Starting phenix.real_space_refine on Sat Feb 17 18:16:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2024/7rli_24531_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2024/7rli_24531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2024/7rli_24531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2024/7rli_24531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2024/7rli_24531_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rli_24531/02_2024/7rli_24531_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 372 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 360 5.16 5 C 43884 2.51 5 N 12300 2.21 5 O 13200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B ASP 307": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C ASP 307": "OD1" <-> "OD2" Residue "C ASP 478": "OD1" <-> "OD2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "D TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D ASP 478": "OD1" <-> "OD2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E ASP 307": "OD1" <-> "OD2" Residue "E ASP 478": "OD1" <-> "OD2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E GLU 701": "OE1" <-> "OE2" Residue "F TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F ASP 307": "OD1" <-> "OD2" Residue "F ASP 478": "OD1" <-> "OD2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F ASP 627": "OD1" <-> "OD2" Residue "F GLU 689": "OE1" <-> "OE2" Residue "F GLU 701": "OE1" <-> "OE2" Residue "G TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G ASP 307": "OD1" <-> "OD2" Residue "G ASP 478": "OD1" <-> "OD2" Residue "G GLU 488": "OE1" <-> "OE2" Residue "G ASP 627": "OD1" <-> "OD2" Residue "G GLU 689": "OE1" <-> "OE2" Residue "G GLU 701": "OE1" <-> "OE2" Residue "H TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H ASP 307": "OD1" <-> "OD2" Residue "H ASP 478": "OD1" <-> "OD2" Residue "H GLU 488": "OE1" <-> "OE2" Residue "H ASP 627": "OD1" <-> "OD2" Residue "H GLU 689": "OE1" <-> "OE2" Residue "H GLU 701": "OE1" <-> "OE2" Residue "I TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I ASP 307": "OD1" <-> "OD2" Residue "I ASP 478": "OD1" <-> "OD2" Residue "I GLU 488": "OE1" <-> "OE2" Residue "I ASP 627": "OD1" <-> "OD2" Residue "I GLU 689": "OE1" <-> "OE2" Residue "I GLU 701": "OE1" <-> "OE2" Residue "J TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 218": "OE1" <-> "OE2" Residue "J ASP 307": "OD1" <-> "OD2" Residue "J ASP 478": "OD1" <-> "OD2" Residue "J GLU 488": "OE1" <-> "OE2" Residue "J ASP 627": "OD1" <-> "OD2" Residue "J GLU 689": "OE1" <-> "OE2" Residue "J GLU 701": "OE1" <-> "OE2" Residue "K TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 218": "OE1" <-> "OE2" Residue "K ASP 307": "OD1" <-> "OD2" Residue "K ASP 478": "OD1" <-> "OD2" Residue "K GLU 488": "OE1" <-> "OE2" Residue "K ASP 627": "OD1" <-> "OD2" Residue "K GLU 689": "OE1" <-> "OE2" Residue "K GLU 701": "OE1" <-> "OE2" Residue "L TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 218": "OE1" <-> "OE2" Residue "L ASP 307": "OD1" <-> "OD2" Residue "L ASP 478": "OD1" <-> "OD2" Residue "L GLU 488": "OE1" <-> "OE2" Residue "L ASP 627": "OD1" <-> "OD2" Residue "L GLU 689": "OE1" <-> "OE2" Residue "L GLU 701": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 69768 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "B" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "C" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "D" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "E" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "F" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "G" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "H" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "I" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "J" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "K" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "L" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'JDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.64, per 1000 atoms: 0.37 Number of scatterers: 69768 At special positions: 0 Unit cell: (173, 177, 185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 360 16.00 P 24 15.00 O 13200 8.00 N 12300 7.00 C 43884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.96 Conformation dependent library (CDL) restraints added in 9.1 seconds 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 384 helices and 48 sheets defined 37.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.46 Creating SS restraints... Processing helix chain 'A' and resid 43 through 46 No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.516A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 230 No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.778A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 449 through 453 Processing helix chain 'A' and resid 455 through 458 No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.994A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.573A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'B' and resid 43 through 46 No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 86 through 92 removed outlier: 3.518A pdb=" N ASN B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.602A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 230 No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.778A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS B 384 " --> pdb=" O ILE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 449 through 453 Processing helix chain 'B' and resid 455 through 458 No H-bonds generated for 'chain 'B' and resid 455 through 458' Processing helix chain 'B' and resid 483 through 490 removed outlier: 3.622A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 553 removed outlier: 3.994A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 568 Processing helix chain 'B' and resid 579 through 586 removed outlier: 4.191A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 749 through 763 Processing helix chain 'C' and resid 43 through 46 No H-bonds generated for 'chain 'C' and resid 43 through 46' Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.517A pdb=" N ASN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 400 No H-bonds generated for 'chain 'C' and resid 398 through 400' Processing helix chain 'C' and resid 408 through 430 removed outlier: 3.626A pdb=" N SER C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 444 No H-bonds generated for 'chain 'C' and resid 442 through 444' Processing helix chain 'C' and resid 449 through 453 Processing helix chain 'C' and resid 455 through 458 No H-bonds generated for 'chain 'C' and resid 455 through 458' Processing helix chain 'C' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 498 Processing helix chain 'C' and resid 501 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 553 removed outlier: 3.994A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 568 Processing helix chain 'C' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.575A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'D' and resid 43 through 46 No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 86 through 89 No H-bonds generated for 'chain 'D' and resid 86 through 89' Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 230 No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 251 through 260 removed outlier: 4.008A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 400 No H-bonds generated for 'chain 'D' and resid 398 through 400' Processing helix chain 'D' and resid 408 through 430 removed outlier: 3.626A pdb=" N SER D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 444 No H-bonds generated for 'chain 'D' and resid 442 through 444' Processing helix chain 'D' and resid 449 through 453 Processing helix chain 'D' and resid 455 through 458 No H-bonds generated for 'chain 'D' and resid 455 through 458' Processing helix chain 'D' and resid 483 through 490 removed outlier: 3.622A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 498 Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 568 Processing helix chain 'D' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 739 Processing helix chain 'D' and resid 749 through 763 Processing helix chain 'E' and resid 43 through 46 No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 86 through 89 No H-bonds generated for 'chain 'E' and resid 86 through 89' Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 230 No H-bonds generated for 'chain 'E' and resid 227 through 230' Processing helix chain 'E' and resid 251 through 260 removed outlier: 4.008A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 282 through 295 removed outlier: 3.777A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 380 " --> pdb=" O GLY E 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS E 384 " --> pdb=" O ILE E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 400 No H-bonds generated for 'chain 'E' and resid 398 through 400' Processing helix chain 'E' and resid 408 through 430 removed outlier: 3.626A pdb=" N SER E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN E 421 " --> pdb=" O GLU E 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 444 No H-bonds generated for 'chain 'E' and resid 442 through 444' Processing helix chain 'E' and resid 449 through 453 Processing helix chain 'E' and resid 455 through 458 No H-bonds generated for 'chain 'E' and resid 455 through 458' Processing helix chain 'E' and resid 483 through 490 removed outlier: 3.622A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 498 Processing helix chain 'E' and resid 501 through 506 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 568 Processing helix chain 'E' and resid 579 through 586 removed outlier: 4.191A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 739 Processing helix chain 'E' and resid 749 through 763 Processing helix chain 'F' and resid 43 through 46 No H-bonds generated for 'chain 'F' and resid 43 through 46' Processing helix chain 'F' and resid 86 through 89 No H-bonds generated for 'chain 'F' and resid 86 through 89' Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 230 No H-bonds generated for 'chain 'F' and resid 227 through 230' Processing helix chain 'F' and resid 251 through 260 removed outlier: 4.008A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 276 Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.778A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F 380 " --> pdb=" O GLY F 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS F 384 " --> pdb=" O ILE F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 400 No H-bonds generated for 'chain 'F' and resid 398 through 400' Processing helix chain 'F' and resid 408 through 430 removed outlier: 3.626A pdb=" N SER F 416 " --> pdb=" O ALA F 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 444 No H-bonds generated for 'chain 'F' and resid 442 through 444' Processing helix chain 'F' and resid 449 through 453 Processing helix chain 'F' and resid 455 through 458 No H-bonds generated for 'chain 'F' and resid 455 through 458' Processing helix chain 'F' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 501 through 506 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 568 Processing helix chain 'F' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 739 Processing helix chain 'F' and resid 749 through 763 Processing helix chain 'G' and resid 43 through 46 No H-bonds generated for 'chain 'G' and resid 43 through 46' Processing helix chain 'G' and resid 86 through 92 removed outlier: 3.518A pdb=" N ASN G 90 " --> pdb=" O ARG G 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN G 91 " --> pdb=" O VAL G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 139 Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE G 216 " --> pdb=" O GLN G 212 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU G 218 " --> pdb=" O ALA G 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) Proline residue: G 223 - end of helix Processing helix chain 'G' and resid 227 through 230 No H-bonds generated for 'chain 'G' and resid 227 through 230' Processing helix chain 'G' and resid 251 through 260 removed outlier: 4.008A pdb=" N ALA G 255 " --> pdb=" O LYS G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 276 Processing helix chain 'G' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE G 290 " --> pdb=" O LEU G 286 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU G 291 " --> pdb=" O ARG G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'G' and resid 350 through 352 No H-bonds generated for 'chain 'G' and resid 350 through 352' Processing helix chain 'G' and resid 355 through 358 Processing helix chain 'G' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE G 380 " --> pdb=" O GLY G 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN G 382 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE G 383 " --> pdb=" O GLU G 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS G 384 " --> pdb=" O ILE G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 400 No H-bonds generated for 'chain 'G' and resid 398 through 400' Processing helix chain 'G' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER G 416 " --> pdb=" O ALA G 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN G 421 " --> pdb=" O GLU G 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP G 428 " --> pdb=" O ARG G 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU G 429 " --> pdb=" O LYS G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 442 through 444 No H-bonds generated for 'chain 'G' and resid 442 through 444' Processing helix chain 'G' and resid 449 through 453 Processing helix