Starting phenix.real_space_refine on Mon Sep 30 08:12:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/09_2024/5wve_6690.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/09_2024/5wve_6690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/09_2024/5wve_6690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/09_2024/5wve_6690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/09_2024/5wve_6690.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/09_2024/5wve_6690.cif" } resolution = 4.4 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= 0.011 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 516 5.16 5 C 49679 2.51 5 N 13585 2.21 5 O 14790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 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: 78605 Number of models: 1 Model: "" Number of chains: 39 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "P" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "Q" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "R" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "S" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 762 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "X" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 742 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "Y" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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} Chain: "C" 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: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" 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: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" 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: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "K" 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: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "M" 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: "N" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 33.82, per 1000 atoms: 0.43 Number of scatterers: 78605 At special positions: 0 Unit cell: (302.84, 308.2, 148.74, 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 516 16.00 P 21 15.00 Mg 7 11.99 O 14790 8.00 N 13585 7.00 C 49679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, 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 Simple disulfide: pdb=" SG CYS C 633 " - pdb=" SG CYS C 663 " distance=2.20 Simple disulfide: pdb=" SG CYS C 675 " - pdb=" SG CYS C 705 " distance=2.02 Simple disulfide: pdb=" SG CYS C 704 " - pdb=" SG CYS C 749 " distance=1.89 Simple disulfide: pdb=" SG CYS C 761 " - pdb=" SG CYS C 804 " distance=2.05 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 846 " distance=2.09 Simple disulfide: pdb=" SG CYS E 633 " - pdb=" SG CYS E 663 " distance=2.20 Simple disulfide: pdb=" SG CYS E 675 " - pdb=" SG CYS E 705 " distance=2.02 Simple disulfide: pdb=" SG CYS E 704 " - pdb=" SG CYS E 749 " distance=1.89 Simple disulfide: pdb=" SG CYS E 761 " - pdb=" SG CYS E 804 " distance=2.05 Simple disulfide: pdb=" SG CYS E 803 " - pdb=" SG CYS E 846 " distance=2.09 Simple disulfide: pdb=" SG CYS G 633 " - pdb=" SG CYS G 663 " distance=2.20 Simple disulfide: pdb=" SG CYS G 675 " - pdb=" SG CYS G 705 " distance=2.02 Simple disulfide: pdb=" SG CYS G 704 " - pdb=" SG CYS G 749 " distance=1.89 Simple disulfide: pdb=" SG CYS G 761 " - pdb=" SG CYS G 804 " distance=2.05 Simple disulfide: pdb=" SG CYS G 803 " - pdb=" SG CYS G 846 " distance=2.09 Simple disulfide: pdb=" SG CYS I 633 " - pdb=" SG CYS I 663 " distance=2.20 Simple disulfide: pdb=" SG CYS I 675 " - pdb=" SG CYS I 705 " distance=2.02 Simple disulfide: pdb=" SG CYS I 704 " - pdb=" SG CYS I 749 " distance=1.89 Simple disulfide: pdb=" SG CYS I 761 " - pdb=" SG CYS I 804 " distance=2.05 Simple disulfide: pdb=" SG CYS I 803 " - pdb=" SG CYS I 846 " distance=2.09 Simple disulfide: pdb=" SG CYS K 633 " - pdb=" SG CYS K 663 " distance=2.19 Simple disulfide: pdb=" SG CYS K 675 " - pdb=" SG CYS K 705 " distance=2.02 Simple disulfide: pdb=" SG CYS K 704 " - pdb=" SG CYS K 749 " distance=1.89 Simple disulfide: pdb=" SG CYS K 761 " - pdb=" SG CYS K 804 " distance=2.05 Simple disulfide: pdb=" SG CYS K 803 " - pdb=" SG CYS K 846 " distance=2.09 Simple disulfide: pdb=" SG CYS M 633 " - pdb=" SG CYS M 663 " distance=2.20 Simple disulfide: pdb=" SG CYS M 675 " - pdb=" SG CYS M 705 " distance=2.02 Simple disulfide: pdb=" SG CYS M 704 " - pdb=" SG CYS M 749 " distance=1.89 Simple disulfide: pdb=" SG CYS M 761 " - pdb=" SG CYS M 804 " distance=2.05 Simple disulfide: pdb=" SG CYS M 803 " - pdb=" SG CYS M 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: 15.33 Conformation dependent library (CDL) restraints added in 7.7 seconds 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18440 Finding SS restraints... Secondary structure from input PDB file: 301 helices and 133 sheets defined 36.7% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.30 Creating SS restraints... Processing helix chain 'A' and resid 107 through 118 removed outlier: 3.557A pdb=" N ARG A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 removed outlier: 4.125A 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: 3.844A 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: 3.675A 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: 4.119A 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: 3.532A 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: 3.670A pdb=" N ILE A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 467 removed outlier: 7.004A 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: 3.834A pdb=" N GLN A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.685A pdb=" N ASN A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.628A 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 518 Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.536A 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: 3.719A pdb=" N ILE A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 550 removed outlier: 3.665A 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 573 through 591 removed outlier: 3.555A pdb=" N LEU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 589 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 4.230A 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: 4.139A pdb=" N CYS A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) removed outlier: 3.917A 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: 3.515A 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: 3.844A 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: 3.526A 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: 3.677A 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: 4.358A 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: 3.647A 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: 3.829A pdb=" N ASP C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.928A 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: 3.530A 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: 3.713A 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: 3.824A 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: 3.668A 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: 3.836A 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: 4.320A pdb=" N LYS C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 495 removed outlier: 3.685A pdb=" N ASN C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.809A 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 518 Processing helix chain 'C' and resid 520 through 533 removed outlier: 3.538A 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: 3.719A pdb=" N ILE C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 550 removed outlier: 3.667A 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: 4.771A 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 573 through 591 removed outlier: 3.554A pdb=" N LEU C 582 " --> pdb=" O GLN C 578 " (cutoff:3.500A) removed outlier: 3.618A 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: 3.918A 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: 3.524A pdb=" N GLU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 3.516A 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: 4.125A pdb=" N LEU E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 170 removed outlier: 3.561A 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: 3.939A pdb=" N LEU E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 207 removed outlier: 3.628A pdb=" N MET E 197 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 3.677A 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: 4.033A 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 309 through 318 removed outlier: 3.743A pdb=" N ILE E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS E 315 " --> pdb=" O HIS E 311 " (cutoff:3.500A) removed outlier: 3.559A 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: 4.118A 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: 3.532A pdb=" N MET E 368 " --> pdb=" O LEU E 364 " (cutoff:3.500A) removed outlier: 3.752A 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: 4.571A 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: 4.338A pdb=" N TYR E 382 " --> pdb=" O ASP E 378 " (cutoff:3.500A) removed outlier: 4.030A 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: 7.003A 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: 3.836A 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: 4.319A pdb=" N LYS E 458 " --> pdb=" O GLN E 454 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN E 463 " --> pdb=" O LYS E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 495 removed outlier: 3.685A pdb=" N ASN E 485 " --> pdb=" O MET E 481 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET E 491 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 492 " --> pdb=" O ALA E 488 " (cutoff:3.500A) removed outlier: 3.627A 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 518 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: 3.719A pdb=" N ILE E 532 " --> pdb=" O GLU E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 550 removed outlier: 3.667A pdb=" N VAL E 540 " --> pdb=" O LYS E 536 " (cutoff:3.500A) removed outlier: 4.075A 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 573 through 591 removed outlier: 3.554A pdb=" N LEU E 582 " --> pdb=" O GLN E 578 " (cutoff:3.500A) removed outlier: 3.616A 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: 4.141A 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: 3.524A pdb=" N GLU F 69 " --> pdb=" O MET F 65 " (cutoff:3.500A) removed outlier: 3.514A 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: 4.126A 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: 3.844A pdb=" N ASP G 170 " --> pdb=" O GLU G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 178 removed outlier: 3.942A 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: 4.030A 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: 3.743A 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: 3.830A pdb=" N ASP G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 348 removed outlier: 4.118A 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: 3.532A pdb=" N MET G 368 " --> pdb=" O LEU G 364 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE G 370 " --> pdb=" O GLU G 366 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU G 373 " --> pdb=" O SER G 369 " (cutoff:3.500A) removed outlier: 4.572A 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: 4.030A pdb=" N THR G 384 " --> pdb=" O LYS G 380 " (cutoff:3.500A) removed outlier: 3.824A 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: 4.148A 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: 6.846A 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: 4.322A pdb=" N LYS G 458 " --> pdb=" O GLN G 454 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN G 463 " --> pdb=" O LYS G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 479 through 495 removed outlier: 3.686A pdb=" N ASN G 485 " --> pdb=" O MET G 481 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET G 491 " --> pdb=" O LEU G 487 " (cutoff:3.500A) removed outlier: 3.810A 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 518 Processing helix chain 'G' and resid 520 through 533 removed outlier: 3.537A pdb=" N GLU G 528 " --> pdb=" O HIS G 524 " (cutoff:3.500A) removed outlier: 4.267A 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: 4.077A pdb=" N LEU G 550 " --> pdb=" O GLU G 546 " (cutoff:3.500A) Processing helix chain 'G' and resid 550 through 555 removed outlier: 4.770A 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 573 through 591 removed outlier: 3.553A pdb=" N LEU G 582 " --> pdb=" O GLN G 578 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP G 589 " --> pdb=" O LYS G 585 " (cutoff:3.500A) removed outlier: 4.229A 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: 3.516A 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: 3.557A pdb=" N ARG I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 143 removed outlier: 4.125A pdb=" N LEU I 143 " --> pdb=" O LYS I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 170 removed outlier: 3.561A 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: 3.940A 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: 3.628A 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: 4.356A pdb=" N HIS I 311 " --> pdb=" O PRO I 307 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER I 312 " --> pdb=" O GLU I 308 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE I 313 " --> pdb=" O GLN I 309 " (cutoff:3.500A) removed outlier: 3.647A 