helix: 0.23 (0.11), residues: 2373 sheet: -1.73 (0.11), residues: 1946 loop : -1.37 (0.09), residues: 4389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP M1201 HIS 0.010 0.001 HIS A 471 PHE 0.033 0.001 PHE K 547 TYR 0.031 0.002 TYR D 97 ARG 0.008 0.000 ARG M 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19900.94 seconds wall clock time: 345 minutes 8.33 seconds (20708.33 seconds total)