chain 'G' and resid 455 through 458 No H-bonds generated for 'chain 'G' and resid 455 through 458' Processing helix chain 'G' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU G 488 " --> pdb=" O ASP G 484 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 498 Processing helix chain 'G' and resid 501 through 506 Processing helix chain 'G' and resid 524 through 534 Processing helix chain 'G' and resid 544 through 553 removed outlier: 3.992A pdb=" N MET G 550 " --> pdb=" O GLU G 546 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP G 551 " --> pdb=" O LEU G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 558 through 568 Processing helix chain 'G' and resid 579 through 586 removed outlier: 4.189A pdb=" N ILE G 582 " --> pdb=" O LEU G 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 609 Processing helix chain 'G' and resid 631 through 634 Processing helix chain 'G' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA G 655 " --> pdb=" O LYS G 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 672 through 678 Processing helix chain 'G' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU G 706 " --> pdb=" O SER G 702 " (cutoff:3.500A) Processing helix chain 'G' and resid 733 through 739 Processing helix chain 'G' and resid 749 through 763 Processing helix chain 'H' and resid 43 through 46 No H-bonds generated for 'chain 'H' and resid 43 through 46' Processing helix chain 'H' and resid 86 through 89 No H-bonds generated for 'chain 'H' and resid 86 through 89' Processing helix chain 'H' and resid 135 through 139 Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE H 216 " --> pdb=" O GLN H 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU H 218 " --> pdb=" O ALA H 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU H 222 " --> pdb=" O GLU H 218 " (cutoff:3.500A) Proline residue: H 223 - end of helix Processing helix chain 'H' and resid 227 through 230 No H-bonds generated for 'chain 'H' and resid 227 through 230' Processing helix chain 'H' and resid 251 through 260 removed outlier: 4.008A pdb=" N ALA H 255 " --> pdb=" O LYS H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 272 through 276 Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE H 290 " --> pdb=" O LEU H 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU H 291 " --> pdb=" O ARG H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'H' and resid 350 through 352 No H-bonds generated for 'chain 'H' and resid 350 through 352' Processing helix chain 'H' and resid 355 through 358 Processing helix chain 'H' and resid 374 through 385 removed outlier: 3.595A pdb=" N GLU H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE H 380 " --> pdb=" O GLY H 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN H 382 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE H 383 " --> pdb=" O GLU H 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS H 384 " --> pdb=" O ILE H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 400 No H-bonds generated for 'chain 'H' and resid 398 through 400' Processing helix chain 'H' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER H 416 " --> pdb=" O ALA H 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN H 421 " --> pdb=" O GLU H 417 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS H 426 " --> pdb=" O ALA H 422 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP H 428 " --> pdb=" O ARG H 424 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU H 429 " --> pdb=" O LYS H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 444 No H-bonds generated for 'chain 'H' and resid 442 through 444' Processing helix chain 'H' and resid 449 through 453 Processing helix chain 'H' and resid 455 through 458 No H-bonds generated for 'chain 'H' and resid 455 through 458' Processing helix chain 'H' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU H 488 " --> pdb=" O ASP H 484 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 498 Processing helix chain 'H' and resid 501 through 506 Processing helix chain 'H' and resid 524 through 534 Processing helix chain 'H' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET H 550 " --> pdb=" O GLU H 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP H 551 " --> pdb=" O LEU H 547 " (cutoff:3.500A) Processing helix chain 'H' and resid 558 through 568 Processing helix chain 'H' and resid 579 through 586 removed outlier: 4.191A pdb=" N ILE H 582 " --> pdb=" O LEU H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 599 through 609 Processing helix chain 'H' and resid 631 through 634 Processing helix chain 'H' and resid 650 through 661 removed outlier: 3.923A pdb=" N ALA H 655 " --> pdb=" O LYS H 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 672 through 678 Processing helix chain 'H' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU H 706 " --> pdb=" O SER H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 733 through 739 Processing helix chain 'H' and resid 749 through 763 Processing helix chain 'I' and resid 43 through 46 No H-bonds generated for 'chain 'I' and resid 43 through 46' Processing helix chain 'I' and resid 86 through 89 No H-bonds generated for 'chain 'I' and resid 86 through 89' Processing helix chain 'I' and resid 135 through 139 Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE I 216 " --> pdb=" O GLN I 212 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS I 217 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU I 218 " --> pdb=" O ALA I 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) Proline residue: I 223 - end of helix Processing helix chain 'I' and resid 227 through 230 No H-bonds generated for 'chain 'I' and resid 227 through 230' Processing helix chain 'I' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA I 255 " --> pdb=" O LYS I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 276 Processing helix chain 'I' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE I 290 " --> pdb=" O LEU I 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU I 291 " --> pdb=" O ARG I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 333 Processing helix chain 'I' and resid 350 through 352 No H-bonds generated for 'chain 'I' and resid 350 through 352' Processing helix chain 'I' and resid 355 through 358 Processing helix chain 'I' and resid 374 through 385 removed outlier: 3.593A pdb=" N GLU I 379 " --> pdb=" O THR I 375 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE I 380 " --> pdb=" O GLY I 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN I 382 " --> pdb=" O LEU I 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE I 383 " --> pdb=" O GLU I 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS I 384 " --> pdb=" O ILE I 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 400 No H-bonds generated for 'chain 'I' and resid 398 through 400' Processing helix chain 'I' and resid 408 through 430 removed outlier: 3.626A pdb=" N SER I 416 " --> pdb=" O ALA I 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN I 421 " --> pdb=" O GLU I 417 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS I 426 " --> pdb=" O ALA I 422 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP I 428 " --> pdb=" O ARG I 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU I 429 " --> pdb=" O LYS I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 442 through 444 No H-bonds generated for 'chain 'I' and resid 442 through 444' Processing helix chain 'I' and resid 449 through 453 Processing helix chain 'I' and resid 455 through 458 No H-bonds generated for 'chain 'I' and resid 455 through 458' Processing helix chain 'I' and resid 483 through 490 removed outlier: 3.622A pdb=" N GLU I 488 " --> pdb=" O ASP I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 498 Processing helix chain 'I' and resid 501 through 506 Processing helix chain 'I' and resid 524 through 534 Processing helix chain 'I' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET I 550 " --> pdb=" O GLU I 546 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP I 551 " --> pdb=" O LEU I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 558 through 568 Processing helix chain 'I' and resid 579 through 586 removed outlier: 4.191A pdb=" N ILE I 582 " --> pdb=" O LEU I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 609 Processing helix chain 'I' and resid 631 through 634 Processing helix chain 'I' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA I 655 " --> pdb=" O LYS I 651 " (cutoff:3.500A) Processing helix chain 'I' and resid 672 through 678 Processing helix chain 'I' and resid 684 through 706 removed outlier: 3.575A pdb=" N GLU I 706 " --> pdb=" O SER I 702 " (cutoff:3.500A) Processing helix chain 'I' and resid 733 through 739 Processing helix chain 'I' and resid 749 through 763 Processing helix chain 'J' and resid 43 through 46 No H-bonds generated for 'chain 'J' and resid 43 through 46' Processing helix chain 'J' and resid 86 through 92 removed outlier: 3.517A pdb=" N ASN J 90 " --> pdb=" O ARG J 86 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN J 91 " --> pdb=" O VAL J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 139 Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 211 through 225 removed outlier: 3.604A pdb=" N GLN J 215 " --> pdb=" O LYS J 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE J 216 " --> pdb=" O GLN J 212 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS J 217 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU J 218 " --> pdb=" O ALA J 214 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU J 222 " --> pdb=" O GLU J 218 " (cutoff:3.500A) Proline residue: J 223 - end of helix Processing helix chain 'J' and resid 227 through 230 No H-bonds generated for 'chain 'J' and resid 227 through 230' Processing helix chain 'J' and resid 251 through 260 removed outlier: 4.006A pdb=" N ALA J 255 " --> pdb=" O LYS J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 276 Processing helix chain 'J' and resid 282 through 295 removed outlier: 3.779A pdb=" N PHE J 290 " --> pdb=" O LEU J 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU J 291 " --> pdb=" O ARG J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 333 Processing helix chain 'J' and resid 350 through 352 No H-bonds generated for 'chain 'J' and resid 350 through 352' Processing helix chain 'J' and resid 355 through 358 Processing helix chain 'J' and resid 374 through 385 removed outlier: 3.594A pdb=" N GLU J 379 " --> pdb=" O THR J 375 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE J 380 " --> pdb=" O GLY J 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN J 382 " --> pdb=" O LEU J 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE J 383 " --> pdb=" O GLU J 379 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS J 384 " --> pdb=" O ILE J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 398 through 400 No H-bonds generated for 'chain 'J' and resid 398 through 400' Processing helix chain 'J' and resid 408 through 430 removed outlier: 3.625A pdb=" N SER J 416 " --> pdb=" O ALA J 412 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN J 421 " --> pdb=" O GLU J 417 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS J 426 " --> pdb=" O ALA J 422 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP J 428 " --> pdb=" O ARG J 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU J 429 " --> pdb=" O LYS J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 444 No H-bonds generated for 'chain 'J' and resid 442 through 444' Processing helix chain 'J' and resid 449 through 453 Processing helix chain 'J' and resid 455 through 458 No H-bonds generated for 'chain 'J' and resid 455 through 458' Processing helix chain 'J' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU J 488 " --> pdb=" O ASP J 484 " (cutoff:3.500A) Processing helix chain 'J' and resid 494 through 498 Processing helix chain 'J' and resid 501 through 506 Processing helix chain 'J' and resid 524 through 534 Processing helix chain 'J' and resid 544 through 553 removed outlier: 3.993A pdb=" N MET J 550 " --> pdb=" O GLU J 546 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP J 551 " --> pdb=" O LEU J 547 " (cutoff:3.500A) Processing helix chain 'J' and resid 558 through 568 Processing helix chain 'J' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE J 582 " --> pdb=" O LEU J 579 " (cutoff:3.500A) Processing helix chain 'J' and resid 599 through 609 Processing helix chain 'J' and resid 631 through 634 Processing helix chain 'J' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA J 655 " --> pdb=" O LYS J 651 " (cutoff:3.500A) Processing helix chain 'J' and resid 672 through 678 Processing helix chain 'J' and resid 684 through 706 removed outlier: 3.573A pdb=" N GLU J 706 " --> pdb=" O SER J 702 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 739 Processing helix chain 'J' and resid 749 through 763 Processing helix chain 'K' and resid 43 through 46 No H-bonds generated for 'chain 'K' and resid 43 through 46' Processing helix chain 'K' and resid 86 through 89 No H-bonds generated for 'chain 'K' and resid 86 through 89' Processing helix chain 'K' and resid 135 through 139 Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN K 215 " --> pdb=" O LYS K 211 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE K 216 " --> pdb=" O GLN K 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS K 217 " --> pdb=" O LEU K 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU K 218 " --> pdb=" O ALA K 214 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU K 222 " --> pdb=" O GLU K 218 " (cutoff:3.500A) Proline residue: K 223 - end of helix Processing