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: 3.832A 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: 4.121A 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: 3.753A pdb=" N ILE I 370 " --> pdb=" O GLU I 366 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.713A pdb=" N ASP I 381 " --> pdb=" O GLU I 377 " (cutoff:3.500A) removed outlier: 4.341A 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: 3.822A 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: 7.001A 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: 4.322A pdb=" N LYS I 458 " --> pdb=" O GLN I 454 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS I 459 " --> pdb=" O ASP I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 479 through 495 removed outlier: 3.686A pdb=" N ASN I 485 " --> pdb=" O MET I 481 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET I 491 " --> pdb=" O LEU I 487 " (cutoff:3.500A) removed outlier: 3.809A 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 518 Processing helix chain 'I' and resid 520 through 533 removed outlier: 3.539A 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: 3.721A 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 573 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: 4.141A 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: 3.522A 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: 4.125A pdb=" N LEU K 143 " --> pdb=" O LYS K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 170 removed outlier: 3.563A 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: 3.938A pdb=" N LEU K 174 " --> pdb=" O ASP K 170 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 207 removed outlier: 3.626A 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: 4.034A 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: 4.573A pdb=" N SER K 312 " --> pdb=" O GLU K 308 " (cutoff:3.500A) removed outlier: 3.745A 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: 3.873A 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: 3.832A 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: 3.878A 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: 3.617A pdb=" N GLU K 373 " --> pdb=" O SER K 369 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET K 374 " --> pdb=" O ILE K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 376 through 386 removed outlier: 3.711A 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: 4.031A 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: 4.148A pdb=" N ASP K 413 " --> pdb=" O GLU K 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE K 414 " --> pdb=" O GLU K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 438 through 467 removed outlier: 7.004A 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: 3.837A pdb=" N GLN K 454 " --> pdb=" O CYS K 450 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP K 455 " --> pdb=" O SER K 451 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS K 458 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS K 459 " --> pdb=" O ASP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 495 removed outlier: 3.686A pdb=" N ASN K 485 " --> pdb=" O MET K 481 " (cutoff:3.500A) removed outlier: 3.619A 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 518 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: 3.720A pdb=" N ILE K 532 " --> pdb=" O GLU K 528 " (cutoff:3.500A) Processing helix chain 'K' and resid 534 through 550 removed outlier: 3.666A 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: 4.771A 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 573 through 591 removed outlier: 3.553A 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: 4.141A pdb=" N CYS K 915 " --> pdb=" O THR K 911 " (cutoff:3.500A) removed outlier: 3.917A 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: 4.124A 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: 3.628A 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: 4.356A pdb=" N HIS M 311 " --> pdb=" O PRO M 307 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 3.743A 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: 3.873A pdb=" N LYS M 315 " --> pdb=" O HIS M 311 " (cutoff:3.500A) removed outlier: 3.559A 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: 3.930A 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: 3.532A 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: 3.714A pdb=" N ASP M 381 " --> pdb=" O GLU M 377 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR M 382 " --> pdb=" O ASP M 378 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR M 384 " --> pdb=" O LYS M 380 " (cutoff:3.500A) removed outlier: 3.823A 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: 4.151A pdb=" N ASP M 413 " --> pdb=" O GLU M 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE M 414 " --> pdb=" O GLU M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 467 removed outlier: 7.004A 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: 3.835A pdb=" N GLN M 454 " --> pdb=" O CYS M 450 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP M 455 " --> pdb=" O SER M 451 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS M 458 " --> pdb=" O GLN M 454 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS M 459 " --> pdb=" O ASP M 455 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN M 463 " --> pdb=" O LYS M 459 " (cutoff:3.500A) Processing helix chain 'M' and resid 479 through 495 removed outlier: 3.685A pdb=" N ASN M 485 " --> pdb=" O MET M 481 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET M 491 " --> pdb=" O LEU M 487 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA M 492 " --> pdb=" O ALA M 488 " (cutoff:3.500A) removed outlier: 3.629A 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 518 Processing helix chain 'M' and resid 520 through 533 removed outlier: 3.537A 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: 4.075A 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 573 through 591 removed outlier: 3.552A 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: 4.229A 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: 3.521A pdb=" N GLU N 69 " --> pdb=" O MET N 65 " (cutoff:3.500A) removed outlier: 3.513A 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 helix chain 'O' and resid 2 through 18 removed outlier: 4.962A pdb=" N GLU O 14 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA O 15 " --> pdb=" O GLN O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 32 removed outlier: 4.106A pdb=" N ILE O 25 " --> pdb=" O LYS O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 45 Processing helix chain 'O' and resid 48 through 61 Processing helix chain 'O' and resid 64 through 78 removed outlier: 3.583A pdb=" N TYR O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 88 Processing helix chain 'O' and resid 89 through 91 No H-bonds generated for 'chain 'O' and resid 89 through 91' Processing helix chain 'P' and resid 2 through 18 removed outlier: 4.962A pdb=" N GLU P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA P 15 " --> pdb=" O GLN P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 32 removed outlier: 4.170A pdb=" N ILE P 25 " --> pdb=" O LYS P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 45 Processing helix chain 'P' and resid 48 through 62 removed outlier: 3.976A pdb=" N LYS P 62 " --> pdb=" O LYS P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 78 removed outlier: 3.585A pdb=" N TYR P 68 " --> pdb=" O ASP P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 88 Processing helix chain 'P' and resid 89 through 91 No H-bonds generated for 'chain 'P' and resid 89 through 91' Processing helix chain 'Q' and resid 2 through 18 removed outlier: 4.962A pdb=" N GLU Q 14 " --> pdb=" O LEU Q 10 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA Q 15 " --> pdb=" O GLN Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 33 removed outlier: 4.171A pdb=" N ILE Q 25 " --> pdb=" O LYS Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 45 Processing helix chain 'Q' and resid 48 through 62 removed outlier: 3.977A pdb=" N LYS Q 62 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 78 removed outlier: 3.584A pdb=" N TYR Q 68 " --> pdb=" O ASP Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 88 Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'R' and resid 2 through 18 removed outlier: 4.962A pdb=" N GLU R 14 " --> pdb=" O LEU R 10 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA R 15 " --> pdb=" O GLN R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 32 removed outlier: 4.105A pdb=" N ILE R 25 " --> pdb=" O LYS R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 45 Processing helix chain 'R' and resid 48 through 62 removed outlier: 3.977A pdb=" N LYS R 62 " --> pdb=" O LYS R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 78 removed outlier: 3.582A pdb=" N TYR R 68 " --> pdb=" O ASP R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 88 Processing helix chain 'R' and resid 89 through 91 No H-bonds generated for 'chain 'R' and resid 89 through 91' Processing helix chain 'S' and resid 2 through 12 Processing helix chain 'S' and resid 12 through 20 Processing helix chain 'S' and resid 25 through 32 Processing helix chain 'S' and resid 36 through 45 Processing helix chain 'S' and resid 50 through 63 removed outlier: 4.019A pdb=" N GLU S 63 " --> pdb=" O ILE S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 79 Processing helix chain 'S' and resid 82 through 95 Processing helix chain 'T' and resid 2 through 12 Processing helix chain 'T' and resid 12 through 20 Processing helix chain 'T' and resid 25 through 32 Processing helix chain 'T' and resid 36 through 45 Processing helix chain 'T' and resid 50 through 63 removed outlier: 4.020A pdb=" N GLU T 63 " --> pdb=" O ILE T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 79 Processing helix chain 'T' and resid 82 through 95 Processing helix chain 'U' and resid 2 through 12 removed outlier: 3.842A pdb=" N ARG U 10 " --> pdb=" O ARG U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 12 through 18 Processing helix chain 'U' and resid 25 through 32 Processing helix chain 'U' and resid 36 through 45 Processing helix chain 'U' and resid 50 through 63 removed outlier: 4.019A pdb=" N GLU U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 Processing helix chain 'U' and resid 82 through 95 Processing helix chain 'V' and resid 2 through 12 Processing helix chain 'V' and resid 12 through 20 Processing helix chain 'V' and resid 25 through 32 Processing helix chain 'V' and resid 36 through 45 Processing helix chain 'V' and resid 50 through 63 removed outlier: 4.020A pdb=" N GLU V 63 " --> pdb=" O ILE V 59 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 79 Processing helix chain 'V' and resid 82 through 95 Processing helix chain 'W' and resid 2 through 12 Processing helix chain 'W' and resid 12 through 20 Processing helix chain 'W' and resid 21 through 24 Processing helix chain 'W' and resid 25 through 32 Processing helix chain 'W' and resid 36 through 45 Processing helix chain 'W' and resid 48 through 61 Processing helix chain 'W' and resid 64 through 78 Processing helix chain 'W' and resid 80 through 89 removed outlier: 4.651A pdb=" N ASP W 89 " --> pdb=" O ALA W 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 20 removed outlier: 5.133A pdb=" N GLU X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA X 15 " --> pdb=" O GLN X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 33 Processing helix chain 'X' and resid 36 through 46 removed outlier: 3.921A pdb=" N GLU X 46 " --> pdb=" O LYS X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 62 removed outlier: 3.633A pdb=" N LYS X 62 " --> pdb=" O LYS X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 78 Processing helix chain 'X' and resid 80 through 89 removed outlier: 4.115A pdb=" N ASP X 89 " --> pdb=" O ALA X 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 12 Processing helix chain 'Y' and resid 12 through 20 Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 45 Processing helix chain 'Y' and resid 50 through 63 removed outlier: 3.719A pdb=" N GLU Y 63 " --> pdb=" O ILE Y 59 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 80 Processing helix chain 'Y' and resid 82 through 94 removed outlier: 3.755A pdb=" N ASN Y 92 " --> pdb=" O PHE Y 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 182 through 188 removed outlier: 3.521A 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: 7.319A pdb=" N THR A 264 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 152 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing sheet with id=AA2, 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: 3.835A pdb=" N TYR A 435 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, 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=AA4, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.485A pdb=" N VAL A 641 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 3.515A 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: 3.653A pdb=" N GLU A 648 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing sheet with id=AA5, 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: 5.148A 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=AA6, 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: 4.670A 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: 5.404A 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=AA7, first strand: chain 'A' and resid 746 through 749 removed outlier: 3.847A 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: 5.164A pdb=" N GLU A 777 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 804 through 806 removed outlier: 5.751A pdb=" N LEU A 823 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 858 removed outlier: 6.865A pdb=" N LEU A 866 " --> pdb=" O VAL A 875 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 928 through 930 removed outlier: 3.790A pdb=" N MET A 936 " --> pdb=" O VAL A 929 " (cutoff:3.500A) removed outlier: 4.227A 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=AB2, first strand: chain 'A' and resid 946 through 947 removed outlier: 3.931A pdb=" N LEU A 946 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 967 through 969 Processing sheet with id=AB4, first strand: chain 'A' and resid 985 through 986 Processing sheet with id=AB5, first strand: chain 'A' and resid 1009 through 1011 Processing sheet with id=AB6, first strand: chain 'A' and resid 1049 through 1052 Processing sheet with id=AB7, 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=AB8, first strand: chain 'A' and resid 1132 through 1135 Processing sheet with id=AB9, first strand: chain 'A' and resid 1182 through 1185 removed outlier: 4.000A 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=AC1, first strand: chain 'A' and resid 1233 through 1235 Processing sheet with id=AC2, 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: 6.351A pdb=" N LEU C 240 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR C 263 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.320A 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=AC3, first strand: chain 'C' and resid 395 through 396 removed outlier: 3.771A 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=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU C 609 " --> pdb=" O LEU C 908 " (cutoff:3.500A) Processing sheet with id=AC5, 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: 3.958A pdb=" N LYS C 643 " --> pdb=" O GLU C 648 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 648 " --> pdb=" O LYS C 643 " (cutoff:3.500A) Processing sheet with id=AC6, 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: 5.145A 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=AC7, 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: 4.582A 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: 4.672A pdb=" N PHE C 707 " --> pdb=" O LEU C 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 715 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 5.406A 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=AC8, first strand: chain 'C' and resid 746 through 749 removed outlier: 3.845A pdb=" N HIS C 748 " --> pdb=" O CYS C 761 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP C 771 " --> pdb=" O GLU C 777 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU C 777 " --> pdb=" O ASP C 771 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 804 through 806 removed outlier: 5.752A pdb=" N LEU C 823 " --> pdb=" O LEU C 832 " (cutoff:3.500A) Processing sheet with id=AD1, 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=AD2, first strand: chain 'C' and resid 928 through 930 removed outlier: 3.792A 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=AD3, first strand: chain 'C' and resid 946 through 947 removed outlier: 3.933A pdb=" N LEU C 946 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 967 through 969 Processing sheet with id=AD5, first strand: chain 'C' and resid 985 through 986 Processing sheet with id=AD6, first strand: chain 'C' and resid 1009 through 1011 Processing sheet with id=AD7, first strand: chain 'C' and resid 1049 through 1052 Processing sheet with id=AD8, first strand: chain 'C' and resid 1090 through 1093 removed outlier: 3.516A pdb=" N SER C1090 " --> pdb=" O SER C1104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1132 through 1135 Processing sheet with id=AE1, 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: 3.572A pdb=" N ALA C1195 " --> pdb=" O ASP C1182 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1233 through 1235 Processing sheet with id=AE3, 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: 6.352A 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: 6.321A pdb=" N LEU E 242 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL E 150 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 7.317A 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=AE4, 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=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 609 through 611 removed outlier: 3.903A pdb=" N LEU E 609 " --> pdb=" O LEU E 908 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 621 through 623 removed outlier: 6.486A pdb=" N VAL E 641 " --> pdb=" O LEU E 650 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 650 " --> pdb=" O VAL E 641 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS E 643 " --> pdb=" O GLU E 648 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU E 648 " --> pdb=" O LYS E 643 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 660 through 665 removed outlier: 3.785A 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: 6.073A pdb=" N LEU E 691 " --> pdb=" O ASN E 685 " (cutoff:3.500A) Processing sheet with id=AE8, 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: 4.672A pdb=" N PHE E 707 " --> pdb=" O LEU E 715 " (cutoff:3.500A) removed outlier: 6.644A 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: 5.977A pdb=" N CYS E 735 " --> pdb=" O ASP E 729 " (cutoff:3.500A) Processing sheet with id=AE9, 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=AF1, first strand: chain 'E' and resid 804 through 806 removed outlier: 5.753A pdb=" N LEU E 823 " --> pdb=" O LEU E 832 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 854 through 858 removed outlier: 6.864A pdb=" N LEU E 866 " --> pdb=" O VAL E 875 " (cutoff:3.500A) Processing sheet with id=AF3, 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: 4.229A 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=AF4, 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=AF5, first strand: chain 'E' and resid 967 through 969 Processing sheet with id=AF6, first strand: chain 'E' and resid 985 through 986 Processing sheet with id=AF7, first strand: chain 'E' and resid 1009 through 1011 Processing sheet with id=AF8, first strand: chain 'E' and resid 1049 through 1052 Processing sheet with id=AF9, first strand: chain 'E' and resid 1090 through 1093 removed outlier: 3.517A pdb=" N SER E1090 " --> pdb=" O SER E1104 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 1132 through 1135 Processing sheet with id=AG2, first strand: chain 'E' and resid 1182 through 1185 removed outlier: 4.002A 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=AG3, first strand: chain 'E' and resid 1233 through 1235 Processing sheet with id=AG4, 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: 6.352A 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: 5.790A 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: 6.099A pdb=" N ILE G 152 " --> pdb=" O THR G 264 " (cutoff:3.500A) Processing sheet with id=AG5, 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=AG5 Processing sheet with id=AG6, first strand: chain 'G' and resid 609 through 611 removed outlier: 3.901A pdb=" N LEU G 609 " --> pdb=" O LEU G 908 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 621 through 623 removed outlier: 6.484A pdb=" N VAL G 641 " --> pdb=" O LEU G 650 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 650 " --> pdb=" O VAL G 641 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS G 643 " --> pdb=" O GLU G 648 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU G 648 " --> pdb=" O LYS G 643 " (cutoff:3.500A) Processing sheet with id=AG8, 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: 6.073A pdb=" N LEU G 691 " --> pdb=" O ASN G 685 " (cutoff:3.500A) Processing sheet with id=AG9, 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: 4.582A pdb=" N CYS G 705 " --> pdb=" O ALA G 717 " (cutoff:3.500A) removed outlier: 7.264A 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: 6.644A 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=AH1, 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: 5.165A pdb=" N GLU G 777 " --> pdb=" O ASP G 771 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 804 through 806 removed outlier: 5.752A pdb=" N LEU G 823 " --> pdb=" O LEU G 832 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 854 through 858 removed outlier: 6.864A pdb=" N LEU G 866 " --> pdb=" O VAL G 875 " (cutoff:3.500A) Processing sheet with id=AH4, 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: 4.229A pdb=" N VAL G 937 " --> pdb=" O ILE G 949 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE G 949 " --> pdb=" O VAL G 937 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 946 through 947 removed outlier: 3.931A pdb=" N LEU G 946 " --> pdb=" O LEU G 959 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 967 through 969 Processing sheet with id=AH7, first strand: chain 'G' and resid 985 through 986 Processing sheet with id=AH8, first strand: chain 'G' and resid 1009 through 1011 Processing sheet with id=AH9, first strand: chain 'G' and resid 1049 through 1052 Processing sheet with id=AI1, first strand: chain 'G' and resid 1090 through 1093 removed outlier: 3.517A pdb=" N SER G1090 " --> pdb=" O SER G1104 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 1132 through 1135 Processing sheet with id=AI3, first strand: chain 'G' and resid 1182 through 1185 removed outlier: 4.002A pdb=" N ASP G1182 " --> pdb=" O ALA G1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G1195 " --> pdb=" O ASP G1182 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 1233 through 1235 Processing sheet with id=AI5, first strand: chain 'I' and resid 182 through 188 removed outlier: 3.521A 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: 7.748A 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: 5.790A pdb=" N VAL I 150 " --> pdb=" O LEU I 262 " (cutoff:3.500A) removed outlier: 7.320A 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=AI6, 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: 3.838A pdb=" N TYR I 435 " --> pdb=" O VAL I 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, 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=AI8, 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: 3.957A 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=AI9, 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=AJ1, 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: 4.672A pdb=" N PHE I 707 " --> pdb=" O LEU I 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU I 715 " --> pdb=" O PHE I 707 " (cutoff:3.500A) removed outlier: 5.406A 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=AJ2, first strand: chain 'I' and resid 746 through 749 removed outlier: 3.847A 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: 5.164A pdb=" N GLU I 777 " --> pdb=" O ASP I 771 " (cutoff:3.500A) Processing sheet with id=AJ3, 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=AJ4, first strand: chain 'I' and resid 854 through 858 removed outlier: 6.866A pdb=" N LEU I 866 " --> pdb=" O VAL I 875 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'I' and resid 928 through 930 removed outlier: 3.790A pdb=" N MET I 936 " --> pdb=" O VAL I 929 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL I 937 " --> pdb=" O ILE I 949 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE I 949 " --> pdb=" O VAL I 937 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'I' and resid 946 through 947 removed outlier: 3.933A pdb=" N LEU I 946 " --> pdb=" O LEU I 959 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'I' and resid 967 through 969 Processing sheet with id=AJ8, first strand: chain 'I' and resid 985 through 986 Processing sheet with id=AJ9, first strand: chain 'I' and resid 1009 through 1011 Processing sheet with id=AK1, first strand: chain 'I' and resid 1049 through 1052 Processing sheet with id=AK2, first strand: chain 'I' and resid 1090 through 1093 removed outlier: 3.515A pdb=" N SER I1090 " --> pdb=" O SER I1104 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'I' and resid 1132 through 1135 Processing sheet with id=AK4, 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: 3.572A pdb=" N ALA I1195 " --> pdb=" O ASP I1182 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'I' and resid 1233 through 1235 Processing sheet with id=AK6, first strand: chain 'K' and resid 182 through 188 removed outlier: 3.523A pdb=" N VAL K 187 " --> pdb=" O ASP K 243 " (cutoff:3.500A) removed outlier: 6.352A 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: 6.321A pdb=" N LEU K 242 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 5.791A 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=AK7, 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: 3.839A pdb=" N TYR K 435 " --> pdb=" O VAL K 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK7 Processing sheet with id=AK8, 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=AK9, 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: 3.517A 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=AL1, first strand: chain 'K' and resid 660 through 665 removed outlier: 3.787A 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=AL2, 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: 4.582A 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: 4.672A 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=AL3, 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: 5.025A pdb=" N ASP K 771 " --> pdb=" O GLU K 777 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU K 777 " --> pdb=" O