helix chain 'K' and resid 227 through 230 No H-bonds generated for 'chain 'K' and resid 227 through 230' Processing helix chain 'K' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA K 255 " --> pdb=" O LYS K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 276 Processing helix chain 'K' and resid 282 through 295 removed outlier: 3.778A pdb=" N PHE K 290 " --> pdb=" O LEU K 286 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 291 " --> pdb=" O ARG K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 333 Processing helix chain 'K' and resid 350 through 352 No H-bonds generated for 'chain 'K' and resid 350 through 352' Processing helix chain 'K' and resid 355 through 358 Processing helix chain 'K' and resid 374 through 385 removed outlier: 3.594A pdb=" N GLU K 379 " --> pdb=" O THR K 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE K 380 " --> pdb=" O GLY K 376 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN K 382 " --> pdb=" O LEU K 378 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE K 383 " --> pdb=" O GLU K 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS K 384 " --> pdb=" O ILE K 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER K 416 " --> pdb=" O ALA K 412 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN K 421 " --> pdb=" O GLU K 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS K 426 " --> pdb=" O ALA K 422 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP K 428 " --> pdb=" O ARG K 424 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU K 429 " --> pdb=" O LYS K 425 " (cutoff:3.500A) Processing helix chain 'K' and resid 442 through 444 No H-bonds generated for 'chain 'K' and resid 442 through 444' Processing helix chain 'K' and resid 449 through 453 Processing helix chain 'K' and resid 455 through 458 No H-bonds generated for 'chain 'K' and resid 455 through 458' Processing helix chain 'K' and resid 483 through 490 removed outlier: 3.623A pdb=" N GLU K 488 " --> pdb=" O ASP K 484 " (cutoff:3.500A) Processing helix chain 'K' and resid 494 through 498 Processing helix chain 'K' and resid 501 through 506 Processing helix chain 'K' and resid 524 through 534 Processing helix chain 'K' and resid 544 through 553 removed outlier: 3.995A pdb=" N MET K 550 " --> pdb=" O GLU K 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP K 551 " --> pdb=" O LEU K 547 " (cutoff:3.500A) Processing helix chain 'K' and resid 558 through 568 Processing helix chain 'K' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE K 582 " --> pdb=" O LEU K 579 " (cutoff:3.500A) Processing helix chain 'K' and resid 599 through 609 Processing helix chain 'K' and resid 631 through 634 Processing helix chain 'K' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA K 655 " --> pdb=" O LYS K 651 " (cutoff:3.500A) Processing helix chain 'K' and resid 672 through 678 Processing helix chain 'K' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU K 706 " --> pdb=" O SER K 702 " (cutoff:3.500A) Processing helix chain 'K' and resid 733 through 739 Processing helix chain 'K' and resid 749 through 763 Processing helix chain 'L' and resid 43 through 46 No H-bonds generated for 'chain 'L' and resid 43 through 46' Processing helix chain 'L' and resid 86 through 89 No H-bonds generated for 'chain 'L' and resid 86 through 89' Processing helix chain 'L' and resid 135 through 139 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 211 through 225 removed outlier: 3.603A pdb=" N GLN L 215 " --> pdb=" O LYS L 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE L 216 " --> pdb=" O GLN L 212 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS L 217 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU L 218 " --> pdb=" O ALA L 214 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 227 through 230 No H-bonds generated for 'chain 'L' and resid 227 through 230' Processing helix chain 'L' and resid 251 through 260 removed outlier: 4.007A pdb=" N ALA L 255 " --> pdb=" O LYS L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 276 Processing helix chain 'L' and resid 282 through 295 removed outlier: 3.778A pdb=" N PHE L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU L 291 " --> pdb=" O ARG L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 333 Processing helix chain 'L' and resid 350 through 352 No H-bonds generated for 'chain 'L' and resid 350 through 352' Processing helix chain 'L' and resid 355 through 358 Processing helix chain 'L' and resid 374 through 385 removed outlier: 3.594A pdb=" N GLU L 379 " --> pdb=" O THR L 375 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE L 380 " --> pdb=" O GLY L 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN L 382 " --> pdb=" O LEU L 378 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE L 383 " --> pdb=" O GLU L 379 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS L 384 " --> pdb=" O ILE L 380 " (cutoff:3.500A) Processing helix chain 'L' and resid 398 through 400 No H-bonds generated for 'chain 'L' and resid 398 through 400' Processing helix chain 'L' and resid 408 through 430 removed outlier: 3.627A pdb=" N SER L 416 " --> pdb=" O ALA L 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN L 421 " --> pdb=" O GLU L 417 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS L 426 " --> pdb=" O ALA L 422 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP L 428 " --> pdb=" O ARG L 424 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU L 429 " --> pdb=" O LYS L 425 " (cutoff:3.500A) Processing helix chain 'L' and resid 442 through 444 No H-bonds generated for 'chain 'L' and resid 442 through 444' Processing helix chain 'L' and resid 449 through 453 Processing helix chain 'L' and resid 455 through 458 No H-bonds generated for 'chain 'L' and resid 455 through 458' Processing helix chain 'L' and resid 483 through 490 removed outlier: 3.621A pdb=" N GLU L 488 " --> pdb=" O ASP L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 498 Processing helix chain 'L' and resid 501 through 506 Processing helix chain 'L' and resid 524 through 534 Processing helix chain 'L' and resid 544 through 553 removed outlier: 3.994A pdb=" N MET L 550 " --> pdb=" O GLU L 546 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP L 551 " --> pdb=" O LEU L 547 " (cutoff:3.500A) Processing helix chain 'L' and resid 558 through 568 Processing helix chain 'L' and resid 579 through 586 removed outlier: 4.190A pdb=" N ILE L 582 " --> pdb=" O LEU L 579 " (cutoff:3.500A) Processing helix chain 'L' and resid 599 through 609 Processing helix chain 'L' and resid 631 through 634 Processing helix chain 'L' and resid 650 through 661 removed outlier: 3.924A pdb=" N ALA L 655 " --> pdb=" O LYS L 651 " (cutoff:3.500A) Processing helix chain 'L' and resid 672 through 678 Processing helix chain 'L' and resid 684 through 706 removed outlier: 3.574A pdb=" N GLU L 706 " --> pdb=" O SER L 702 " (cutoff:3.500A) Processing helix chain 'L' and resid 733 through 739 Processing helix chain 'L' and resid 749 through 763 Processing sheet with id= A, first strand: chain 'A' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 58 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 163 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 154 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 156 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 159 " --> pdb=" O GLY A 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 365 through 367 removed outlier: 7.134A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 643 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL B 57 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 58 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.945A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 163 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 156 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 159 " --> pdb=" O GLY B 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 365 through 367 removed outlier: 7.134A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 641 through 645 removed outlier: 4.047A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 643 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL C 57 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 58 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE C 152 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C 163 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 156 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 159 " --> pdb=" O GLY C 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 365 through 367 removed outlier: 7.133A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 643 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 66 through 70 removed outlier: 3.678A pdb=" N VAL D 57 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 58 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE D 163 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 154 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 156 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG D 159 " --> pdb=" O GLY D 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 365 through 367 removed outlier: 7.135A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 643 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E 58 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE E 152 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE E 163 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 154 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY E 156 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG E 159 " --> pdb=" O GLY E 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 365 through 367 removed outlier: 7.134A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 643 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU F 58 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE F 152 " --> pdb=" O PHE F 163 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE F 163 " --> pdb=" O PHE F 152 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 154 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL F 161 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY F 156 " --> pdb=" O ARG F 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG F 159 " --> pdb=" O GLY F 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 365 through 367 removed outlier: 7.133A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.678A pdb=" N VAL G 57 " --> pdb=" O CYS G 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU G 58 " --> pdb=" O GLN G 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN G 103 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE G 152 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE G 163 " --> pdb=" O PHE G 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL G 154 " --> pdb=" O VAL G 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL G 161 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY G 156 " --> pdb=" O ARG G 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG G 159 " --> pdb=" O GLY G 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'G' and resid 365 through 367 removed outlier: 7.135A pdb=" N ALA G 299 " --> pdb=" O ILE G 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET G 344 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE G 301 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA G 346 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE G 303 " --> pdb=" O ALA G 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE G 265 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE G 302 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE G 267 " --> pdb=" O PHE G 302 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN G 641 " --> pdb=" O GLY G 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE G 643 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE G 619 " --> pdb=" O VAL G 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE G 516 " --> pdb=" O ILE G 619 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY G 621 " --> pdb=" O PHE G 516 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY G 518 " --> pdb=" O GLY G 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR G 623 " --> pdb=" O GLY G 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE G 620 " --> pdb=" O CYS G 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU G 574 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA G 622 " --> pdb=" O LEU G 574 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE G 576 " --> pdb=" O ALA G 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN G 538 " --> pdb=" O VAL G 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE G 575 " --> pdb=" O ASN G 538 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE G 540 " --> pdb=" O PHE G 575 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL H 57 " --> pdb=" O CYS H 69 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU H 58 " --> pdb=" O GLN H 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN H 103 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE H 152 " --> pdb=" O PHE H 163 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE H 163 " --> pdb=" O PHE H 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL H 154 " --> pdb=" O VAL H 161 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL H 161 " --> pdb=" O VAL H 154 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY H 156 " --> pdb=" O ARG H 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG H 159 " --> pdb=" O GLY H 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'H' and resid 365 through 367 removed outlier: 7.134A pdb=" N ALA H 299 " --> pdb=" O ILE H 342 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET H 344 " --> pdb=" O ALA H 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE H 301 " --> pdb=" O MET H 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA H 346 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE H 303 " --> pdb=" O ALA H 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE H 265 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE H 302 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE H 267 " --> pdb=" O PHE H 302 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN H 641 " --> pdb=" O GLY H 513 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 643 " --> pdb=" O LEU H 515 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE H 619 " --> pdb=" O VAL H 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE H 516 " --> pdb=" O ILE H 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY H 621 " --> pdb=" O PHE H 516 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY H 518 " --> pdb=" O GLY H 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR H 623 " --> pdb=" O GLY H 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE H 620 " --> pdb=" O CYS H 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU H 574 " --> pdb=" O ILE H 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA H 622 " --> pdb=" O LEU H 574 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE H 576 " --> pdb=" O ALA H 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN H 538 " --> pdb=" O VAL H 573 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE H 575 " --> pdb=" O ASN H 538 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE H 540 " --> pdb=" O PHE H 575 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 66 through 70 removed outlier: 3.678A pdb=" N VAL I 57 " --> pdb=" O CYS I 69 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU I 58 " --> pdb=" O GLN I 103 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN I 103 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 151 through 156 removed outlier: 3.945A pdb=" N PHE I 152 " --> pdb=" O PHE I 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE I 163 " --> pdb=" O PHE I 152 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL I 154 " --> pdb=" O VAL I 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL I 161 " --> pdb=" O VAL I 154 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY I 156 " --> pdb=" O ARG I 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG I 159 " --> pdb=" O GLY I 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'I' and resid 365 through 367 removed outlier: 7.135A pdb=" N ALA I 299 " --> pdb=" O ILE I 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET I 344 " --> pdb=" O ALA I 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE I 301 " --> pdb=" O MET I 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA I 346 " --> pdb=" O ILE I 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE I 303 " --> pdb=" O ALA I 346 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE I 265 " --> pdb=" O ILE I 300 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE I 302 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE I 267 " --> pdb=" O PHE I 302 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN I 641 " --> pdb=" O GLY I 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE I 643 " --> pdb=" O LEU I 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE I 619 " --> pdb=" O VAL I 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE I 516 " --> pdb=" O ILE I 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY I 621 " --> pdb=" O PHE I 516 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY I 518 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR I 623 " --> pdb=" O GLY I 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE I 620 " --> pdb=" O CYS I 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU I 574 " --> pdb=" O ILE I 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA I 622 " --> pdb=" O LEU I 574 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE I 576 " --> pdb=" O ALA I 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN I 538 " --> pdb=" O VAL I 573 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE I 575 " --> pdb=" O ASN I 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE I 540 " --> pdb=" O PHE I 575 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'J' and resid 66 through 70 removed outlier: 3.678A pdb=" N VAL J 57 " --> pdb=" O CYS J 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU J 58 " --> pdb=" O GLN J 103 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN J 103 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'J' and resid 151 through 156 removed outlier: 3.944A pdb=" N PHE J 152 " --> pdb=" O PHE J 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE J 163 " --> pdb=" O PHE J 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL J 154 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL J 161 " --> pdb=" O VAL J 154 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY J 156 " --> pdb=" O ARG J 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG J 159 " --> pdb=" O GLY J 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'J' and resid 365 through 367 removed outlier: 7.135A pdb=" N ALA J 299 " --> pdb=" O ILE J 342 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N MET J 344 " --> pdb=" O ALA J 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE J 301 " --> pdb=" O MET J 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA J 346 " --> pdb=" O ILE J 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE J 303 " --> pdb=" O ALA J 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE J 265 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE J 302 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE J 267 " --> pdb=" O PHE J 302 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'J' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN J 641 " --> pdb=" O GLY J 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE J 643 " --> pdb=" O LEU J 515 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE J 619 " --> pdb=" O VAL J 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE J 516 " --> pdb=" O ILE J 619 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY J 621 " --> pdb=" O PHE J 516 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY J 518 " --> pdb=" O GLY J 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR J 623 " --> pdb=" O GLY J 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE J 620 " --> pdb=" O CYS J 572 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU J 574 " --> pdb=" O ILE J 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA J 622 " --> pdb=" O LEU J 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE J 576 " --> pdb=" O ALA J 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN J 538 " --> pdb=" O VAL J 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE J 575 " --> pdb=" O ASN J 538 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE J 540 " --> pdb=" O PHE J 575 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'K' and resid 66 through 70 removed outlier: 3.678A pdb=" N VAL K 57 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU K 58 " --> pdb=" O GLN K 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN K 103 " --> pdb=" O LEU K 58 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'K' and resid 151 through 156 removed outlier: 3.945A pdb=" N PHE K 152 " --> pdb=" O PHE K 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE K 163 " --> pdb=" O PHE K 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL K 154 " --> pdb=" O VAL K 161 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL K 161 " --> pdb=" O VAL K 154 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY K 156 " --> pdb=" O ARG K 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG K 159 " --> pdb=" O GLY K 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'K' and resid 365 through 367 removed outlier: 7.134A pdb=" N ALA K 299 " --> pdb=" O ILE K 342 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N MET K 344 " --> pdb=" O ALA K 299 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE K 301 " --> pdb=" O MET K 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA K 346 " --> pdb=" O ILE K 301 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE K 303 " --> pdb=" O ALA K 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE K 265 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE K 302 " --> pdb=" O PHE K 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE K 267 " --> pdb=" O PHE K 302 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN K 641 " --> pdb=" O GLY K 513 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE K 643 " --> pdb=" O LEU K 515 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE K 619 " --> pdb=" O VAL K 514 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE K 516 " --> pdb=" O ILE K 619 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY K 621 " --> pdb=" O PHE K 516 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLY K 518 " --> pdb=" O GLY K 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR K 623 " --> pdb=" O GLY K 518 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ILE K 620 " --> pdb=" O CYS K 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU K 574 " --> pdb=" O ILE K 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA K 622 " --> pdb=" O LEU K 574 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE K 576 " --> pdb=" O ALA K 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN K 538 " --> pdb=" O VAL K 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE K 575 " --> pdb=" O ASN K 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE K 540 " --> pdb=" O PHE K 575 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'L' and resid 66 through 70 removed outlier: 3.679A pdb=" N VAL L 57 " --> pdb=" O CYS L 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU L 58 " --> pdb=" O GLN L 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN L 103 " --> pdb=" O LEU L 58 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'L' and resid 151 through 156 removed outlier: 3.945A pdb=" N PHE L 152 " --> pdb=" O PHE L 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE L 163 " --> pdb=" O PHE L 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL L 154 " --> pdb=" O VAL L 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL L 161 " --> pdb=" O VAL L 154 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY L 156 " --> pdb=" O ARG L 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG L 159 " --> pdb=" O GLY L 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'L' and resid 365 through 367 removed outlier: 7.135A pdb=" N ALA L 299 " --> pdb=" O ILE L 342 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET L 344 " --> pdb=" O ALA L 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE L 301 " --> pdb=" O MET L 344 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA L 346 " --> pdb=" O ILE L 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE L 303 " --> pdb=" O ALA L 346 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N PHE L 265 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE L 302 " --> pdb=" O PHE L 265 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE L 267 " --> pdb=" O PHE L 302 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 641 through 645 removed outlier: 4.046A pdb=" N GLN L 641 " --> pdb=" O GLY L 513 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE L 643 " --> pdb=" O LEU L 515 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE L 619 " --> pdb=" O VAL L 514 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE L 516 " --> pdb=" O ILE L 619 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY L 621 " --> pdb=" O PHE L 516 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY L 518 " --> pdb=" O GLY L 621 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR L 623 " --> pdb=" O GLY L 518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE L 620 " --> pdb=" O CYS L 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU L 574 " --> pdb=" O ILE L 620 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA L 622 " --> pdb=" O LEU L 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE L 576 " --> pdb=" O ALA L 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN L 538 " --> pdb=" O VAL L 573 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE L 575 " --> pdb=" O ASN L 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE L 540 " --> pdb=" O PHE L 575 " (cutoff:3.500A) 1649 hydrogen bonds defined for protein. 4695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.14 Time building geometry restraints manager: 22.