ASP K 771 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'K' and resid 804 through 806 removed outlier: 5.749A pdb=" N LEU K 823 " --> pdb=" O LEU K 832 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'K' and resid 854 through 858 removed outlier: 6.863A pdb=" N LEU K 866 " --> pdb=" O VAL K 875 " (cutoff:3.500A) Processing sheet with id=AL6, 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: 4.227A pdb=" N VAL K 937 " --> pdb=" O ILE K 949 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE K 949 " --> pdb=" O VAL K 937 " (cutoff:3.500A) Processing sheet with id=AL7, 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=AL8, first strand: chain 'K' and resid 967 through 969 Processing sheet with id=AL9, first strand: chain 'K' and resid 985 through 986 Processing sheet with id=AM1, first strand: chain 'K' and resid 1009 through 1011 Processing sheet with id=AM2, first strand: chain 'K' and resid 1049 through 1052 Processing sheet with id=AM3, first strand: chain 'K' and resid 1090 through 1093 removed outlier: 3.517A pdb=" N SER K1090 " --> pdb=" O SER K1104 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'K' and resid 1132 through 1135 Processing sheet with id=AM5, first strand: chain 'K' and resid 1182 through 1185 removed outlier: 4.002A pdb=" N ASP K1182 " --> pdb=" O ALA K1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA K1195 " --> pdb=" O ASP K1182 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'K' and resid 1233 through 1235 Processing sheet with id=AM7, 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: 7.318A 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=AM8, first strand: chain 'M' and resid 395 through 396 removed outlier: 3.772A 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=AM8 Processing sheet with id=AM9, 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=AN1, first strand: chain 'M' and resid 621 through 623 removed outlier: 6.487A 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=AN2, 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: 5.148A 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=AN3, 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: 7.261A pdb=" N ALA M 717 " --> pdb=" O CYS M 705 " (cutoff:3.500A) removed outlier: 4.672A 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=AN4, first strand: chain 'M' and resid 746 through 749 removed outlier: 3.844A pdb=" N HIS M 748 " --> pdb=" O CYS M 761 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASP M 771 " --> pdb=" O GLU M 777 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU M 777 " --> pdb=" O ASP M 771 " (cutoff:3.500A) Processing sheet with id=AN5, 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=AN6, 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=AN7, first strand: chain 'M' and resid 928 through 930 removed outlier: 3.790A 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: 4.522A pdb=" N ILE M 949 " --> pdb=" O VAL M 937 " (cutoff:3.500A) Processing sheet with id=AN8, 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=AN9, first strand: chain 'M' and resid 967 through 969 Processing sheet with id=AO1, first strand: chain 'M' and resid 985 through 986 Processing sheet with id=AO2, first strand: chain 'M' and resid 1009 through 1011 Processing sheet with id=AO3, first strand: chain 'M' and resid 1049 through 1052 Processing sheet with id=AO4, 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=AO5, first strand: chain 'M' and resid 1132 through 1135 Processing sheet with id=AO6, 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=AO7, first strand: chain 'M' and resid 1233 through 1235 2860 hydrogen bonds defined for protein. 8094 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: 48.15 Time building geometry restraints manager: 18.25 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: 26796 1.37 - 1.55: 52476 1.55 - 1.73: 235 1.73 - 1.92: 728 1.92 - 2.10: 21 Bond restraints: 80256 Sorted by residual: bond pdb=" C TRP K1179 " pdb=" N VAL K1180 " ideal model delta sigma weight residual 1.332 1.190 0.142 1.36e-02 5.41e+03 1.09e+02 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 6.94e+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 6.87e+01 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 ... (remaining 80251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 106473 3.90 - 7.79: 1886 7.79 - 11.69: 126 11.69 - 15.59: 37 15.59 - 19.48: 21 Bond angle restraints: 108543 Sorted by residual: angle pdb=" PB DTP E1301 " pdb=" O3B DTP E1301 " pdb=" PG DTP E1301 " ideal model delta sigma weight residual 139.87 120.39 19.48 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PB DTP A1301 " pdb=" O3B DTP A1301 " pdb=" PG DTP A1301 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB DTP I1301 " pdb=" O3B DTP I1301 " pdb=" PG DTP I1301 " ideal model delta sigma weight residual 139.87 120.49 19.38 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 139.87 120.52 19.35 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB DTP M1301 " pdb=" O3B DTP M1301 " pdb=" PG DTP M1301 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 ... (remaining 108538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.25: 43815 26.25 - 52.49: 3430 52.49 - 78.74: 942 78.74 - 104.98: 124 104.98 - 131.23: 7 Dihedral angle restraints: 48318 sinusoidal: 19896 harmonic: 28422 Sorted by residual: dihedral pdb=" CB CYS M 761 " pdb=" SG CYS M 761 " pdb=" SG CYS M 804 " pdb=" CB CYS M 804 " ideal model delta sinusoidal sigma weight residual 93.00 174.18 -81.18 1 1.00e+01 1.00e-02 8.13e+01 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 93.00 174.14 -81.14 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS E 761 " pdb=" SG CYS E 761 " pdb=" SG CYS E 804 " pdb=" CB CYS E 804 " ideal model delta sinusoidal sigma weight residual 93.00 174.13 -81.13 1 1.00e+01 1.00e-02 8.12e+01 ... (remaining 48315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 9998 0.096 - 0.192: 1594 0.192 - 0.288: 338 0.288 - 0.383: 49 0.383 - 0.479: 14 Chirality restraints: 11993 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 5.74e+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 G 153 " pdb=" N HIS G 153 " pdb=" C HIS G 153 " pdb=" CB HIS G 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 11990 not shown) Planarity restraints: 13790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG T 52 " -0.677 9.50e-02 1.11e+02 3.04e-01 5.62e+01 pdb=" NE ARG T 52 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG T 52 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG T 52 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG T 52 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE M 560 " -0.102 5.00e-02 4.00e+02 1.60e-01 4.09e+01 pdb=" N PRO M 561 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO M 561 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO M 561 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 560 " 0.102 5.00e-02 4.00e+02 1.60e-01 4.08e+01 pdb=" N PRO C 561 " -0.276 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.079 5.00e-02 4.00e+02 ... (remaining 13787 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 245 2.17 - 2.86: 31395 2.86 - 3.54: 113575 3.54 - 4.22: 188169 4.22 - 4.90: 312439 Nonbonded interactions: 645823 Sorted by model distance: nonbonded pdb=" OG SER A 141 " pdb=" CD1 LEU W 10 " model vdw 1.493 3.460 nonbonded pdb=" O TRP E 483 " pdb=" CB LEU E 487 " model vdw 1.816 2.752 nonbonded pdb=" O TRP C 483 " pdb=" CB LEU C 487 " model vdw 1.816 2.752 nonbonded pdb=" O TRP G 483 " pdb=" CB LEU G 487 " model vdw 1.816 2.752 nonbonded pdb=" O TRP A 483 " pdb=" CB LEU A 487 " model vdw 1.816 2.752 ... (remaining 645818 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' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = (chain 'W' and resid 1 through 91) selection = (chain 'X' and resid 1 through 91) } ncs_group { reference = (chain 'S' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = (chain 'T' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = (chain 'U' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = (chain 'V' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = chain 'Y' } 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: 15.020 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: 0.080 Extract box with map and model: 2.470 Check model and map are aligned: 0.450 Set scattering table: 0.580 Process input model: 156.670 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.680 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: 0.020 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1510 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 0.217 80256 Z= 0.526 Angle : 1.345 19.482 108543 Z= 0.941 Chirality : 0.076 0.479 11993 Planarity : 0.010 0.304 13790 Dihedral : 19.501 131.230 29773 Min Nonbonded Distance : 1.493 Molprobity Statistics. All-atom Clashscore : 69.05 Ramachandran Plot: Outliers : 3.39 % Allowed : 7.12 % Favored : 89.49 % Rotamer: Outliers : 16.86 % Allowed : 10.68 % Favored : 72.46 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.09), residues: 9716 helix: 0.00 (0.09), residues: 3194 sheet: -1.64 (0.16), residues: 1148 loop : -0.43 (0.09), residues: 5374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 249 HIS 0.014 0.001 HIS L 33 PHE 0.055 0.002 PHE R 34 TYR 0.044 0.004 TYR P 72 ARG 0.024 0.001 ARG S 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2773 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1467 poor density : 1306 time to evaluate : 6.803 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 153 HIS cc_start: 0.4058 (p-80) cc_final: 0.3718 (p90) REVERT: A 261 LEU cc_start: 0.2615 (OUTLIER) cc_final: 0.1839 (tt) REVERT: A 273 VAL cc_start: 0.5594 (OUTLIER) cc_final: 0.5344 (p) REVERT: A 352 ARG cc_start: 0.5408 (OUTLIER) cc_final: 0.4884 (mmp-170) REVERT: A 568 LEU cc_start: -0.3074 (OUTLIER) cc_final: -0.4189 (tt) REVERT: A 588 VAL cc_start: 0.3416 (OUTLIER) cc_final: 0.3102 (t) REVERT: A 600 LYS cc_start: 0.0813 (OUTLIER) cc_final: -0.1111 (ptpt) REVERT: A 643 LYS cc_start: 0.0102 (OUTLIER) cc_final: -0.0329 (tmtt) REVERT: A 739 MET cc_start: -0.3745 (mtm) cc_final: -0.3970 (mtt) REVERT: A 885 VAL cc_start: -0.0107 (OUTLIER) cc_final: -0.0674 (p) REVERT: A 914 VAL cc_start: 0.0004 (OUTLIER) cc_final: -0.0427 (m) REVERT: A 925 GLU cc_start: -0.0820 (OUTLIER) cc_final: -0.2253 (tt0) REVERT: A 936 MET cc_start: 0.1877 (mtp) cc_final: 0.1179 (ptm) REVERT: A 1191 MET cc_start: -0.2525 (mtm) cc_final: -0.3831 (tmm) REVERT: A 1235 VAL cc_start: 0.3773 (OUTLIER) cc_final: 0.3194 (p) REVERT: A 1243 ILE cc_start: 0.5813 (mt) cc_final: 0.5382 (mt) REVERT: C 174 LEU cc_start: 0.2170 (OUTLIER) cc_final: 0.0788 (tp) REVERT: C 252 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7012 (mmmm) REVERT: C 273 VAL cc_start: 0.0822 (OUTLIER) cc_final: 0.0591 (p) REVERT: C 442 VAL cc_start: 0.3946 (OUTLIER) cc_final: 0.3658 (p) REVERT: C 473 LEU cc_start: -0.2829 (OUTLIER) cc_final: -0.3616 (mt) REVERT: C 550 LEU cc_start: -0.2377 (OUTLIER) cc_final: -0.2766 (pp) REVERT: C 588 VAL cc_start: -0.3523 (OUTLIER) cc_final: -0.3802 (t) REVERT: C 651 LEU cc_start: -0.2294 (OUTLIER) cc_final: -0.3722 (mt) REVERT: C 879 ARG cc_start: 0.0027 (OUTLIER) cc_final: -0.2100 (mmm160) REVERT: C 1168 LEU cc_start: 0.1759 (OUTLIER) cc_final: 0.1073 (mt) REVERT: C 1181 THR cc_start: 0.1591 (OUTLIER) cc_final: 0.1178 (p) REVERT: E 149 TRP cc_start: 0.1019 (m-10) cc_final: 0.0432 (m-10) REVERT: E 213 SER cc_start: 0.6620 (OUTLIER) cc_final: 0.6332 (t) REVERT: E 261 LEU cc_start: -0.2869 (OUTLIER) cc_final: -0.3875 (tt) REVERT: E 268 SER cc_start: 0.6077 (OUTLIER) cc_final: 0.5815 (m) REVERT: E 473 LEU cc_start: -0.3704 (OUTLIER) cc_final: -0.5830 (mp) REVERT: E 588 VAL cc_start: -0.1763 (OUTLIER) cc_final: -0.2456 (p) REVERT: E 646 THR cc_start: -0.3352 (OUTLIER) cc_final: -0.3684 (t) REVERT: E 879 ARG cc_start: 0.1266 (OUTLIER) cc_final: 0.0326 (mmm160) REVERT: E 999 ARG cc_start: 0.2514 (OUTLIER) cc_final: 0.0546 (tpt90) REVERT: E 1183 LEU cc_start: -0.1038 (OUTLIER) cc_final: -0.1542 (mt) REVERT: F 50 ASP cc_start: 0.3522 (m-30) cc_final: 0.3211 (m-30) REVERT: G 202 LEU cc_start: 0.6996 (tp) cc_final: 0.6451 (tp) REVERT: G 325 SER cc_start: -0.0442 (OUTLIER) cc_final: -0.0842 (p) REVERT: G 473 LEU cc_start: -0.3589 (OUTLIER) cc_final: -0.5135 (mp) REVERT: G 504 MET cc_start: -0.2539 (mtp) cc_final: -0.2801 (mtm) REVERT: G 530 ARG cc_start: 0.0005 (OUTLIER) cc_final: -0.0308 (ttp-170) REVERT: G 531 HIS cc_start: -0.3750 (OUTLIER) cc_final: -0.4190 (t-170) REVERT: G 603 ILE cc_start: 0.0213 (OUTLIER) cc_final: -0.0213 (pt) REVERT: G 651 LEU cc_start: -0.1891 (OUTLIER) cc_final: -0.2724 (mt) REVERT: G 1171 GLU cc_start: 0.1450 (OUTLIER) cc_final: 0.0727 (pt0) REVERT: G 1183 LEU cc_start: -0.1660 (OUTLIER) cc_final: -0.2194 (mp) REVERT: I 127 VAL cc_start: 0.5298 (OUTLIER) cc_final: 0.5003 (p) REVERT: I 160 LYS cc_start: 0.0918 (OUTLIER) cc_final: 0.0541 (mttt) REVERT: I 230 LEU cc_start: 0.7255 (mt) cc_final: 0.6808 (mp) REVERT: I 450 CYS cc_start: 0.2802 (OUTLIER) cc_final: 0.2403 (t) REVERT: I 522 LEU cc_start: -0.2893 (OUTLIER) cc_final: -0.3151 (mp) REVERT: I 530 ARG cc_start: 0.1016 (OUTLIER) cc_final: -0.0968 (ttm170) REVERT: I 531 HIS cc_start: -0.3847 (OUTLIER) cc_final: -0.6213 (t70) REVERT: I 553 HIS cc_start: 0.0672 (OUTLIER) cc_final: -0.0600 (t70) REVERT: I 568 LEU cc_start: -0.1417 (OUTLIER) cc_final: -0.2747 (tp) REVERT: I 651 LEU cc_start: -0.1725 (OUTLIER) cc_final: -0.2108 (mt) REVERT: I 687 MET cc_start: -0.1868 (ttp) cc_final: -0.3677 (ptp) REVERT: I 802 LYS cc_start: -0.0490 (mmtt) cc_final: -0.2092 (mptt) REVERT: I 925 GLU cc_start: -0.2133 (OUTLIER) cc_final: -0.2763 (pt0) REVERT: I 936 MET cc_start: -0.1284 (mtp) cc_final: -0.2533 (ttt) REVERT: I 1221 LYS cc_start: -0.0754 (OUTLIER) cc_final: -0.2921 (tptt) REVERT: I 1235 VAL cc_start: 0.5467 (OUTLIER) cc_final: 0.4158 (p) REVERT: I 1247 LEU cc_start: 0.1586 (OUTLIER) cc_final: 0.1100 (mp) REVERT: I 1248 GLU cc_start: 0.3056 (OUTLIER) cc_final: 0.2755 (pt0) REVERT: K 160 LYS cc_start: 0.2950 (OUTLIER) cc_final: 0.2693 (tttt) REVERT: K 202 LEU cc_start: 0.7487 (tp) cc_final: 0.7176 (tp) REVERT: K 239 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6440 (tp) REVERT: K 290 LYS cc_start: 0.1472 (OUTLIER) cc_final: 0.0640 (mtmt) REVERT: K 374 MET cc_start: -0.0316 (OUTLIER) cc_final: -0.0651 (ptt) REVERT: K 397 THR cc_start: -0.3593 (OUTLIER) cc_final: -0.3850 (p) REVERT: K 449 ASN cc_start: -0.1269 (OUTLIER) cc_final: -0.2718 (t0) REVERT: K 473 LEU cc_start: -0.3110 (OUTLIER) cc_final: -0.4109 (mp) REVERT: K 522 LEU cc_start: 0.4326 (OUTLIER) cc_final: 0.2365 (mp) REVERT: K 533 LEU cc_start: -0.5701 (OUTLIER) cc_final: -0.5963 (mp) REVERT: K 572 GLU cc_start: -0.1864 (OUTLIER) cc_final: -0.3046 (tm-30) REVERT: K 633 CYS cc_start: 0.1406 (OUTLIER) cc_final: 0.0104 (m) REVERT: K 643 LYS cc_start: -0.1152 (OUTLIER) cc_final: -0.2411 (tttp) REVERT: K 739 MET cc_start: -0.2290 (mtm) cc_final: -0.2742 (mtm) REVERT: K 925 GLU cc_start: -0.0701 (OUTLIER) cc_final: -0.3669 (tm-30) REVERT: K 926 VAL cc_start: 0.4053 (m) cc_final: 0.3086 (m) REVERT: K 936 MET cc_start: -0.2290 (mtp) cc_final: -0.3096 (ttt) REVERT: K 948 LEU cc_start: -0.2313 (OUTLIER) cc_final: -0.2762 (mt) REVERT: K 1078 GLU cc_start: 0.4150 (OUTLIER) cc_final: 0.2757 (pt0) REVERT: K 1171 GLU cc_start: 0.1724 (OUTLIER) cc_final: 0.0879 (mm-30) REVERT: K 1192 LEU cc_start: 0.2942 (OUTLIER) cc_final: 0.2412 (tt) REVERT: M 206 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6089 (tp) REVERT: M 283 GLU cc_start: 0.3702 (OUTLIER) cc_final: 0.3145 (mp0) REVERT: M 405 ASP cc_start: 0.4106 (OUTLIER) cc_final: 0.3628 (t0) REVERT: M 449 ASN cc_start: 0.2496 (OUTLIER) cc_final: 0.1745 (t0) REVERT: M 600 LYS cc_start: 0.3555 (OUTLIER) cc_final: 0.1672 (pttm) REVERT: M 619 TYR cc_start: -0.1169 (OUTLIER) cc_final: -0.1765 (m-80) REVERT: M 633 CYS cc_start: 0.1318 (OUTLIER) cc_final: 0.0715 (m) REVERT: M 643 LYS cc_start: -0.0459 (OUTLIER) cc_final: -0.1465 (tttt) REVERT: M 648 GLU cc_start: -0.2376 (OUTLIER) cc_final: -0.3540 (pm20) REVERT: M 659 GLU cc_start: -0.0958 (OUTLIER) cc_final: -0.2248 (mt-10) REVERT: M 739 MET cc_start: -0.2175 (mtm) cc_final: -0.2680 (mtm) REVERT: M 948 LEU cc_start: -0.3994 (OUTLIER) cc_final: -0.4467 (mp) REVERT: M 1165 CYS cc_start: -0.4199 (OUTLIER) cc_final: -0.5450 (t) REVERT: M 1215 THR cc_start: 0.3233 (OUTLIER) cc_final: 0.2919 (t) REVERT: M 1248 GLU cc_start: 0.4223 (OUTLIER) cc_final: 0.3342 (pm20) REVERT: Q 42 LYS cc_start: 0.6956 (mttp) cc_final: 0.6671 (tptp) REVERT: S 36 ARG cc_start: -0.1928 (OUTLIER) cc_final: -0.2285 (mmt-90) REVERT: T 1 MET cc_start: -0.3534 (ttm) cc_final: -0.5268 (tpp) REVERT: T 8 LEU cc_start: -0.0716 (OUTLIER) cc_final: -0.1151 (tp) REVERT: U 1 MET cc_start: -0.1396 (ttm) cc_final: -0.1627 (ttm) REVERT: W 26 MET cc_start: -0.1074 (mtm) cc_final: -0.1276 (mtt) outliers start: 1467 outliers final: 255 residues processed: 2444 average time/residue: 0.7917 time to fit residues: 3210.0698 Evaluate side-chains 1192 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 851 time to evaluate : 6.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 816 optimal weight: 5.9990 chunk 732 optimal weight: 20.0000 chunk 406 optimal weight: 8.9990 chunk 250 optimal weight: 1.9990 chunk 494 optimal weight: 7.9990 chunk 391 optimal weight: 1.9990 chunk 757 optimal weight: 0.9980 chunk 293 optimal weight: 0.3980 chunk 460 optimal weight: 9.9990 chunk 564 optimal weight: 5.9990 chunk 878 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 347 ASN A 420 ASN A 454 GLN A 477 GLN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN A 703 ASN A 709 ASN A 840 HIS ** A1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 HIS ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN B 52 ASN C 235 HIS C 257 GLN C 420 ASN C 463 GLN ** C 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 HIS C 545 GLN ** C 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN C 640 GLN C 709 ASN C 904 GLN ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN D 52 ASN E 137 GLN E 257 GLN E 429 ASN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN ** E 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 545 GLN E 562 ASN E 583 GLN E 599 ASN E 706 HIS E 709 ASN E 840 HIS E 904 GLN ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN G 183 HIS G 235 HIS ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 ASN ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 553 HIS G 562 ASN ** G 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 GLN ** G 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 904 GLN ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 GLN I 201 ASN I 235 HIS I 347 ASN ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 438 HIS I 449 ASN I 463 GLN I 477 GLN ** I 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 553 HIS I 565 GLN I 583 GLN I 703 ASN I 709 ASN I 737 ASN I 904 GLN ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1219 ASN ** I1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS K 153 HIS ** K 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 201 ASN ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 311 HIS K 347 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 GLN K 477 GLN ** K 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 545 GLN K 562 ASN K 583 GLN K 703 ASN K 709 ASN K 840 HIS K 904 GLN K1001 GLN ** K1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN M 183 HIS ** M 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 347 ASN ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 454 GLN M 463 GLN M 477 GLN M 553 HIS ** M 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 562 ASN M 578 GLN M 583 GLN M 703 ASN M 709 ASN M 904 GLN ** M 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN O 28 HIS O 45 ASN O 65 ASN P 28 HIS P 45 ASN P 51 GLN P 65 ASN Q 45 ASN Q 51 GLN Q 65 ASN Q 88 HIS R 11 GLN R 28 HIS R 45 ASN R 50 GLN R 65 ASN S 24 GLN S 38 HIS S 44 GLN S 82 GLN ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 44 GLN T 82 GLN U 21 GLN U 82 GLN V 44 GLN V 82 GLN W 7 ASN W 11 GLN W 12 HIS W 45 ASN W 51 GLN X 7 ASN X 11 GLN X 51 GLN Y 44 GLN Total number of N/Q/H flips: 125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1910 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 80256 Z= 0.288 Angle : 0.875 15.923 108543 Z= 0.454 Chirality : 0.049 0.360 11993 Planarity : 0.006 0.086 13790 Dihedral : 8.661 126.862 10669 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.80 % Allowed : 6.47 % Favored : 92.72 % Rotamer: Outliers : 0.15 % Allowed : 3.87 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.29 (0.08), residues: 9716 helix: 0.00 (0.08), residues: 3332 sheet: -1.74 (0.12), residues: 1547 loop : -1.08 (0.09), residues: 4837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP I 404 HIS 0.018 0.002 HIS T 38 PHE 0.036 0.002 PHE G 298 TYR 0.033 0.003 TYR I 278 ARG 0.019 0.001 ARG D 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 994 time to evaluate : 7.001 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLN cc_start: 0.6245 (pp30) cc_final: 0.5965 (pp30) REVERT: A 160 LYS cc_start: 0.4675 (mtmt) cc_final: 0.3452 (ttmm) REVERT: A 255 ASP cc_start: 0.6277 (t0) cc_final: 0.6033 (t0) REVERT: A 353 ILE cc_start: 0.5741 (mt) cc_final: 0.5230 (mt) REVERT: A 477 GLN cc_start: 0.4191 (OUTLIER) cc_final: 0.3487 (pt0) REVERT: A 687 MET cc_start: 0.1744 (mpp) cc_final: 0.1262 (mpp) REVERT: A 701 GLN cc_start: 0.2391 (pm20) cc_final: 0.1666 (pm20) REVERT: A 739 MET cc_start: -0.3840 (mtm) cc_final: -0.4699 (mtt) REVERT: A 879 ARG cc_start: 0.2561 (mtm180) cc_final: 0.2227 (tmt170) REVERT: C 136 ILE cc_start: 0.4570 (pt) cc_final: 0.4328 (pt) REVERT: C 359 TYR cc_start: 0.5535 (t80) cc_final: 0.5285 (t80) REVERT: C 540 VAL cc_start: 0.4412 (t) cc_final: 0.4197 (t) REVERT: C 592 MET cc_start: -0.2999 (mtp) cc_final: -0.4273 (ttm) REVERT: C 687 MET cc_start: -0.0907 (pmm) cc_final: -0.1378 (pmm) REVERT: C 1191 MET cc_start: 0.0908 (tmm) cc_final: 0.0291 (tmm) REVERT: E 504 MET cc_start: -0.3981 (mtp) cc_final: -0.4205 (mtp) REVERT: E 840 HIS cc_start: 0.4238 (m-70) cc_final: 0.3509 (m-70) REVERT: G 257 GLN cc_start: 0.5155 (mt0) cc_final: 0.4889 (mm-40) REVERT: G 504 MET cc_start: -0.2417 (mtp) cc_final: -0.2660 (mtp) REVERT: G 592 MET cc_start: -0.2814 (mtm) cc_final: -0.3279 (ptp) REVERT: I 206 LEU cc_start: 0.7836 (tp) cc_final: 0.7597 (tt) REVERT: I 274 MET cc_start: 0.2182 (tpp) cc_final: 0.1109 (ptm) REVERT: I 368 MET cc_start: 0.2639 (mtt) cc_final: 0.2389 (mtm) REVERT: I 687 MET cc_start: -0.0796 (ttp) cc_final: -0.2753 (ptp) REVERT: I 739 MET cc_start: -0.3711 (mtt) cc_final: -0.3967 (mpp) REVERT: I 802 LYS cc_start: -0.0452 (mmtt) cc_final: -0.2270 (mptt) REVERT: K 195 LEU cc_start: 0.5468 (mt) cc_final: 0.5264 (mt) REVERT: K 358 SER cc_start: 0.5930 (m) cc_final: 0.5496 (p) REVERT: K 368 MET cc_start: 0.4644 (mmt) cc_final: 0.3607 (mtm) REVERT: K 739 MET cc_start: -0.2345 (mtm) cc_final: -0.2779 (mtm) REVERT: K 936 MET cc_start: -0.2227 (mtp) cc_final: -0.3042 (ttt) REVERT: M 739 MET cc_start: -0.2030 (mtm) cc_final: -0.2989 (mtm) REVERT: O 59 MET cc_start: -0.1366 (ttp) cc_final: -0.1662 (ttm) REVERT: P 26 MET cc_start: 0.6458 (mtt) cc_final: 0.5979 (mmt) REVERT: T 1 MET cc_start: -0.3222 (ttm) cc_final: -0.5121 (tpp) REVERT: U 15 ARG cc_start: 0.1926 (mmp-170) cc_final: 0.1170 (mmp80) REVERT: U 64 THR cc_start: 0.3792 (p) cc_final: 0.3538 (p) REVERT: V 1 MET cc_start: 0.0427 (ttp) cc_final: -0.0877 (ptm) REVERT: W 55 MET cc_start: 0.0283 (ptp) cc_final: -0.1796 (ppp) outliers start: 13 outliers final: 1 residues processed: 1006 average time/residue: 0.7860 time to fit residues: 1338.9142 Evaluate side-chains 676 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 674 time to evaluate : 6.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 488 optimal weight: 30.0000 chunk 272 optimal weight: 0.9990 chunk 730 optimal weight: 4.9990 chunk 597 optimal weight: 30.0000 chunk 242 optimal weight: 6.9990 chunk 879 optimal weight: 1.9990 chunk 950 optimal weight: 10.0000 chunk 783 optimal weight: 8.9990 chunk 872 optimal weight: 0.9990 chunk 299 optimal weight: 9.9990 chunk 705 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN A 477 GLN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS A 974 GLN ** A1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 ASN C 137 GLN C 153 HIS C 183 HIS ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 416 GLN ** C 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 HIS ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 ASN D 52 ASN E 153 HIS E 183 HIS ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN ** E 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 553 HIS E 562 ASN ** E 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 HIS ** G 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 562 ASN ** G 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 579 GLN G 706 HIS G 881 HIS ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 208 GLN I 449 ASN I 452 GLN I 463 GLN I 477 GLN ** I 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 565 GLN ** I 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 698 HIS I 703 ASN ** I 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1224 HIS I1237 ASN J 52 ASN K 137 GLN ** K 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 257 GLN ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 HIS K 449 ASN ** K 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 524 HIS ** K 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 562 ASN K 565 GLN K 579 GLN ** K1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1126 HIS ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1224 HIS ** M 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 452 GLN M 477 GLN ** M 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 524 HIS M 545 GLN M 562 ASN M 565 GLN ** M 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1224 HIS ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2234 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 80256 Z= 0.259 Angle : 0.771 10.954 108543 Z= 0.400 Chirality : 0.046 0.288 11993 Planarity : 0.005 0.148 13790 Dihedral : 8.432 119.822 10669 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.90 % Favored : 92.42 % Rotamer: Outliers : 0.09 % Allowed : 3.89 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.30 (0.08), residues: 9716 helix: -0.01 (0.09), residues: 3283 sheet: -1.61 (0.12), residues: 1540 loop : -1.14 (0.09), residues: 4893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C1201 HIS 0.012 0.001 HIS T 38 PHE 0.043 0.002 PHE M 526 TYR 0.043 0.003 TYR C 435 ARG 0.015 0.001 ARG E1051 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 889 time to evaluate : 6.814 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: A 110 VAL cc_start: 0.5639 (t) cc_final: 0.5286 (t) REVERT: A 255 ASP cc_start: 0.6596 (t0) cc_final: 0.6369 (t0) REVERT: A 701 GLN cc_start: 0.2538 (pm20) cc_final: 0.1684 (pm20) REVERT: A 739 MET cc_start: -0.4059 (mtm) cc_final: -0.4500 (mtt) REVERT: C 191 ASP cc_start: 0.4619 (p0) cc_final: 0.4100 (p0) REVERT: C 384 THR cc_start: 0.5570 (m) cc_final: 0.5171 (m) REVERT: C 687 MET cc_start: -0.1069 (pmm) cc_final: -0.1629 (pmm) REVERT: E 504 MET cc_start: -0.3654 (mtp) cc_final: -0.3892 (mtp) REVERT: E 592 MET cc_start: -0.2399 (ttm) cc_final: -0.4287 (ttp) REVERT: E 840 HIS cc_start: 0.4906 (m-70) cc_final: 0.4296 (m90) REVERT: G 533 LEU cc_start: -0.0114 (mp) cc_final: -0.0467 (mp) REVERT: G 1018 LEU cc_start: -0.2037 (OUTLIER) cc_final: -0.2247 (tt) REVERT: I 206 LEU cc_start: 0.8332 (tp) cc_final: 0.8086 (tp) REVERT: I 274 MET cc_start: 0.3858 (tpp) cc_final: 0.3309 (tpp) REVERT: I 355 LYS cc_start: 0.4863 (tptt) cc_final: 0.3553 (pttt) REVERT: I 687 MET cc_start: -0.0152 (ttp) cc_final: -0.1729 (ptp) REVERT: I 802 LYS cc_start: -0.0212 (mmtt) cc_final: -0.2021 (mptt) REVERT: K 202 LEU cc_start: 0.7758 (tp) cc_final: 0.7520 (tp) REVERT: K 368 MET cc_start: 0.5084 (mmt) cc_final: 0.4601 (mmm) REVERT: K 449 ASN cc_start: 0.0774 (OUTLIER) cc_final: 0.0202 (t0) REVERT: K 739 MET cc_start: -0.1972 (mtm) cc_final: -0.2421 (mtm) REVERT: K 797 MET cc_start: -0.1412 (ttt) cc_final: -0.1909 (ttm) REVERT: K 936 MET cc_start: -0.1686 (mtp) cc_final: -0.2860 (ttt) REVERT: M 248 SER cc_start: 0.4792 (m) cc_final: 0.4446 (p) REVERT: M 321 PRO cc_start: 0.6978 (Cg_endo) cc_final: 0.6716 (Cg_exo) REVERT: M 358 SER cc_start: 0.5850 (m) cc_final: 0.5571 (p) REVERT: M 406 MET cc_start: 0.4879 (tmm) cc_final: 0.4446 (mmt) REVERT: M 411 VAL cc_start: 0.6001 (t) cc_final: 0.5553 (t) REVERT: M 464 PHE cc_start: 0.2648 (t80) cc_final: 0.2397 (t80) REVERT: M 687 MET cc_start: 0.2121 (mmt) cc_final: 0.1846 (mmm) REVERT: M 729 ASP cc_start: 0.6270 (t0) cc_final: 0.5749 (m-30) REVERT: M 739 MET cc_start: -0.2238 (mtm) cc_final: -0.2909 (mtm) REVERT: M 1016 LYS cc_start: 0.4837 (mmmt) cc_final: 0.4475 (mmtm) REVERT: O 59 MET cc_start: -0.0800 (ttp) cc_final: -0.1141 (ttm) REVERT: T 1 MET cc_start: -0.2978 (ttm) cc_final: -0.5050 (tpp) REVERT: U 64 THR cc_start: 0.3346 (p) cc_final: 0.3024 (p) outliers start: 8 outliers final: 0 residues processed: 896 average time/residue: 0.7737 time to fit residues: 1193.8670 Evaluate side-chains 672 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 670 time to evaluate : 6.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 869 optimal weight: 2.9990 chunk 661 optimal weight: 7.9990 chunk 456 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 419 optimal weight: 9.9990 chunk 590 optimal weight: 10.0000 chunk 882 optimal weight: 7.9990 chunk 934 optimal weight: 0.7980 chunk 461 optimal weight: 10.0000 chunk 836 optimal weight: 9.9990 chunk 251 optimal weight: 0.9980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS A 477 GLN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 997 GLN ** A1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS C 257 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN C 416 GLN C 441 GLN ** C 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 HIS ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 HIS ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN E 171 HIS E 257 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN E 477 GLN E 524 HIS ** E 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 524 HIS G 562 ASN G 565 GLN ** G 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1095 HIS G1219 ASN I 311 HIS I 336 ASN ** I 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 GLN I 583 GLN ** I 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1219 ASN K 153 HIS ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 336 ASN K 420 ASN K 438 HIS ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 562 ASN K 703 ASN ** K1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1055 ASN K1095 HIS ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 420 ASN ** M 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 703 ASN ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1095 HIS ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 HIS R 50 GLN ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2410 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 80256 Z= 0.239 Angle : 0.744 10.822 108543 Z= 0.383 Chirality : 0.045 0.265 11993 Planarity : 0.005 0.116 13790 Dihedral : 8.351 137.496 10669 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.01 % Favored : 92.34 % Rotamer: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.08), residues: 9716 helix: -0.08 (0.09), residues: 3317 sheet: -1.89 (0.12), residues: 1582 loop : -1.26 (0.09), residues: 4817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 249 HIS 0.016 0.001 HIS G1084 PHE 0.043 0.002 PHE C 526 TYR 0.027 0.002 TYR I 278 ARG 0.010 0.001 ARG K1152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 847 time to evaluate : 6.890 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: A 110 VAL cc_start: 0.6098 (t) cc_final: 0.5812 (t) REVERT: A 255 ASP cc_start: 0.6859 (t0) cc_final: 0.6387 (t0) REVERT: A 257 GLN cc_start: 0.5736 (mt0) cc_final: 0.5477 (mt0) REVERT: A 411 VAL cc_start: 0.7632 (m) cc_final: 0.7409 (m) REVERT: A 687 MET cc_start: 0.2242 (mpp) cc_final: 0.2011 (mpp) REVERT: A 701 GLN cc_start: 0.2536 (pm20) cc_final: 0.1643 (pm20) REVERT: A 739 MET cc_start: -0.3903 (mtm) cc_final: -0.4361 (mtt) REVERT: C 191 ASP cc_start: 0.5038 (p0) cc_final: 0.4716 (p0) REVERT: C 257 GLN cc_start: 0.4163 (tt0) cc_final: 0.3535 (tt0) REVERT: C 687 MET cc_start: -0.1008 (pmm) cc_final: -0.1640 (pmm) REVERT: E 199 LEU cc_start: 0.7196 (mt) cc_final: 0.6965 (mt) REVERT: E 592 MET cc_start: -0.2182 (ttm) cc_final: -0.3159 (ttt) REVERT: E 840 HIS cc_start: 0.5079 (m-70) cc_final: 0.4719 (m90) REVERT: G 196 LEU cc_start: 0.6033 (mt) cc_final: 0.5761 (mt) REVERT: G 199 LEU cc_start: 0.7285 (mt) cc_final: 0.7055 (mt) REVERT: G 592 MET cc_start: -0.1712 (ptt) cc_final: -0.2131 (ptt) REVERT: G 1191 MET cc_start: -0.0341 (tmm) cc_final: -0.1378 (tmm) REVERT: I 262 LEU cc_start: 0.6451 (tp) cc_final: 0.6136 (tt) REVERT: I 355 LYS cc_start: 0.5102 (tptt) cc_final: 0.3823 (pttt) REVERT: I 687 MET cc_start: 0.0016 (ttp) cc_final: -0.1642 (ptp) REVERT: I 739 MET cc_start: -0.2825 (mpp) cc_final: -0.3121 (mpp) REVERT: I 802 LYS cc_start: -0.0528 (mmtt) cc_final: -0.2237 (mptt) REVERT: I 921 MET cc_start: -0.3115 (mtt) cc_final: -0.3459 (mtt) REVERT: I 936 MET cc_start: -0.1544 (ttt) cc_final: -0.1984 (ttt) REVERT: K 202 LEU cc_start: 0.7784 (tp) cc_final: 0.7563 (tp) REVERT: K 321 PRO cc_start: 0.7832 (Cg_endo) cc_final: 0.7530 (Cg_exo) REVERT: K 368 MET cc_start: 0.4715 (mmt) cc_final: 0.4415 (mmm) REVERT: K 739 MET cc_start: -0.1849 (mtm) cc_final: -0.2193 (mtm) REVERT: K 797 MET cc_start: -0.0987 (ttt) cc_final: -0.1585 (ttm) REVERT: K 936 MET cc_start: -0.1763 (mtp) cc_final: -0.4109 (ttt) REVERT: M 248 SER cc_start: 0.5797 (m) cc_final: 0.5554 (p) REVERT: M 256 SER cc_start: 0.8065 (m) cc_final: 0.7814 (t) REVERT: M 301 MET cc_start: 0.2078 (ptp) cc_final: 0.1178 (ptp) REVERT: M 390 GLN cc_start: 0.4096 (mp10) cc_final: 0.3860 (mp10) REVERT: M 406 MET cc_start: 0.5692 (tmm) cc_final: 0.4472 (mmt) REVERT: M 729 ASP cc_start: 0.5654 (t0) cc_final: 0.5438 (m-30) REVERT: M 739 MET cc_start: -0.2492 (mtm) cc_final: -0.2842 (mtm) REVERT: M 936 MET cc_start: -0.0923 (ttp) cc_final: -0.1602 (ttm) REVERT: O 26 MET cc_start: -0.0899 (ptt) cc_final: -0.1571 (ptt) REVERT: O 59 MET cc_start: -0.0556 (ttp) cc_final: -0.1058 (ttm) REVERT: Q 55 MET cc_start: 0.6955 (ppp) cc_final: 0.6157 (tmm) REVERT: T 1 MET cc_start: -0.2924 (ttm) cc_final: -0.4990 (tpp) REVERT: U 1 MET cc_start: -0.1053 (ttt) cc_final: -0.1269 (ttm) REVERT: X 29 MET cc_start: 0.2493 (tmm) cc_final: 0.1491 (mtt) outliers start: 2 outliers final: 0 residues processed: 849 average time/residue: 0.7285 time to fit residues: 1074.3868 Evaluate side-chains 643 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 643 time to evaluate : 6.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 778 optimal weight: 4.9990 chunk 530 optimal weight: 6.9990 chunk 13 optimal weight: 0.0470 chunk 695 optimal weight: 20.0000 chunk 385 optimal weight: 8.9990 chunk 797 optimal weight: 20.0000 chunk 646 optimal weight: 0.0010 chunk 1 optimal weight: 0.3980 chunk 477 optimal weight: 30.0000 chunk 838 optimal weight: 40.0000 chunk 235 optimal weight: 0.9980 overall best weight: 1.2886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS A 477 GLN A 531 HIS A 565 GLN A1028 GLN A1095 HIS ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 GLN C 429 ASN C 441 GLN ** C 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN ** C 565 GLN ** 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** ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN E 153 HIS E 257 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN E 477 GLN ** E 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 GLN ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 GLN I 583 GLN I 827 HIS ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1121 HIS ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1219 ASN ** K 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 420 ASN K 438 HIS ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 553 HIS K 562 ASN K 579 GLN ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 420 ASN M 438 HIS ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 477 GLN ** M 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 GLN ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2397 moved from start: 0.7301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 80256 Z= 0.188 Angle : 0.679 10.873 108543 Z= 0.350 Chirality : 0.043 0.214 11993 Planarity : 0.004 0.084 13790 Dihedral : 8.079 148.710 10669 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.71 % Favored : 92.63 % Rotamer: Outliers : 0.02 % Allowed : 2.44 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.39 (0.08), residues: 9716 helix: 0.05 (0.09), residues: 3321 sheet: -1.80 (0.12), residues: 1638 loop : -1.23 (0.09), residues: 4757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP K 246 HIS 0.008 0.001 HIS G 698 PHE 0.037 0.002 PHE M 526 TYR 0.029 0.002 TYR A 529 ARG 0.017 0.000 ARG G 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 838 time to evaluate : 6.911 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: A 110 VAL cc_start: 0.6165 (t) cc_final: 0.5856 (t) REVERT: A 255 ASP cc_start: 0.6405 (t0) cc_final: 0.6092 (t0) REVERT: A 277 LYS cc_start: 0.7800 (mmtt) cc_final: 0.7492 (mttm) REVERT: A 301 MET cc_start: 0.4533 (ppp) cc_final: 0.3812 (ppp) REVERT: A 687 MET cc_start: 0.2281 (mpp) cc_final: 0.1977 (mpp) REVERT: A 701 GLN cc_start: 0.2372 (pm20) cc_final: 0.1692 (pm20) REVERT: A 739 MET cc_start: -0.3917 (mtm) cc_final: -0.4333 (mtt) REVERT: C 136 ILE cc_start: 0.7217 (pt) cc_final: 0.6979 (pt) REVERT: C 359 TYR cc_start: 0.6532 (t80) cc_final: 0.6234 (t80) REVERT: C 411 VAL cc_start: 0.3811 (t) cc_final: 0.3566 (t) REVERT: C 687 MET cc_start: -0.1131 (pmm) cc_final: -0.1591 (pmm) REVERT: E 257 GLN cc_start: 0.3807 (tt0) cc_final: 0.3602 (tt0) REVERT: F 80 MET cc_start: -0.1707 (tmm) cc_final: -0.2044 (tmm) REVERT: G 136 ILE cc_start: 0.5657 (tt) cc_final: 0.5454 (tt) REVERT: G 199 LEU cc_start: 0.7209 (mt) cc_final: 0.6984 (mt) REVERT: G 739 MET cc_start: 0.4002 (tmm) cc_final: 0.3215 (tpp) REVERT: G 1191 MET cc_start: -0.0345 (tmm) cc_final: -0.1311 (tmm) REVERT: I 433 PHE cc_start: 0.0798 (m-10) cc_final: 0.0391 (m-10) REVERT: I 687 MET cc_start: -0.0009 (ttp) cc_final: -0.1718 (ptp) REVERT: I 739 MET cc_start: -0.2517 (mpp) cc_final: -0.2946 (mpp) REVERT: I 921 MET cc_start: -0.3263 (mtt) cc_final: -0.3652 (mtt) REVERT: I 936 MET cc_start: -0.1161 (ttt) cc_final: -0.1995 (ttt) REVERT: K 321 PRO cc_start: 0.7939 (Cg_endo) cc_final: 0.7641 (Cg_exo) REVERT: K 739 MET cc_start: -0.1980 (mtm) cc_final: -0.2291 (mtm) REVERT: K 797 MET cc_start: -0.0989 (ttt) cc_final: -0.1382 (ttm) REVERT: K 936 MET cc_start: -0.1764 (mtp) cc_final: -0.4230 (ttt) REVERT: M 256 SER cc_start: 0.8574 (m) cc_final: 0.8057 (t) REVERT: M 406 MET cc_start: 0.5745 (tmm) cc_final: 0.4554 (mmt) REVERT: M 739 MET cc_start: -0.2393 (mtm) cc_final: -0.2818 (mtm) REVERT: M 936 MET cc_start: -0.1092 (ttp) cc_final: -0.1810 (ttm) REVERT: O 59 MET cc_start: -0.0388 (ttp) cc_final: -0.0937 (ttm) REVERT: Q 58 LYS cc_start: 0.9041 (pptt) cc_final: 0.8562 (tmmt) REVERT: Q 59 MET cc_start: 0.6614 (ttm) cc_final: 0.6221 (ttm) REVERT: S 1 MET cc_start: 0.0717 (ttm) cc_final: 0.0458 (mtt) REVERT: T 1 MET cc_start: -0.2737 (ttm) cc_final: -0.4754 (tpt) REVERT: U 39 MET cc_start: 0.1661 (mmt) cc_final: 0.1079 (mmm) outliers start: 2 outliers final: 0 residues processed: 840 average time/residue: 0.7191 time to fit residues: 1054.0985 Evaluate side-chains 653 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 653 time to evaluate : 6.