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 12204 1.31 - 1.44: 16656 1.44 - 1.56: 41477 1.56 - 1.69: 79 1.69 - 1.82: 576 Bond restraints: 70992 Sorted by residual: bond pdb=" C02 JDP J 901 " pdb=" N31 JDP J 901 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C02 JDP A 901 " pdb=" N31 JDP A 901 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C02 JDP F 901 " pdb=" N31 JDP F 901 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C02 JDP D 901 " pdb=" N31 JDP D 901 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C02 JDP I 901 " pdb=" N31 JDP I 901 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.86e+01 ... (remaining 70987 not shown) Histogram of bond angle deviations from ideal: 99.36 - 109.72: 8120 109.72 - 120.08: 58444 120.08 - 130.45: 29172 130.45 - 140.81: 204 140.81 - 151.17: 12 Bond angle restraints: 95952 Sorted by residual: angle pdb=" C11 JDP A 901 " pdb=" C10 JDP A 901 " pdb=" N12 JDP A 901 " ideal model delta sigma weight residual 124.18 151.17 -26.99 3.00e+00 1.11e-01 8.10e+01 angle pdb=" C11 JDP I 901 " pdb=" C10 JDP I 901 " pdb=" N12 JDP I 901 " ideal model delta sigma weight residual 124.18 151.17 -26.99 3.00e+00 1.11e-01 8.09e+01 angle pdb=" C11 JDP K 901 " pdb=" C10 JDP K 901 " pdb=" N12 JDP K 901 " ideal model delta sigma weight residual 124.18 151.13 -26.95 3.00e+00 1.11e-01 8.07e+01 angle pdb=" C11 JDP J 901 " pdb=" C10 JDP J 901 " pdb=" N12 JDP J 901 " ideal model delta sigma weight residual 124.18 151.12 -26.94 3.00e+00 1.11e-01 8.06e+01 angle pdb=" C11 JDP H 901 " pdb=" C10 JDP H 901 " pdb=" N12 JDP H 901 " ideal model delta sigma weight residual 124.18 151.11 -26.93 3.00e+00 1.11e-01 8.06e+01 ... (remaining 95947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.18: 40958 27.18 - 54.36: 2630 54.36 - 81.54: 182 81.54 - 108.72: 60 108.72 - 135.89: 30 Dihedral angle restraints: 43860 sinusoidal: 18492 harmonic: 25368 Sorted by residual: dihedral pdb=" CA GLN K 760 " pdb=" C GLN K 760 " pdb=" N THR K 761 " pdb=" CA THR K 761 " ideal model delta harmonic sigma weight residual 180.00 147.20 32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA GLN J 760 " pdb=" C GLN J 760 " pdb=" N THR J 761 " pdb=" CA THR J 761 " ideal model delta harmonic sigma weight residual 180.00 147.25 32.75 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA GLN C 760 " pdb=" C GLN C 760 " pdb=" N THR C 761 " pdb=" CA THR C 761 " ideal model delta harmonic sigma weight residual 180.00 147.25 32.75 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 43857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 8686 0.058 - 0.117: 1832 0.117 - 0.175: 150 0.175 - 0.234: 12 0.234 - 0.292: 24 Chirality restraints: 10704 Sorted by residual: chirality pdb=" CA GLN A 760 " pdb=" N GLN A 760 " pdb=" C GLN A 760 " pdb=" CB GLN A 760 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLN G 760 " pdb=" N GLN G 760 " pdb=" C GLN G 760 " pdb=" CB GLN G 760 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLN I 760 " pdb=" N GLN I 760 " pdb=" C GLN I 760 " pdb=" CB GLN I 760 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 10701 not shown) Planarity restraints: 12636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 349 " 0.295 9.50e-02 1.11e+02 1.32e-01 1.11e+01 pdb=" NE ARG H 349 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG H 349 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG H 349 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 349 " 0.295 9.50e-02 1.11e+02 1.32e-01 1.11e+01 pdb=" NE ARG D 349 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 349 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 349 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 349 " 0.294 9.50e-02 1.11e+02 1.32e-01 1.10e+01 pdb=" NE ARG I 349 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG I 349 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG I 349 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG I 349 " 0.014 2.00e-02 2.50e+03 ... (remaining 12633 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 85 2.17 - 2.85: 24284 2.85 - 3.53: 100252 3.53 - 4.22: 166203 4.22 - 4.90: 274875 Nonbonded interactions: 565699 Sorted by model distance: nonbonded pdb=" NE2 GLN B 760 " pdb=" NE2 GLN J 760 " model vdw 1.481 3.200 nonbonded pdb=" NE2 GLN A 760 " pdb=" NE2 GLN K 760 " model vdw 1.609 3.200 nonbonded pdb=" NE2 GLN E 760 " pdb=" NE2 GLN G 760 " model vdw 1.724 3.200 nonbonded pdb=" NE2 GLN D 760 " pdb=" NE2 GLN H 760 " model vdw 1.745 3.200 nonbonded pdb=" NE2 GLN C 760 " pdb=" NE2 GLN I 760 " model vdw 1.757 3.200 ... (remaining 565694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.310 Construct map_model_manager: 0.060 Extract box with map and model: 15.150 Check model and map are aligned: 0.760 Set scattering table: 0.450 Process input model: 134.860 Find NCS groups from input model: 3.950 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.005 0.107 70992 Z= 0.305 Angle : 0.952 26.994 95952 Z= 0.474 Chirality : 0.048 0.292 10704 Planarity : 0.006 0.132 12636 Dihedral : 16.841 135.895 27420 Min Nonbonded Distance : 1.481 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.32 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 24.47 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.09), residues: 8772 helix: -0.62 (0.09), residues: 3168 sheet: 0.11 (0.21), residues: 720 loop : -1.53 (0.09), residues: 4884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 551 HIS 0.010 0.001 HIS B 340 PHE 0.027 0.001 PHE F 516 TYR 0.021 0.002 TYR B 138 ARG 0.010 0.001 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 5.808 Fit side-chains REVERT: B 757 MET cc_start: 0.8025 (mtp) cc_final: 0.7585 (mmp) REVERT: C 45 LYS cc_start: 0.7405 (mmmt) cc_final: 0.6805 (mmmm) REVERT: C 138 TYR cc_start: 0.7759 (p90) cc_final: 0.7512 (p90) REVERT: E 138 TYR cc_start: 0.7740 (p90) cc_final: 0.7482 (p90) REVERT: E 757 MET cc_start: 0.7987 (mtp) cc_final: 0.7739 (mmp) REVERT: F 45 LYS cc_start: 0.7398 (mmmt) cc_final: 0.6875 (mmtp) REVERT: F 138 TYR cc_start: 0.7848 (p90) cc_final: 0.7503 (p90) REVERT: F 387 ASN cc_start: 0.8117 (p0) cc_final: 0.7416 (p0) REVERT: G 45 LYS cc_start: 0.7579 (mmmt) cc_final: 0.6975 (mmtp) REVERT: H 275 MET cc_start: 0.8649 (mpt) cc_final: 0.8291 (mmm) REVERT: J 46 MET cc_start: 0.7091 (pmm) cc_final: 0.6788 (pmm) REVERT: J 757 MET cc_start: 0.8033 (mtp) cc_final: 0.7794 (mmp) REVERT: K 45 LYS cc_start: 0.7574 (mmmt) cc_final: 0.6950 (mmtp) REVERT: K 138 TYR cc_start: 0.7838 (p90) cc_final: 0.7537 (p90) REVERT: K 757 MET cc_start: 0.8093 (mtp) cc_final: 0.7807 (mmp) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.6135 time to fit residues: 464.8718 Evaluate side-chains 391 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 5.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 739 optimal weight: 6.9990 chunk 663 optimal weight: 3.9990 chunk 368 optimal weight: 30.0000 chunk 226 optimal weight: 20.0000 chunk 447 optimal weight: 30.0000 chunk 354 optimal weight: 2.9990 chunk 686 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 chunk 417 optimal weight: 4.9990 chunk 511 optimal weight: 20.0000 chunk 795 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 215 GLN A 285 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN A 602 ASN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 215 GLN B 285 ASN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN B 602 ASN ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 GLN C 43 GLN C 215 GLN C 285 ASN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN D 215 GLN D 285 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN F 285 ASN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 401 ASN G 602 ASN ** G 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 764 GLN H 215 GLN H 285 ASN H 327 GLN ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 401 ASN ** H 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN I 215 GLN I 285 ASN I 327 GLN ** I 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN ** I 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN J 215 GLN ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 401 ASN J 602 ASN ** J 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN K 215 GLN K 285 ASN ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 ASN K 602 ASN ** K 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 215 GLN L 285 ASN ** L 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 401 ASN ** L 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 70992 Z= 0.502 Angle : 0.780 10.457 95952 Z= 0.385 Chirality : 0.052 0.297 10704 Planarity : 0.006 0.063 12636 Dihedral : 11.503 140.551 9852 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.38 % Favored : 94.32 % Rotamer: Outliers : 5.31 % Allowed : 19.61 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.75 (0.09), residues: 8772 helix: -1.01 (0.08), residues: 3576 sheet: -0.22 (0.17), residues: 936 loop : -1.44 (0.09), residues: 4260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 551 HIS 0.013 0.002 HIS C 384 PHE 0.045 0.003 PHE F 516 TYR 0.065 0.004 TYR J 138 ARG 0.007 0.001 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 398 poor density : 430 time to evaluate : 5.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7967 (pt) REVERT: A 268 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9421 (tm) REVERT: A 286 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9124 (pt) REVERT: B 458 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8060 (pp30) REVERT: B 578 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8554 (pt0) REVERT: C 58 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8210 (pt) REVERT: C 84 MET cc_start: 0.7387 (tpt) cc_final: 0.7139 (tpt) REVERT: C 148 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6066 (mmtm) REVERT: C 275 MET cc_start: 0.9047 (mmm) cc_final: 0.8788 (mmm) REVERT: C 387 ASN cc_start: 0.8209 (p0) cc_final: 0.7926 (p0) REVERT: C 460 ASN cc_start: 0.8637 (t0) cc_final: 0.8329 (t0) REVERT: D 58 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7901 (pt) REVERT: D 158 MET cc_start: 0.7244 (tpp) cc_final: 0.5802 (tpt) REVERT: D 211 LYS cc_start: 0.8740 (tmtm) cc_final: 0.8418 (tptp) REVERT: D 268 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9417 (tm) REVERT: D 286 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9137 (pt) REVERT: E 45 LYS cc_start: 0.7739 (mmmt) cc_final: 0.7059 (mmtm) REVERT: E 46 MET cc_start: 0.7982 (pmm) cc_final: 0.7748 (pmm) REVERT: E 58 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8076 (pt) REVERT: E 332 MET cc_start: 0.8902 (ttp) cc_final: 0.8682 (mtp) REVERT: E 458 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7715 (pp30) REVERT: E 578 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8532 (pt0) REVERT: F 84 MET cc_start: 0.7048 (tpt) cc_final: 0.6726 (tpt) REVERT: F 139 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: F 148 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6150 (mmtm) REVERT: F 427 MET cc_start: 0.6068 (mmm) cc_final: 0.5813 (ttm) REVERT: G 268 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9410 (tm) REVERT: G 286 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9168 (pt) REVERT: H 58 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8076 (pt) REVERT: H 578 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8500 (pt0) REVERT: I 58 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8147 (pt) REVERT: I 148 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.5886 (mmtm) REVERT: I 158 MET cc_start: 0.7111 (tpp) cc_final: 0.6159 (tpt) REVERT: J 46 MET cc_start: 0.7398 (pmm) cc_final: 0.7043 (pmm) REVERT: J 58 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7905 (pt) REVERT: J 84 MET cc_start: 0.6798 (tpt) cc_final: 0.6579 (tpt) REVERT: J 211 LYS cc_start: 0.8731 (tmtm) cc_final: 0.8441 (tptp) REVERT: J 286 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9167 (pt) REVERT: J 458 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8109 (pm20) REVERT: K 148 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6058 (mmtm) REVERT: K 427 MET cc_start: 0.6482 (mmm) cc_final: 0.6173 (ttt) REVERT: K 460 ASN cc_start: 0.8376 (t0) cc_final: 0.8168 (t0) REVERT: K 578 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8542 (pt0) REVERT: L 58 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8171 (pt) REVERT: L 84 MET cc_start: 0.7352 (tpt) cc_final: 0.7129 (tpt) REVERT: L 387 ASN cc_start: 0.8277 (p0) cc_final: 0.7900 (p0) outliers start: 398 outliers final: 132 residues processed: 808 average time/residue: 0.6638 time to fit residues: 925.6827 Evaluate side-chains 513 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 354 time to evaluate : 5.