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 314 optimal weight: 40.0000 chunk 841 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 548 optimal weight: 5.9990 chunk 230 optimal weight: 0.0040 chunk 935 optimal weight: 40.0000 chunk 776 optimal weight: 10.0000 chunk 433 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 309 optimal weight: 30.0000 chunk 491 optimal weight: 30.0000 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 468 HIS A 477 GLN ** A 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 GLN ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 HIS ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 827 HIS ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1126 HIS ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN E 121 GLN E 137 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN E 346 GLN E 416 GLN ** E 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN ** E 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN E 685 ASN E 698 HIS ** E 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1176 HIS F 52 ASN ** G 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 GLN ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 ASN ** G 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 HIS ** I 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 524 HIS I 545 GLN ** I 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 942 HIS ** I1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1176 HIS I1237 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 HIS ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 GLN ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 562 ASN K 565 GLN ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 257 GLN ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 344 GLN M 349 GLN M 438 HIS ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 463 GLN M 477 GLN ** M 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 565 GLN ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN Q 77 HIS ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 GLN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3021 moved from start: 0.9159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 80256 Z= 0.366 Angle : 0.893 13.904 108543 Z= 0.459 Chirality : 0.050 0.586 11993 Planarity : 0.006 0.166 13790 Dihedral : 8.926 167.607 10669 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.12 % Favored : 91.19 % Rotamer: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.98 (0.08), residues: 9716 helix: -0.69 (0.08), residues: 3298 sheet: -2.00 (0.11), residues: 1743 loop : -1.39 (0.09), residues: 4675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.004 TRP G 184 HIS 0.030 0.002 HIS K 521 PHE 0.042 0.003 PHE C 425 TYR 0.041 0.003 TYR G 278 ARG 0.019 0.001 ARG I1152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 795 time to evaluate : 6.874 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: A 110 VAL cc_start: 0.6983 (t) cc_final: 0.6715 (t) REVERT: A 251 LEU cc_start: 0.8274 (mt) cc_final: 0.8020 (mt) REVERT: A 481 MET cc_start: 0.5448 (pmm) cc_final: 0.5152 (pmm) REVERT: C 245 VAL cc_start: 0.8665 (t) cc_final: 0.8432 (t) REVERT: C 322 LEU cc_start: 0.7790 (tp) cc_final: 0.7544 (tp) REVERT: C 485 ASN cc_start: 0.2479 (OUTLIER) cc_final: 0.1993 (t0) REVERT: C 687 MET cc_start: -0.0729 (pmm) cc_final: -0.1286 (pmm) REVERT: E 232 LEU cc_start: 0.6438 (tt) cc_final: 0.6125 (tt) REVERT: E 504 MET cc_start: -0.2932 (mtp) cc_final: -0.3194 (mtp) REVERT: G 739 MET cc_start: 0.3278 (tmm) cc_final: 0.1880 (ttt) REVERT: G 814 MET cc_start: 0.0902 (tpt) cc_final: 0.0468 (tpt) REVERT: G 1191 MET cc_start: 0.0297 (tmm) cc_final: -0.0659 (tmm) REVERT: I 687 MET cc_start: -0.0567 (ttp) cc_final: -0.1714 (mpp) REVERT: I 739 MET cc_start: -0.1807 (mpp) cc_final: -0.2298 (mpp) REVERT: I 921 MET cc_start: -0.3192 (mtt) cc_final: -0.3491 (mtm) REVERT: I 936 MET cc_start: -0.1168 (ttt) cc_final: -0.2290 (ttt) REVERT: K 245 VAL cc_start: 0.6825 (t) cc_final: 0.6623 (t) REVERT: K 292 LEU cc_start: 0.6138 (mt) cc_final: 0.5811 (mt) REVERT: K 739 MET cc_start: -0.1411 (mtm) cc_final: -0.1862 (mtt) REVERT: K 921 MET cc_start: -0.0978 (mtt) cc_final: -0.1371 (mmt) REVERT: K 936 MET cc_start: -0.2062 (mtp) cc_final: -0.3584 (ttt) REVERT: M 225 ASP cc_start: 0.5695 (m-30) cc_final: 0.5492 (m-30) REVERT: M 257 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6994 (pp30) REVERT: M 406 MET cc_start: 0.5415 (tmm) cc_final: 0.4696 (mpp) REVERT: M 411 VAL cc_start: 0.6605 (t) cc_final: 0.6152 (t) REVERT: M 739 MET cc_start: -0.2081 (mtm) cc_final: -0.2323 (mtm) REVERT: M 814 MET cc_start: 0.0481 (ttt) cc_final: -0.2773 (mtt) REVERT: M 936 MET cc_start: -0.1143 (ttp) cc_final: -0.1854 (ttm) REVERT: M 1016 LYS cc_start: 0.5343 (mmmt) cc_final: 0.4764 (mmmt) REVERT: P 26 MET cc_start: 0.4667 (mmt) cc_final: 0.4217 (mmm) REVERT: P 59 MET cc_start: 0.0109 (ttm) cc_final: -0.0125 (ttp) REVERT: Q 58 LYS cc_start: 0.8846 (pptt) cc_final: 0.8170 (tmmt) REVERT: Q 59 MET cc_start: 0.6625 (ttm) cc_final: 0.5871 (ptt) REVERT: S 1 MET cc_start: 0.1300 (ttm) cc_final: -0.0171 (mtt) REVERT: U 15 ARG cc_start: 0.3587 (mmp-170) cc_final: 0.2724 (mmp80) REVERT: U 39 MET cc_start: 0.1758 (mmt) cc_final: 0.1176 (mmm) outliers start: 5 outliers final: 1 residues processed: 799 average time/residue: 0.7299 time to fit residues: 1013.4995 Evaluate side-chains 587 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 584 time to evaluate : 6.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 902 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 533 optimal weight: 5.9990 chunk 683 optimal weight: 4.9990 chunk 529 optimal weight: 0.9990 chunk 787 optimal weight: 0.9990 chunk 522 optimal weight: 0.6980 chunk 932 optimal weight: 20.0000 chunk 583 optimal weight: 9.9990 chunk 568 optimal weight: 20.0000 chunk 430 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS A 477 GLN A 614 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 416 GLN C 565 GLN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 698 HIS C 737 ASN ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN E 134 ASN E 137 GLN E 257 GLN ** E 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN ** E 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 HIS E 531 HIS E 543 ASN E 747 ASN E 851 GLN ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1126 HIS F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 GLN G 449 ASN G 477 GLN ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 208 GLN ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 477 GLN ** I1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1028 GLN ** I1031 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1095 HIS ** K 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 HIS ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 344 GLN ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 477 GLN ** M 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 531 HIS ** M 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 HIS ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2940 moved from start: 0.9524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 80256 Z= 0.233 Angle : 0.727 13.353 108543 Z= 0.373 Chirality : 0.045 0.309 11993 Planarity : 0.005 0.098 13790 Dihedral : 8.406 177.929 10669 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.90 % Favored : 92.50 % Rotamer: Outliers : 0.02 % Allowed : 1.59 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.78 (0.08), residues: 9716 helix: -0.41 (0.09), residues: 3316 sheet: -1.87 (0.12), residues: 1722 loop : -1.39 (0.09), residues: 4678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 404 HIS 0.011 0.001 HIS K 521 PHE 0.037 0.002 PHE G1213 TYR 0.037 0.002 TYR A 529 ARG 0.011 0.001 ARG I 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 800 time to evaluate : 6.987 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: A 136 ILE cc_start: 0.8959 (pt) cc_final: 0.8695 (pt) REVERT: A 163 LEU cc_start: 0.7919 (mt) cc_final: 0.7644 (mm) REVERT: A 251 LEU cc_start: 0.8413 (mt) cc_final: 0.8069 (mt) REVERT: A 481 MET cc_start: 0.5649 (pmm) cc_final: 0.5370 (pmm) REVERT: A 701 GLN cc_start: 0.1631 (pm20) cc_final: 0.1277 (pm20) REVERT: A 1191 MET cc_start: -0.2339 (mtm) cc_final: -0.4281 (ttp) REVERT: C 308 GLU cc_start: 0.4614 (tp30) cc_final: 0.4343 (tp30) REVERT: C 322 LEU cc_start: 0.7857 (tp) cc_final: 0.7586 (tp) REVERT: C 687 MET cc_start: 0.0039 (pmm) cc_final: -0.0675 (pmm) REVERT: E 240 LEU cc_start: 0.6779 (mm) cc_final: 0.6356 (mt) REVERT: G 155 MET cc_start: 0.4143 (ptt) cc_final: 0.3847 (ptp) REVERT: G 202 LEU cc_start: 0.7841 (tp) cc_final: 0.7562 (tp) REVERT: G 1191 MET cc_start: -0.0190 (tmm) cc_final: -0.1126 (tmm) REVERT: I 198 LYS cc_start: 0.7482 (mmmt) cc_final: 0.6767 (mmmm) REVERT: I 245 VAL cc_start: 0.8577 (t) cc_final: 0.8299 (t) REVERT: I 484 TYR cc_start: 0.1028 (m-80) cc_final: 0.0794 (m-80) REVERT: I 687 MET cc_start: -0.0583 (ttp) cc_final: -0.1704 (mpp) REVERT: I 739 MET cc_start: -0.1858 (mpp) cc_final: -0.2311 (mpp) REVERT: I 921 MET cc_start: -0.3568 (mtt) cc_final: -0.3865 (mtt) REVERT: I 936 MET cc_start: -0.1218 (ttt) cc_final: -0.2339 (ttt) REVERT: K 225 ASP cc_start: 0.5903 (m-30) cc_final: 0.5695 (m-30) REVERT: K 245 VAL cc_start: 0.6854 (t) cc_final: 0.6497 (t) REVERT: K 264 THR cc_start: 0.6392 (t) cc_final: 0.6157 (t) REVERT: K 301 MET cc_start: 0.6260 (ppp) cc_final: 0.5873 (ppp) REVERT: K 739 MET cc_start: -0.1811 (mtm) cc_final: -0.2181 (mtt) REVERT: K 797 MET cc_start: -0.1344 (ttt) cc_final: -0.1853 (ttm) REVERT: K 936 MET cc_start: -0.2655 (mtp) cc_final: -0.4315 (ttt) REVERT: M 201 ASN cc_start: 0.6478 (m110) cc_final: 0.5546 (m110) REVERT: M 202 LEU cc_start: 0.9145 (pp) cc_final: 0.8849 (pp) REVERT: M 205 ARG cc_start: 0.7645 (ttm110) cc_final: 0.7262 (ttm110) REVERT: M 225 ASP cc_start: 0.6105 (m-30) cc_final: 0.5899 (m-30) REVERT: M 412 GLU cc_start: 0.6354 (tp30) cc_final: 0.5308 (tp30) REVERT: M 936 MET cc_start: -0.1241 (ttp) cc_final: -0.1894 (ttm) REVERT: N 65 MET cc_start: 0.3562 (tpt) cc_final: 0.3223 (tpp) REVERT: P 26 MET cc_start: 0.4669 (mmt) cc_final: 0.4257 (mmm) REVERT: P 59 MET cc_start: 0.0416 (ttm) cc_final: 0.0186 (ttp) REVERT: Q 58 LYS cc_start: 0.8880 (pptt) cc_final: 0.8231 (tmmt) REVERT: S 1 MET cc_start: 0.1179 (ttm) cc_final: 0.0408 (mtt) REVERT: U 39 MET cc_start: 0.1480 (mmt) cc_final: 0.1002 (mmm) REVERT: V 1 MET cc_start: -0.1031 (ttt) cc_final: -0.1240 (ttt) outliers start: 2 outliers final: 0 residues processed: 802 average time/residue: 0.7446 time to fit residues: 1033.0991 Evaluate side-chains 612 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 612 time to evaluate : 6.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 576 optimal weight: 6.9990 chunk 372 optimal weight: 0.8980 chunk 556 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 592 optimal weight: 10.0000 chunk 634 optimal weight: 1.9990 chunk 460 optimal weight: 30.0000 chunk 86 optimal weight: 9.9990 chunk 732 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS A 477 GLN ** A 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 416 GLN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** E 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN ** E 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 ASN ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 ASN ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN ** I 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 GLN I 531 HIS ** I 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 257 GLN ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 HIS ** K 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 562 ASN ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 827 HIS ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 438 HIS ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 477 GLN ** M 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 553 HIS ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 HIS ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3038 moved from start: 1.0134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 80256 Z= 0.236 Angle : 0.735 17.313 108543 Z= 0.375 Chirality : 0.045 0.273 11993 Planarity : 0.005 0.096 13790 Dihedral : 8.295 177.163 10669 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.61 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.71 (0.08), residues: 9716 helix: -0.27 (0.09), residues: 3253 sheet: -1.81 (0.12), residues: 1715 loop : -1.42 (0.09), residues: 4748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP C 249 HIS 0.020 0.001 HIS M 656 PHE 0.027 0.002 PHE A 787 TYR 0.032 0.002 TYR A 529 ARG 0.016 0.001 ARG E 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 801 time to evaluate : 6.859 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: A 163 LEU cc_start: 0.7779 (mt) cc_final: 0.7561 (mm) REVERT: A 251 LEU cc_start: 0.8303 (mt) cc_final: 0.7984 (mt) REVERT: A 687 MET cc_start: 0.4237 (mpp) cc_final: 0.3967 (mpp) REVERT: A 701 GLN cc_start: 0.2168 (pm20) cc_final: 0.1699 (pm20) REVERT: A 1191 MET cc_start: -0.2408 (mtm) cc_final: -0.4328 (ttp) REVERT: C 257 GLN cc_start: 0.7267 (tt0) cc_final: 0.6839 (tt0) REVERT: C 268 SER cc_start: 0.8497 (p) cc_final: 0.8284 (p) REVERT: C 322 LEU cc_start: 0.7554 (tp) cc_final: 0.7183 (tp) REVERT: C 687 MET cc_start: -0.0101 (pmm) cc_final: -0.0736 (pmm) REVERT: D 80 MET cc_start: 0.0179 (ppp) cc_final: -0.0140 (ppp) REVERT: E 221 GLU cc_start: 0.6587 (tm-30) cc_final: 0.6348 (tm-30) REVERT: E 232 LEU cc_start: 0.6155 (tt) cc_final: 0.5930 (tp) REVERT: E 326 LEU cc_start: 0.5844 (tt) cc_final: 0.5598 (tt) REVERT: E 368 MET cc_start: 0.2888 (ptt) cc_final: 0.2342 (ptt) REVERT: F 80 MET cc_start: -0.1707 (tmm) cc_final: -0.2206 (tmm) REVERT: G 232 LEU cc_start: 0.8042 (pp) cc_final: 0.7311 (tt) REVERT: G 294 ILE cc_start: 0.5735 (tp) cc_final: 0.5481 (tp) REVERT: G 921 MET cc_start: -0.3423 (mmm) cc_final: -0.3722 (mmm) REVERT: G 1191 MET cc_start: 0.0051 (tmm) cc_final: -0.0829 (tmm) REVERT: I 198 LYS cc_start: 0.7472 (mmmt) cc_final: 0.6944 (mmmm) REVERT: I 285 SER cc_start: 0.7366 (p) cc_final: 0.7148 (t) REVERT: I 372 VAL cc_start: 0.7406 (t) cc_final: 0.7195 (t) REVERT: I 388 ILE cc_start: 0.8078 (mp) cc_final: 0.7867 (mt) REVERT: I 687 MET cc_start: -0.0190 (ttp) cc_final: -0.1430 (mpp) REVERT: I 921 MET cc_start: -0.3176 (mtt) cc_final: -0.3400 (mtt) REVERT: I 936 MET cc_start: -0.1357 (ttt) cc_final: -0.2414 (ttt) REVERT: K 187 VAL cc_start: 0.8134 (t) cc_final: 0.7922 (t) REVERT: K 264 THR cc_start: 0.6848 (t) cc_final: 0.6629 (t) REVERT: K 274 MET cc_start: 0.7108 (ptm) cc_final: 0.6360 (ppp) REVERT: K 739 MET cc_start: -0.1465 (mtm) cc_final: -0.1916 (mtt) REVERT: K 797 MET cc_start: -0.1020 (ttt) cc_final: -0.1480 (ttm) REVERT: K 936 MET cc_start: -0.2872 (mtp) cc_final: -0.4183 (ttt) REVERT: M 277 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8209 (mttp) REVERT: M 283 GLU cc_start: 0.4989 (pp20) cc_final: 0.4667 (pp20) REVERT: M 440 LEU cc_start: 0.6063 (mt) cc_final: 0.5469 (mt) REVERT: M 739 MET cc_start: -0.1678 (mtm) cc_final: -0.1920 (mtm) REVERT: M 936 MET cc_start: -0.1317 (ttp) cc_final: -0.1952 (ttm) REVERT: N 65 MET cc_start: 0.3050 (tpt) cc_final: 0.2227 (tpp) REVERT: P 26 MET cc_start: 0.4706 (mmt) cc_final: 0.4348 (mmm) REVERT: P 59 MET cc_start: 0.0438 (ttm) cc_final: 0.0185 (ttp) REVERT: Q 58 LYS cc_start: 0.9022 (pptt) cc_final: 0.8397 (tmmt) REVERT: S 1 MET cc_start: 0.1754 (ttm) cc_final: -0.0982 (mmt) REVERT: S 39 MET cc_start: 0.1724 (mpp) cc_final: -0.0356 (mtt) REVERT: U 39 MET cc_start: 0.2106 (mmt) cc_final: 0.1802 (mmm) REVERT: W 26 MET cc_start: 0.1614 (mpp) cc_final: 0.1396 (mtm) outliers start: 0 outliers final: 0 residues processed: 801 average time/residue: 0.7264 time to fit residues: 1017.5001 Evaluate side-chains 603 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 603 time to evaluate : 6.