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 313 ARG Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 139 PHE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 458 GLN Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 558 ASN Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 215 GLN Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 221 GLU Chi-restraints excluded: chain H residue 313 ARG Chi-restraints excluded: chain H residue 464 LEU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 484 ASP Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 578 GLU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 313 ARG Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 458 GLN Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 484 ASP Chi-restraints excluded: chain I residue 515 LEU Chi-restraints excluded: chain I residue 558 ASN Chi-restraints excluded: chain I residue 578 GLU Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 148 LYS Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 221 GLU Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain J residue 313 ARG Chi-restraints excluded: chain J residue 458 GLN Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 484 ASP Chi-restraints excluded: chain J residue 515 LEU Chi-restraints excluded: chain J residue 578 GLU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 LYS Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 464 LEU Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 484 ASP Chi-restraints excluded: chain K residue 515 LEU Chi-restraints excluded: chain K residue 550 MET Chi-restraints excluded: chain K residue 578 GLU Chi-restraints excluded: chain K residue 611 MET Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 146 ILE Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 221 GLU Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 313 ARG Chi-restraints excluded: chain L residue 381 LEU Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 458 GLN Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 484 ASP Chi-restraints excluded: chain L residue 515 LEU Chi-restraints excluded: chain L residue 558 ASN Chi-restraints excluded: chain L residue 578 GLU Chi-restraints excluded: chain L residue 640 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 442 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 662 optimal weight: 20.0000 chunk 541 optimal weight: 2.9990 chunk 219 optimal weight: 30.0000 chunk 796 optimal weight: 0.9980 chunk 860 optimal weight: 9.9990 chunk 709 optimal weight: 0.6980 chunk 790 optimal weight: 0.8980 chunk 271 optimal weight: 0.6980 chunk 639 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 624 ASN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 337 GLN ** C 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 337 GLN G 43 GLN G 285 ASN ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN G 624 ASN ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 337 GLN ** I 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN K 285 ASN ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 602 ASN ** K 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN L 337 GLN L 533 ASN L 624 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 70992 Z= 0.196 Angle : 0.613 9.451 95952 Z= 0.286 Chirality : 0.046 0.291 10704 Planarity : 0.004 0.072 12636 Dihedral : 11.323 134.553 9852 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.41 % Favored : 95.31 % Rotamer: Outliers : 3.29 % Allowed : 21.79 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -1.34 (0.09), residues: 8772 helix: -0.61 (0.09), residues: 3492 sheet: -0.09 (0.18), residues: 936 loop : -1.25 (0.09), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 454 HIS 0.008 0.001 HIS B 340 PHE 0.032 0.001 PHE B 516 TYR 0.026 0.002 TYR L 138 ARG 0.005 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 394 time to evaluate : 5.905 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: A 58 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7986 (pt) REVERT: A 158 MET cc_start: 0.7305 (tpt) cc_final: 0.6140 (tpt) REVERT: A 218 GLU cc_start: 0.8756 (pp20) cc_final: 0.8087 (pp20) REVERT: A 268 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9409 (tm) REVERT: B 84 MET cc_start: 0.7458 (tpt) cc_final: 0.7206 (tpp) REVERT: B 138 TYR cc_start: 0.7536 (p90) cc_final: 0.6885 (p90) REVERT: B 217 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8995 (mmtp) REVERT: B 420 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8946 (mm) REVERT: B 508 MET cc_start: 0.8697 (ttt) cc_final: 0.8487 (ttt) REVERT: C 58 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8266 (pt) REVERT: C 84 MET cc_start: 0.7264 (tpt) cc_final: 0.6987 (tpt) REVERT: C 138 TYR cc_start: 0.7082 (p90) cc_final: 0.6820 (p90) REVERT: C 148 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6526 (mmtm) REVERT: C 275 MET cc_start: 0.9037 (mmm) cc_final: 0.8780 (mmm) REVERT: C 387 ASN cc_start: 0.8102 (p0) cc_final: 0.7842 (p0) REVERT: C 460 ASN cc_start: 0.8618 (t0) cc_final: 0.8340 (t0) REVERT: D 58 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7981 (pt) REVERT: D 84 MET cc_start: 0.6866 (tpt) cc_final: 0.6454 (tpp) REVERT: D 148 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.5446 (mptt) REVERT: D 211 LYS cc_start: 0.8753 (tmtm) cc_final: 0.8422 (tptp) REVERT: E 45 LYS cc_start: 0.7651 (mmmt) cc_final: 0.6955 (mmtp) REVERT: E 46 MET cc_start: 0.7937 (pmm) cc_final: 0.7732 (pmm) REVERT: E 84 MET cc_start: 0.6957 (tpt) cc_final: 0.6729 (tpt) REVERT: E 158 MET cc_start: 0.7273 (tpp) cc_final: 0.6591 (tpp) REVERT: E 420 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8876 (mm) REVERT: F 138 TYR cc_start: 0.7395 (p90) cc_final: 0.6833 (p90) REVERT: F 139 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: F 148 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6085 (mmtm) REVERT: F 211 LYS cc_start: 0.8738 (tptp) cc_final: 0.8535 (tptp) REVERT: F 427 MET cc_start: 0.5999 (mmm) cc_final: 0.5788 (ttm) REVERT: G 158 MET cc_start: 0.7108 (tpt) cc_final: 0.6126 (tpt) REVERT: H 46 MET cc_start: 0.7942 (pmm) cc_final: 0.7726 (pmm) REVERT: H 58 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8090 (pt) REVERT: H 84 MET cc_start: 0.7377 (tpt) cc_final: 0.6939 (tpp) REVERT: H 138 TYR cc_start: 0.6961 (p90) cc_final: 0.6714 (p90) REVERT: H 420 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8906 (mm) REVERT: I 58 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8148 (pt) REVERT: I 387 ASN cc_start: 0.7977 (p0) cc_final: 0.7598 (p0) REVERT: J 46 MET cc_start: 0.7550 (pmm) cc_final: 0.7152 (pmm) REVERT: J 58 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7882 (pt) REVERT: J 84 MET cc_start: 0.6852 (tpt) cc_final: 0.6570 (tpt) REVERT: J 148 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.5327 (mptt) REVERT: J 211 LYS cc_start: 0.8730 (tmtm) cc_final: 0.8383 (tptp) REVERT: J 286 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9111 (pt) REVERT: K 84 MET cc_start: 0.7021 (tpt) cc_final: 0.6770 (tpt) REVERT: K 148 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.5969 (mmtm) REVERT: L 58 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8201 (pt) REVERT: L 84 MET cc_start: 0.7232 (tpt) cc_final: 0.6965 (tpt) REVERT: L 275 MET cc_start: 0.9021 (mmm) cc_final: 0.8749 (mmm) REVERT: L 387 ASN cc_start: 0.8049 (p0) cc_final: 0.7598 (p0) REVERT: L 460 ASN cc_start: 0.8640 (t0) cc_final: 0.8381 (t0) outliers start: 247 outliers final: 88 residues processed: 618 average time/residue: 0.6361 time to fit residues: 678.2599 Evaluate side-chains 459 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 352 time to evaluate : 5.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 139 PHE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 464 LEU Chi-restraints excluded: chain G residue 550 MET Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 221 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 332 MET Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 550 MET Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 148 LYS Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 221 GLU Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 448 THR Chi-restraints excluded: chain J residue 550 MET Chi-restraints excluded: chain K residue 148 LYS Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 221 GLU Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 640 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 787 optimal weight: 20.0000 chunk 599 optimal weight: 10.0000 chunk 413 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 380 optimal weight: 40.0000 chunk 535 optimal weight: 3.9990 chunk 799 optimal weight: 0.4980 chunk 846 optimal weight: 9.9990 chunk 417 optimal weight: 0.5980 chunk 758 optimal weight: 0.0270 chunk 228 optimal weight: 8.9990 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 215 GLN ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 70992 Z= 0.200 Angle : 0.579 11.715 95952 Z= 0.270 Chirality : 0.045 0.291 10704 Planarity : 0.004 0.064 12636 Dihedral : 11.257 133.384 9852 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.12 % Favored : 95.61 % Rotamer: Outliers : 3.25 % Allowed : 22.49 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -1.08 (0.09), residues: 8772 helix: -0.39 (0.09), residues: 3552 sheet: 0.07 (0.18), residues: 924 loop : -1.11 (0.09), residues: 4296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 551 HIS 0.006 0.001 HIS B 340 PHE 0.029 0.001 PHE B 516 TYR 0.020 0.002 TYR E 134 ARG 0.005 0.000 ARG J 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 382 time to evaluate : 5.941 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: A 158 MET cc_start: 0.7381 (tpt) cc_final: 0.6319 (tpt) REVERT: B 291 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8334 (pm20) REVERT: B 420 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8905 (mm) REVERT: B 508 MET cc_start: 0.8711 (ttt) cc_final: 0.8503 (ttt) REVERT: C 58 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8299 (pt) REVERT: C 138 TYR cc_start: 0.6975 (p90) cc_final: 0.6675 (p90) REVERT: C 275 MET cc_start: 0.9029 (mmm) cc_final: 0.8743 (mmm) REVERT: C 460 ASN cc_start: 0.8649 (t0) cc_final: 0.8388 (t0) REVERT: D 58 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7987 (pt) REVERT: D 148 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.5499 (mptt) REVERT: D 158 MET cc_start: 0.7664 (tpp) cc_final: 0.7099 (tpt) REVERT: D 211 LYS cc_start: 0.8751 (tmtm) cc_final: 0.8431 (tptp) REVERT: D 291 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: D 558 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8159 (m-40) REVERT: E 45 LYS cc_start: 0.7650 (mmmt) cc_final: 0.6971 (mmtm) REVERT: E 46 MET cc_start: 0.7994 (pmm) cc_final: 0.7781 (pmm) REVERT: E 84 MET cc_start: 0.6699 (tpt) cc_final: 0.6417 (tpp) REVERT: E 148 LYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6161 (mmtm) REVERT: E 420 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8849 (mm) REVERT: F 84 MET cc_start: 0.6764 (tpt) cc_final: 0.6347 (tpp) REVERT: F 139 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: F 148 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6142 (mmtm) REVERT: F 158 MET cc_start: 0.7204 (tpt) cc_final: 0.6717 (tpt) REVERT: F 211 LYS cc_start: 0.8685 (tptp) cc_final: 0.8454 (tptp) REVERT: F 427 MET cc_start: 0.6058 (mmm) cc_final: 0.5837 (tpp) REVERT: G 211 LYS cc_start: 0.8703 (tmtm) cc_final: 0.8410 (tptp) REVERT: G 291 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: G 449 MET cc_start: 0.8150 (tpp) cc_final: 0.7848 (tpp) REVERT: G 561 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: H 46 MET cc_start: 0.7956 (pmm) cc_final: 0.7735 (pmm) REVERT: H 84 MET cc_start: 0.7124 (tpt) cc_final: 0.6642 (tpp) REVERT: H 138 TYR cc_start: 0.7105 (p90) cc_final: 0.6840 (p90) REVERT: H 148 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6109 (mmtm) REVERT: H 217 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8456 (mmmt) REVERT: H 420 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8830 (mm) REVERT: I 58 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8174 (pt) REVERT: I 84 MET cc_start: 0.7181 (tpt) cc_final: 0.6888 (tpp) REVERT: I 387 ASN cc_start: 0.8001 (p0) cc_final: 0.7694 (p0) REVERT: J 46 MET cc_start: 0.7602 (pmm) cc_final: 0.7141 (pmm) REVERT: J 58 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7971 (pt) REVERT: J 138 TYR cc_start: 0.6997 (p90) cc_final: 0.6763 (p90) REVERT: J 148 LYS cc_start: 0.6521 (OUTLIER) cc_final: 0.5850 (mmtm) REVERT: J 158 MET cc_start: 0.6722 (tpt) cc_final: 0.5836 (tpt) REVERT: J 211 LYS cc_start: 0.8740 (tmtm) cc_final: 0.8387 (tptp) REVERT: J 286 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9130 (pt) REVERT: J 388 MET cc_start: 0.8062 (mmm) cc_final: 0.7728 (mtm) REVERT: K 84 MET cc_start: 0.6871 (tpt) cc_final: 0.6568 (tpp) REVERT: K 148 LYS cc_start: 0.6770 (OUTLIER) cc_final: 0.6237 (mmtm) REVERT: L 58 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8197 (pt) REVERT: L 84 MET cc_start: 0.7091 (tpt) cc_final: 0.6669 (tpp) REVERT: L 218 GLU cc_start: 0.8653 (pp20) cc_final: 0.8062 (pp20) REVERT: L 387 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7855 (p0) outliers start: 244 outliers final: 139 residues processed: 596 average time/residue: 0.6262 time to fit residues: 646.0612 Evaluate side-chains 507 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 345 time to evaluate : 5.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 139 PHE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 464 LEU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 550 MET Chi-restraints excluded: chain G residue 561 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 382 GLN Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 464 LEU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 515 LEU Chi-restraints excluded: chain I residue 550 MET Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 148 LYS Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 221 GLU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain J residue 291 GLU Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain K residue 148 LYS Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 291 GLU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 382 GLN Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 515 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 221 GLU Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 387 ASN Chi-restraints excluded: chain L residue 388 MET Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 515 LEU Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 640 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 705 optimal weight: 0.9990 chunk 480 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 630 optimal weight: 0.9980 chunk 349 optimal weight: 8.9990 chunk 722 optimal weight: 2.9990 chunk 585 optimal weight: 0.0270 chunk 1 optimal weight: 30.0000 chunk 432 optimal weight: 4.9990 chunk 760 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 602 ASN G 285 ASN ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 602 ASN ** H 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 ASN ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 602 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 70992 Z= 0.168 Angle : 0.581 12.950 95952 Z= 0.266 Chirality : 0.045 0.293 10704 Planarity : 0.004 0.063 12636 Dihedral : 11.150 131.224 9852 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.02 % Favored : 95.70 % Rotamer: Outliers : 2.95 % Allowed : 22.97 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.93 (0.09), residues: 8772 helix: -0.26 (0.09), residues: 3552 sheet: 0.10 (0.18), residues: 924 loop : -1.02 (0.10), residues: 4296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 551 HIS 0.008 0.001 HIS E 340 PHE 0.025 0.001 PHE B 516 TYR 0.019 0.001 TYR A 134 ARG 0.006 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 365 time to evaluate : 6.020 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: A 158 MET cc_start: 0.7399 (tpt) cc_final: 0.6293 (tpt) REVERT: A 211 LYS cc_start: 0.8704 (tmtm) cc_final: 0.8429 (tptp) REVERT: A 388 MET cc_start: 0.9035 (ptp) cc_final: 0.8827 (ptp) REVERT: B 420 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8889 (mm) REVERT: B 578 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8484 (pt0) REVERT: C 58 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8261 (pt) REVERT: C 84 MET cc_start: 0.7022 (tpt) cc_final: 0.6566 (tpp) REVERT: C 138 TYR cc_start: 0.7018 (p90) cc_final: 0.6793 (p90) REVERT: C 148 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6049 (mmtm) REVERT: C 275 MET cc_start: 0.9032 (mmm) cc_final: 0.8768 (mmm) REVERT: C 460 ASN cc_start: 0.8647 (t0) cc_final: 0.8433 (t0) REVERT: D 58 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7977 (pt) REVERT: D 84 MET cc_start: 0.6757 (tpt) cc_final: 0.6461 (tpp) REVERT: D 148 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.5846 (mmtm) REVERT: D 158 MET cc_start: 0.7636 (tpp) cc_final: 0.7089 (tpt) REVERT: D 211 LYS cc_start: 0.8748 (tmtm) cc_final: 0.8434 (tptp) REVERT: D 420 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8927 (mm) REVERT: E 45 LYS cc_start: 0.7655 (mmmt) cc_final: 0.6993 (mmtm) REVERT: E 46 MET cc_start: 0.8006 (pmm) cc_final: 0.7804 (pmm) REVERT: E 84 MET cc_start: 0.6755 (tpt) cc_final: 0.6512 (tpp) REVERT: E 148 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6168 (mmtm) REVERT: E 420 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8802 (mm) REVERT: E 578 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8445 (pt0) REVERT: F 84 MET cc_start: 0.6913 (tpt) cc_final: 0.6488 (tpp) REVERT: F 139 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: F 148 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6141 (mmtm) REVERT: F 158 MET cc_start: 0.7310 (tpt) cc_final: 0.6832 (tpt) REVERT: F 211 LYS cc_start: 0.8670 (tptp) cc_final: 0.8458 (tptp) REVERT: F 388 MET cc_start: 0.9132 (ptp) cc_final: 0.8866 (ptp) REVERT: F 678 MET cc_start: 0.9164 (mmp) cc_final: 0.8926 (mmp) REVERT: G 148 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.5946 (mmtm) REVERT: G 211 LYS cc_start: 0.8694 (tmtm) cc_final: 0.8372 (tptp) REVERT: H 46 MET cc_start: 0.8003 (pmm) cc_final: 0.7787 (pmm) REVERT: H 84 MET cc_start: 0.7126 (tpt) cc_final: 0.6694 (tpp) REVERT: H 138 TYR cc_start: 0.7070 (p90) cc_final: 0.6829 (p90) REVERT: H 148 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6090 (mmtm) REVERT: H 420 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8837 (mm) REVERT: I 58 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8153 (pt) REVERT: I 84 MET cc_start: 0.7134 (tpt) cc_final: 0.6916 (tpp) REVERT: I 134 TYR cc_start: 0.8405 (m-80) cc_final: 0.7982 (m-80) REVERT: I 138 TYR cc_start: 0.7280 (p90) cc_final: 0.7014 (p90) REVERT: I 148 LYS cc_start: 0.6471 (OUTLIER) cc_final: 0.5858 (mmtm) REVERT: I 387 ASN cc_start: 0.8038 (p0) cc_final: 0.7757 (p0) REVERT: J 46 MET cc_start: 0.7571 (pmm) cc_final: 0.7166 (pmm) REVERT: J 84 MET cc_start: 0.6718 (tpt) cc_final: 0.6422 (tpp) REVERT: J 138 TYR cc_start: 0.6884 (p90) cc_final: 0.6679 (p90) REVERT: J 158 MET cc_start: 0.6556 (tpt) cc_final: 0.6167 (tpt) REVERT: J 211 LYS cc_start: 0.8721 (tmtm) cc_final: 0.8372 (tptp) REVERT: J 286 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9130 (pt) REVERT: K 84 MET cc_start: 0.6962 (tpt) cc_final: 0.6688 (tpp) REVERT: K 148 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.5997 (mmtm) REVERT: K 578 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8465 (pt0) REVERT: L 58 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8188 (pt) REVERT: L 84 MET cc_start: 0.6975 (tpt) cc_final: 0.6612 (tpp) REVERT: L 218 GLU cc_start: 0.8631 (pp20) cc_final: 0.8075 (pp20) REVERT: L 387 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7718 (p0) outliers start: 221 outliers final: 117 residues processed: 564 average time/residue: 0.6356 time to fit residues: 621.5105 Evaluate side-chains 482 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 343 time to evaluate : 5.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 139 PHE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 464 LEU Chi-restraints excluded: chain G residue 550 MET Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 382 GLN Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 550 MET Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 550 MET Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 148 LYS Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 221 GLU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 515 LEU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 515 LEU Chi-restraints excluded: chain K residue 578 GLU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 221 GLU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 387 ASN Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 578 GLU Chi-restraints excluded: chain L residue 640 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 284 optimal weight: 3.9990 chunk 762 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 497 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 847 optimal weight: 5.9990 chunk 703 optimal weight: 1.9990 chunk 392 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 280 optimal weight: 0.7980 chunk 444 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 760 GLN J 285 ASN ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 70992 Z= 0.205 Angle : 0.580 11.893 95952 Z= 0.269 Chirality : 0.045 0.291 10704 Planarity : 0.004 0.061 12636 Dihedral : 11.169 132.367 9852 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.07 % Favored : 95.66 % Rotamer: Outliers : 3.28 % Allowed : 22.75 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.80 (0.09), residues: 8772 helix: -0.13 (0.09), residues: 3564 sheet: 0.11 (0.18), residues: 924 loop : -0.95 (0.10), residues: 4284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 551 HIS 0.005 0.001 HIS E 340 PHE 0.027 0.001 PHE L 516 TYR 0.022 0.001 TYR E 134 ARG 0.008 0.000 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 364 time to evaluate : 5.983 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: A 138 TYR cc_start: 0.7384 (p90) cc_final: 0.7017 (p90) REVERT: A 158 MET cc_start: 0.7552 (tpt) cc_final: 0.6474 (tpt) REVERT: A 211 LYS cc_start: 0.8685 (tmtm) cc_final: 0.8380 (tptp) REVERT: B 84 MET cc_start: 0.7202 (tpt) cc_final: 0.7001 (tpt) REVERT: B 420 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8837 (mm) REVERT: B 449 MET cc_start: 0.8220 (tpp) cc_final: 0.7880 (tpp) REVERT: B 578 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8484 (pt0) REVERT: B 678 MET cc_start: 0.9086 (mmm) cc_final: 0.8801 (mmp) REVERT: C 84 MET cc_start: 0.7072 (tpt) cc_final: 0.6628 (tpp) REVERT: C 138 TYR cc_start: 0.7075 (p90) cc_final: 0.6847 (p90) REVERT: C 148 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6024 (tppt) REVERT: C 158 MET cc_start: 0.7180 (tpt) cc_final: 0.6541 (tpt) REVERT: D 84 MET cc_start: 0.6876 (tpt) cc_final: 0.6592 (tpp) REVERT: D 148 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.5872 (mmtm) REVERT: D 158 MET cc_start: 0.7716 (tpp) cc_final: 0.7288 (tpt) REVERT: D 211 LYS cc_start: 0.8698 (tmtm) cc_final: 0.8395 (tptp) REVERT: D 291 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: E 45 LYS cc_start: 0.7676 (mmmt) cc_final: 0.7013 (mmtm) REVERT: E 148 LYS cc_start: 0.6675 (OUTLIER) cc_final: 0.6114 (mmtm) REVERT: E 420 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8862 (mm) REVERT: E 550 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8540 (mtm) REVERT: E 578 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: F 84 MET cc_start: 0.6961 (tpt) cc_final: 0.6733 (tpt) REVERT: F 139 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: F 148 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6270 (tppt) REVERT: F 211 LYS cc_start: 0.8689 (tptp) cc_final: 0.8481 (tptp) REVERT: F 388 MET cc_start: 0.9190 (ptp) cc_final: 0.8989 (ptp) REVERT: G 148 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.5986 (mmtm) REVERT: G 211 LYS cc_start: 0.8639 (tmtm) cc_final: 0.8301 (tptp) REVERT: G 291 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8304 (pm20) REVERT: H 46 MET cc_start: 0.8024 (pmm) cc_final: 0.7815 (pmm) REVERT: H 84 MET cc_start: 0.7240 (tpt) cc_final: 0.6995 (tpt) REVERT: H 138 TYR cc_start: 0.7128 (p90) cc_final: 0.6885 (p90) REVERT: H 148 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6095 (mmtm) REVERT: H 420 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8791 (mm) REVERT: I 58 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8173 (pt) REVERT: I 84 MET cc_start: 0.7136 (tpt) cc_final: 0.6910 (tpp) REVERT: I 148 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.5950 (mmtm) REVERT: I 387 ASN cc_start: 0.8058 (p0) cc_final: 0.7744 (p0) REVERT: J 46 MET cc_start: 0.7719 (pmm) cc_final: 0.7376 (pmm) REVERT: J 84 MET cc_start: 0.6799 (tpt) cc_final: 0.6523 (tpp) REVERT: J 138 TYR cc_start: 0.6887 (p90) cc_final: 0.6677 (p90) REVERT: J 158 MET cc_start: 0.6337 (tpt) cc_final: 0.5857 (tpt) REVERT: J 211 LYS cc_start: 0.8689 (tmtm) cc_final: 0.8327 (tptp) REVERT: J 286 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9121 (pt) REVERT: K 84 MET cc_start: 0.6869 (tpt) cc_final: 0.6661 (tpp) REVERT: K 148 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6015 (mmtm) REVERT: K 349 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7988 (mtm-85) REVERT: K 449 MET cc_start: 0.8163 (tpp) cc_final: 0.7839 (tpp) REVERT: K 578 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8483 (pt0) REVERT: L 58 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8150 (pt) REVERT: L 84 MET cc_start: 0.6933 (tpt) cc_final: 0.6596 (tpp) outliers start: 246 outliers final: 157 residues processed: 585 average time/residue: 0.6381 time to fit residues: 648.7705 Evaluate side-chains 520 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 342 time to evaluate : 5.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 139 PHE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 380 ILE Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 464 LEU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 550 MET Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 269 ILE Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 382 GLN Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 467 THR Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 550 MET Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 515 LEU Chi-restraints excluded: chain I residue 550 MET Chi-restraints excluded: chain I residue 578 GLU Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 148 LYS Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 221 GLU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain J residue 291 GLU Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 515 LEU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 515 LEU Chi-restraints excluded: chain K residue 578 GLU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 146 ILE Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 221 GLU Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 484 ASP Chi-restraints excluded: chain L residue 515 LEU Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 578 GLU Chi-restraints excluded: chain L residue 640 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 817 optimal weight: 30.0000 chunk 95 optimal weight: 6.9990 chunk 482 optimal weight: 0.2980 chunk 618 optimal weight: 8.9990 chunk 479 optimal weight: 40.0000 chunk 713 optimal weight: 8.9990 chunk 473 optimal weight: 9.9990 chunk 844 optimal weight: 6.9990 chunk 528 optimal weight: 20.0000 chunk 514 optimal weight: 40.0000 chunk 389 optimal weight: 0.8980 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 ASN ** J 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 70992 Z= 0.510 Angle : 0.758 12.926 95952 Z= 0.374 Chirality : 0.050 0.303 10704 Planarity : 0.006 0.172 12636 Dihedral : 11.697 156.947 9852 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.20 % Favored : 94.53 % Rotamer: Outliers : 3.52 % Allowed : 22.56 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -1.13 (0.09), residues: 8772 helix: -0.55 (0.09), residues: 3684 sheet: -0.05 (0.17), residues: 900 loop : -0.98 (0.10), residues: 4188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 454 HIS 0.010 0.001 HIS J 384 PHE 0.040 0.003 PHE B 516 TYR 0.019 0.003 TYR B 203 ARG 0.018 0.001 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 344 time to evaluate : 5.899 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: A 387 ASN cc_start: 0.8492 (p0) cc_final: 0.8241 (p0) REVERT: A 449 MET cc_start: 0.8288 (tpp) cc_final: 0.8017 (tpp) REVERT: A 550 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8618 (mtm) REVERT: B 458 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8346 (pm20) REVERT: B 578 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8569 (pt0) REVERT: C 84 MET cc_start: 