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 847 optimal weight: 50.0000 chunk 892 optimal weight: 40.0000 chunk 814 optimal weight: 20.0000 chunk 868 optimal weight: 7.9990 chunk 522 optimal weight: 0.8980 chunk 378 optimal weight: 1.9990 chunk 682 optimal weight: 10.0000 chunk 266 optimal weight: 0.8980 chunk 784 optimal weight: 2.9990 chunk 821 optimal weight: 20.0000 chunk 865 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** A 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 GLN ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN ** E 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 ASN ** E1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 GLN ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 ASN ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 HIS ** G 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 737 ASN ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 477 GLN ** I 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 257 GLN ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 257 GLN ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 438 HIS ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 477 GLN ** M 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3098 moved from start: 1.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 80256 Z= 0.232 Angle : 0.726 12.569 108543 Z= 0.371 Chirality : 0.045 0.366 11993 Planarity : 0.004 0.126 13790 Dihedral : 8.145 173.868 10669 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.12 % Favored : 92.27 % Rotamer: Outliers : 0.02 % Allowed : 0.57 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.70 (0.08), residues: 9716 helix: -0.24 (0.09), residues: 3259 sheet: -1.82 (0.12), residues: 1729 loop : -1.42 (0.09), residues: 4728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 404 HIS 0.010 0.001 HIS M 656 PHE 0.049 0.002 PHE I 350 TYR 0.035 0.002 TYR A 529 ARG 0.013 0.001 ARG A 879 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 784 time to evaluate : 6.947 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: A 163 LEU cc_start: 0.8034 (mt) cc_final: 0.7797 (mm) REVERT: A 251 LEU cc_start: 0.8501 (mt) cc_final: 0.8264 (mt) REVERT: A 424 LEU cc_start: 0.8679 (tp) cc_final: 0.8454 (tp) REVERT: A 437 LEU cc_start: 0.8722 (mt) cc_final: 0.8501 (mt) REVERT: A 701 GLN cc_start: 0.1903 (pm20) cc_final: 0.1443 (pm20) REVERT: A 1191 MET cc_start: -0.2183 (mtm) cc_final: -0.4354 (ttp) REVERT: B 80 MET cc_start: 0.5580 (tmm) cc_final: 0.5346 (tmm) REVERT: C 257 GLN cc_start: 0.7274 (tt0) cc_final: 0.6956 (tt0) REVERT: C 268 SER cc_start: 0.7821 (p) cc_final: 0.7541 (p) REVERT: C 491 MET cc_start: 0.1231 (tmm) cc_final: 0.0889 (tmm) REVERT: C 687 MET cc_start: -0.0215 (pmm) cc_final: -0.0817 (pmm) REVERT: E 301 MET cc_start: 0.3425 (tmm) cc_final: 0.3192 (tmm) REVERT: E 326 LEU cc_start: 0.6277 (tt) cc_final: 0.6016 (tt) REVERT: E 739 MET cc_start: 0.2417 (tpp) cc_final: 0.1703 (tpp) REVERT: F 80 MET cc_start: -0.2009 (tmm) cc_final: -0.2317 (tmm) REVERT: G 294 ILE cc_start: 0.6034 (tp) cc_final: 0.5752 (tp) REVERT: G 295 LEU cc_start: 0.5752 (mt) cc_final: 0.5281 (mt) REVERT: G 301 MET cc_start: 0.3826 (tmm) cc_final: 0.3418 (tmm) REVERT: G 419 VAL cc_start: 0.6317 (t) cc_final: 0.5623 (t) REVERT: G 921 MET cc_start: -0.3673 (mmm) cc_final: -0.3976 (mmm) REVERT: G 1191 MET cc_start: 0.0144 (tmm) cc_final: -0.0743 (tmm) REVERT: I 198 LYS cc_start: 0.7428 (mmmt) cc_final: 0.6852 (mmmm) REVERT: I 359 TYR cc_start: 0.7077 (t80) cc_final: 0.6584 (t80) REVERT: I 388 ILE cc_start: 0.8413 (mp) cc_final: 0.8089 (mt) REVERT: I 484 TYR cc_start: 0.1414 (m-80) cc_final: 0.1111 (m-80) REVERT: I 687 MET cc_start: 0.0060 (ttp) cc_final: -0.1063 (mtm) REVERT: I 739 MET cc_start: -0.1893 (mpp) cc_final: -0.2249 (mpp) REVERT: I 921 MET cc_start: -0.2970 (mtt) cc_final: -0.3180 (mtt) REVERT: I 936 MET cc_start: -0.1278 (ttt) cc_final: -0.2398 (ttt) REVERT: I 1191 MET cc_start: -0.1263 (tpp) cc_final: -0.1486 (ttt) REVERT: K 225 ASP cc_start: 0.5812 (m-30) cc_final: 0.4796 (m-30) REVERT: K 274 MET cc_start: 0.7108 (ptm) cc_final: 0.6431 (ppp) REVERT: K 739 MET cc_start: -0.1700 (mtm) cc_final: -0.2110 (mtt) REVERT: K 936 MET cc_start: -0.2811 (mtp) cc_final: -0.3662 (ttt) REVERT: M 283 GLU cc_start: 0.5300 (pp20) cc_final: 0.5057 (pp20) REVERT: M 301 MET cc_start: 0.3584 (ptp) cc_final: 0.3228 (ptp) REVERT: M 375 LEU cc_start: 0.6992 (mm) cc_final: 0.6766 (mm) REVERT: M 406 MET cc_start: 0.7335 (mpp) cc_final: 0.6892 (mpp) REVERT: M 440 LEU cc_start: 0.6739 (mt) cc_final: 0.5976 (mt) REVERT: M 936 MET cc_start: -0.1608 (ttp) cc_final: -0.2013 (ttm) REVERT: P 26 MET cc_start: 0.4564 (mmt) cc_final: 0.4214 (mmm) REVERT: Q 58 LYS cc_start: 0.8854 (pptt) cc_final: 0.8436 (tmmt) REVERT: S 1 MET cc_start: 0.2111 (ttm) cc_final: 0.1316 (mmm) REVERT: U 39 MET cc_start: 0.1860 (mmt) cc_final: 0.1642 (mmm) outliers start: 2 outliers final: 1 residues processed: 786 average time/residue: 0.7578 time to fit residues: 1045.8562 Evaluate side-chains 599 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 598 time to evaluate : 6.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 570 optimal weight: 5.9990 chunk 918 optimal weight: 8.9990 chunk 560 optimal weight: 6.9990 chunk 435 optimal weight: 40.0000 chunk 638 optimal weight: 0.9980 chunk 963 optimal weight: 9.9990 chunk 886 optimal weight: 5.9990 chunk 767 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 592 optimal weight: 4.9990 chunk 470 optimal weight: 40.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** A 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 HIS ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 HIS ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS C 477 GLN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN E 477 GLN ** E 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 ASN ** E1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 GLN ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 HIS G 565 GLN ** G 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 931 GLN ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 477 GLN ** I 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 257 GLN ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 438 HIS ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 477 GLN ** M 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3258 moved from start: 1.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 80256 Z= 0.280 Angle : 0.778 17.509 108543 Z= 0.397 Chirality : 0.047 0.317 11993 Planarity : 0.005 0.141 13790 Dihedral : 8.260 172.884 10669 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.03 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.86 (0.08), residues: 9716 helix: -0.43 (0.09), residues: 3301 sheet: -1.89 (0.12), residues: 1729 loop : -1.49 (0.09), residues: 4686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 404 HIS 0.033 0.001 HIS E 881 PHE 0.053 0.002 PHE I 350 TYR 0.044 0.003 TYR E 619 ARG 0.019 0.001 ARG K 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 768 time to evaluate : 6.942 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: A 251 LEU cc_start: 0.8465 (mt) cc_final: 0.8204 (mt) REVERT: A 701 GLN cc_start: 0.1827 (pm20) cc_final: 0.1285 (pm20) REVERT: A 1191 MET cc_start: -0.2645 (mtm) cc_final: -0.4562 (ttp) REVERT: C 201 ASN cc_start: 0.6477 (m-40) cc_final: 0.6264 (m-40) REVERT: C 268 SER cc_start: 0.7864 (p) cc_final: 0.7494 (p) REVERT: C 297 LEU cc_start: 0.7514 (mt) cc_final: 0.7240 (tp) REVERT: C 378 ASP cc_start: 0.5191 (p0) cc_final: 0.4912 (p0) REVERT: C 592 MET cc_start: -0.3043 (ptm) cc_final: -0.4231 (ptt) REVERT: C 687 MET cc_start: 0.0195 (pmm) cc_final: -0.0089 (pmm) REVERT: C 814 MET cc_start: 0.4491 (mmp) cc_final: 0.3185 (tpp) REVERT: E 326 LEU cc_start: 0.6817 (tt) cc_final: 0.6571 (tt) REVERT: G 294 ILE cc_start: 0.6875 (tp) cc_final: 0.6661 (tp) REVERT: G 301 MET cc_start: 0.3618 (tmm) cc_final: 0.3378 (tmm) REVERT: G 419 VAL cc_start: 0.6594 (t) cc_final: 0.6214 (t) REVERT: G 1191 MET cc_start: 0.0509 (tmm) cc_final: -0.0162 (tmm) REVERT: I 301 MET cc_start: 0.6802 (ppp) cc_final: 0.5297 (tmm) REVERT: I 388 ILE cc_start: 0.8763 (mp) cc_final: 0.8558 (mt) REVERT: I 687 MET cc_start: 0.0568 (ttp) cc_final: -0.0604 (mtm) REVERT: I 936 MET cc_start: -0.0930 (ttt) cc_final: -0.2076 (ttt) REVERT: K 274 MET cc_start: 0.7438 (ptm) cc_final: 0.6873 (ppp) REVERT: K 292 LEU cc_start: 0.5963 (mt) cc_final: 0.5726 (mt) REVERT: K 415 LEU cc_start: 0.5597 (mt) cc_final: 0.5115 (tt) REVERT: K 739 MET cc_start: -0.1370 (mtm) cc_final: -0.1668 (mtt) REVERT: K 797 MET cc_start: -0.0329 (ttt) cc_final: -0.0978 (ttm) REVERT: M 283 GLU cc_start: 0.5272 (pp20) cc_final: 0.5039 (pp20) REVERT: M 406 MET cc_start: 0.7312 (mpp) cc_final: 0.6697 (mpp) REVERT: M 440 LEU cc_start: 0.6735 (mt) cc_final: 0.6100 (mt) REVERT: M 936 MET cc_start: -0.1433 (ttp) cc_final: -0.1856 (ttm) REVERT: P 26 MET cc_start: 0.4571 (mmt) cc_final: 0.4330 (mmm) REVERT: P 59 MET cc_start: 0.0778 (ttm) cc_final: 0.0568 (ttt) REVERT: Q 58 LYS cc_start: 0.8913 (pptt) cc_final: 0.8291 (tmmt) REVERT: Q 59 MET cc_start: 0.6761 (tmm) cc_final: 0.6485 (tmm) REVERT: S 1 MET cc_start: 0.2832 (ttm) cc_final: 0.0331 (mmm) REVERT: S 39 MET cc_start: 0.1649 (mpp) cc_final: -0.0571 (mtt) REVERT: U 39 MET cc_start: 0.2070 (mmt) cc_final: 0.1767 (mmm) REVERT: V 1 MET cc_start: -0.1066 (ttt) cc_final: -0.1296 (ttt) REVERT: W 26 MET cc_start: 0.1545 (mpp) cc_final: 0.1259 (mtm) outliers start: 0 outliers final: 0 residues processed: 768 average time/residue: 0.7040 time to fit residues: 949.6243 Evaluate side-chains 590 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 590 time to evaluate : 6.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 609 optimal weight: 0.2980 chunk 817 optimal weight: 20.0000 chunk 235 optimal weight: 0.6980 chunk 707 optimal weight: 40.0000 chunk 113 optimal weight: 8.9990 chunk 213 optimal weight: 20.0000 chunk 768 optimal weight: 0.8980 chunk 321 optimal weight: 0.0070 chunk 788 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** A 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS C 471 HIS ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 HIS ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN E 153 HIS E 235 HIS ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 HIS E 553 HIS E 747 ASN ** E1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 441 GLN I 477 GLN ** I 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 257 GLN ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 551 ASN ** K 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 171 HIS ** M 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 309 GLN M 438 HIS ** M 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 551 ASN ** M 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1237 ASN ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.127184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.107614 restraints weight = 674104.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.107779 restraints weight = 473965.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.108146 restraints weight = 330142.629| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 1.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 80256 Z= 0.193 Angle : 0.709 12.533 108543 Z= 0.359 Chirality : 0.044 0.262 11993 Planarity : 0.004 0.112 13790 Dihedral : 7.955 175.091 10669 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.21 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.71 (0.08), residues: 9716 helix: -0.20 (0.09), residues: 3302 sheet: -1.80 (0.12), residues: 1701 loop : -1.50 (0.09), residues: 4713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 404 HIS 0.015 0.001 HIS G 490 PHE 0.056 0.002 PHE I 350 TYR 0.033 0.002 TYR K 278 ARG 0.012 0.001 ARG E 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19758.45 seconds wall clock time: 345 minutes 43.43 seconds (20743.43 seconds total)