0.7461 (tpt) cc_final: 0.7139 (tpp) REVERT: C 138 TYR cc_start: 0.6995 (p90) cc_final: 0.6749 (p90) REVERT: C 550 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8767 (mtm) REVERT: C 689 GLU cc_start: 0.8237 (pt0) cc_final: 0.8029 (pt0) REVERT: D 84 MET cc_start: 0.7372 (tpt) cc_final: 0.6966 (tpp) REVERT: D 211 LYS cc_start: 0.8657 (tmtm) cc_final: 0.8325 (tptp) REVERT: E 84 MET cc_start: 0.7906 (tpp) cc_final: 0.7669 (tpp) REVERT: E 148 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.6052 (tppt) REVERT: E 420 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8819 (mm) REVERT: E 578 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: F 139 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: F 211 LYS cc_start: 0.8709 (tptp) cc_final: 0.8488 (tptp) REVERT: G 148 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6347 (tppt) REVERT: G 211 LYS cc_start: 0.8688 (tmtm) cc_final: 0.8351 (tptp) REVERT: G 387 ASN cc_start: 0.8510 (p0) cc_final: 0.8240 (p0) REVERT: H 84 MET cc_start: 0.7237 (tpt) cc_final: 0.6954 (tpp) REVERT: H 138 TYR cc_start: 0.7221 (p90) cc_final: 0.6867 (p90) REVERT: H 148 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6168 (mmtm) REVERT: H 420 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8900 (mm) REVERT: H 550 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8647 (mtm) REVERT: I 387 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8178 (p0) REVERT: I 449 MET cc_start: 0.8198 (tpp) cc_final: 0.7965 (tpp) REVERT: J 46 MET cc_start: 0.7883 (pmm) cc_final: 0.7591 (pmm) REVERT: J 84 MET cc_start: 0.7235 (tpt) cc_final: 0.6791 (tpp) REVERT: J 138 TYR cc_start: 0.6887 (p90) cc_final: 0.6601 (p90) REVERT: J 158 MET cc_start: 0.6744 (tpt) cc_final: 0.6346 (tpt) REVERT: J 211 LYS cc_start: 0.8707 (tmtm) cc_final: 0.8326 (tptp) REVERT: J 458 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: K 148 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.6053 (mmtm) REVERT: K 449 MET cc_start: 0.8099 (tpp) cc_final: 0.7763 (tpp) REVERT: K 578 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8563 (pt0) REVERT: L 84 MET cc_start: 0.7378 (tpt) cc_final: 0.7129 (tpp) REVERT: L 158 MET cc_start: 0.7590 (tpp) cc_final: 0.6674 (tpt) REVERT: L 388 MET cc_start: 0.9058 (ptp) cc_final: 0.8771 (ptp) REVERT: L 550 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8743 (mtm) outliers start: 264 outliers final: 178 residues processed: 584 average time/residue: 0.6492 time to fit residues: 651.8848 Evaluate side-chains 518 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 323 time to evaluate : 5.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 139 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 458 GLN Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 332 MET Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 382 GLN Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 467 THR Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 484 ASP Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 550 MET Chi-restraints excluded: chain I residue 66 GLU Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 458 GLN Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 484 ASP Chi-restraints excluded: chain I residue 515 LEU Chi-restraints excluded: chain I residue 550 MET Chi-restraints excluded: chain I residue 558 ASN Chi-restraints excluded: chain I residue 578 GLU Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain I residue 668 LYS Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 148 LYS Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 382 GLN Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 458 GLN Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 484 ASP Chi-restraints excluded: chain J residue 515 LEU Chi-restraints excluded: chain J residue 558 ASN Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 LYS Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 382 GLN Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 427 MET Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 484 ASP Chi-restraints excluded: chain K residue 515 LEU Chi-restraints excluded: chain K residue 578 GLU Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 146 ILE Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 221 GLU Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 458 GLN Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 484 ASP Chi-restraints excluded: chain L residue 515 LEU Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 578 GLU Chi-restraints excluded: chain L residue 640 ASP Chi-restraints excluded: chain L residue 668 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 522 optimal weight: 30.0000 chunk 337 optimal weight: 0.5980 chunk 504 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 536 optimal weight: 5.9990 chunk 575 optimal weight: 3.9990 chunk 417 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 663 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 70992 Z= 0.190 Angle : 0.625 11.940 95952 Z= 0.291 Chirality : 0.046 0.335 10704 Planarity : 0.004 0.074 12636 Dihedral : 11.398 154.021 9852 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.15 % Favored : 95.58 % Rotamer: Outliers : 2.25 % Allowed : 23.83 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.97 (0.09), residues: 8772 helix: -0.31 (0.09), residues: 3636 sheet: -0.34 (0.17), residues: 924 loop : -0.91 (0.10), residues: 4212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 551 HIS 0.004 0.001 HIS E 340 PHE 0.032 0.001 PHE K 516 TYR 0.018 0.002 TYR C 134 ARG 0.011 0.000 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 367 time to evaluate : 5.921 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: A 211 LYS cc_start: 0.8662 (tmtm) cc_final: 0.8368 (tptp) REVERT: B 420 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8845 (mm) REVERT: B 578 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8475 (pt0) REVERT: C 84 MET cc_start: 0.7313 (tpt) cc_final: 0.6936 (tpt) REVERT: C 138 TYR cc_start: 0.7003 (p90) cc_final: 0.6639 (p90) REVERT: C 550 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8661 (mtm) REVERT: D 84 MET cc_start: 0.7257 (tpt) cc_final: 0.6871 (tpp) REVERT: D 211 LYS cc_start: 0.8672 (tmtm) cc_final: 0.8352 (tptp) REVERT: E 84 MET cc_start: 0.7826 (tpp) cc_final: 0.7624 (tpp) REVERT: E 420 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8727 (mm) REVERT: E 578 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: F 84 MET cc_start: 0.7038 (tpt) cc_final: 0.6609 (tpt) REVERT: F 139 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: F 550 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8625 (mtm) REVERT: F 757 MET cc_start: 0.8048 (mmp) cc_final: 0.7845 (mmp) REVERT: G 158 MET cc_start: 0.6820 (tpp) cc_final: 0.6406 (tpp) REVERT: G 211 LYS cc_start: 0.8632 (tmtm) cc_final: 0.8276 (tptp) REVERT: H 84 MET cc_start: 0.7196 (tpt) cc_final: 0.6923 (tpp) REVERT: H 138 TYR cc_start: 0.7104 (p90) cc_final: 0.6840 (p90) REVERT: H 148 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6128 (mmtm) REVERT: H 420 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8764 (mm) REVERT: I 387 ASN cc_start: 0.8213 (p0) cc_final: 0.7986 (p0) REVERT: J 46 MET cc_start: 0.7889 (pmm) cc_final: 0.7562 (pmm) REVERT: J 84 MET cc_start: 0.7116 (tpt) cc_final: 0.6694 (tpp) REVERT: J 138 TYR cc_start: 0.6863 (OUTLIER) cc_final: 0.6661 (p90) REVERT: J 158 MET cc_start: 0.6576 (tpt) cc_final: 0.5648 (tpt) REVERT: J 211 LYS cc_start: 0.8639 (tmtm) cc_final: 0.8269 (tptp) REVERT: J 388 MET cc_start: 0.7923 (mmp) cc_final: 0.7588 (mtp) REVERT: J 449 MET cc_start: 0.8298 (tpp) cc_final: 0.7995 (tpp) REVERT: K 578 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: L 84 MET cc_start: 0.7216 (tpt) cc_final: 0.7000 (tpp) REVERT: L 211 LYS cc_start: 0.8551 (tmtm) cc_final: 0.8348 (tptp) REVERT: L 550 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8611 (mtm) outliers start: 169 outliers final: 125 residues processed: 523 average time/residue: 0.6609 time to fit residues: 596.4949 Evaluate side-chains 477 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 340 time to evaluate : 5.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 139 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 269 ILE Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 269 ILE Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 382 GLN Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 467 THR Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 66 GLU Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 300 ILE Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 578 GLU Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 382 GLN Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 578 GLU Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 221 GLU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 578 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 768 optimal weight: 5.9990 chunk 808 optimal weight: 20.0000 chunk 737 optimal weight: 7.9990 chunk 786 optimal weight: 9.9990 chunk 473 optimal weight: 9.9990 chunk 342 optimal weight: 0.6980 chunk 617 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 710 optimal weight: 1.9990 chunk 744 optimal weight: 9.9990 chunk 784 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 70992 Z= 0.278 Angle : 0.638 12.191 95952 Z= 0.301 Chirality : 0.046 0.316 10704 Planarity : 0.004 0.067 12636 Dihedral : 11.471 155.604 9852 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.63 % Favored : 95.10 % Rotamer: Outliers : 2.19 % Allowed : 23.84 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.87 (0.09), residues: 8772 helix: -0.26 (0.09), residues: 3636 sheet: -0.28 (0.17), residues: 924 loop : -0.83 (0.10), residues: 4212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.004 0.001 HIS E 340 PHE 0.033 0.002 PHE H 516 TYR 0.026 0.002 TYR J 134 ARG 0.008 0.000 ARG J 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 344 time to evaluate : 5.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8640 (tmtm) cc_final: 0.8318 (tptp) REVERT: A 349 ARG cc_start: 0.8573 (ttm110) cc_final: 0.8365 (ttm-80) REVERT: B 420 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8886 (mm) REVERT: B 578 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8527 (pt0) REVERT: C 84 MET cc_start: 0.7295 (tpt) cc_final: 0.6974 (tpt) REVERT: C 138 TYR cc_start: 0.7034 (p90) cc_final: 0.6692 (p90) REVERT: C 158 MET cc_start: 0.7728 (tpt) cc_final: 0.6799 (tpt) REVERT: C 449 MET cc_start: 0.7971 (tpp) cc_final: 0.7693 (tpp) REVERT: C 550 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8653 (mtm) REVERT: D 84 MET cc_start: 0.7258 (tpt) cc_final: 0.6893 (tpp) REVERT: D 211 LYS cc_start: 0.8692 (tmtm) cc_final: 0.8363 (tptp) REVERT: E 84 MET cc_start: 0.7960 (tpp) cc_final: 0.7719 (tpt) REVERT: E 420 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8693 (mm) REVERT: E 578 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8534 (pt0) REVERT: F 84 MET cc_start: 0.7086 (tpt) cc_final: 0.6631 (tpt) REVERT: F 139 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7340 (m-80) REVERT: F 449 MET cc_start: 0.8006 (tpp) cc_final: 0.7732 (tpp) REVERT: G 211 LYS cc_start: 0.8659 (tmtm) cc_final: 0.8329 (tptp) REVERT: H 84 MET cc_start: 0.7118 (tpt) cc_final: 0.6872 (tpp) REVERT: H 138 TYR cc_start: 0.7233 (p90) cc_final: 0.6870 (p90) REVERT: H 148 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.5999 (tppt) REVERT: H 420 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8782 (mm) REVERT: I 387 ASN cc_start: 0.8332 (p0) cc_final: 0.7802 (p0) REVERT: J 46 MET cc_start: 0.7912 (pmm) cc_final: 0.7599 (pmm) REVERT: J 84 MET cc_start: 0.7169 (tpt) cc_final: 0.6767 (tpp) REVERT: J 138 TYR cc_start: 0.6940 (p90) cc_final: 0.6728 (p90) REVERT: J 211 LYS cc_start: 0.8680 (tmtm) cc_final: 0.8311 (tptp) REVERT: J 449 MET cc_start: 0.8296 (tpp) cc_final: 0.8056 (tpp) REVERT: K 578 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: L 550 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8609 (mtm) outliers start: 164 outliers final: 131 residues processed: 499 average time/residue: 0.6345 time to fit residues: 550.3749 Evaluate side-chains 478 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 337 time to evaluate : 5.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 139 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 269 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 464 LEU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 269 ILE Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 382 GLN Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 467 THR Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 578 GLU Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 484 ASP Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 382 GLN Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 578 GLU Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 221 GLU Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 300 ILE Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 578 GLU Chi-restraints excluded: chain L residue 611 MET Chi-restraints excluded: chain L residue 640 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 516 optimal weight: 2.9990 chunk 831 optimal weight: 6.9990 chunk 507 optimal weight: 5.9990 chunk 394 optimal weight: 7.9990 chunk 578 optimal weight: 5.9990 chunk 872 optimal weight: 6.9990 chunk 803 optimal weight: 0.0050 chunk 694 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 536 optimal weight: 0.9980 chunk 426 optimal weight: 0.5980 overall best weight: 2.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 70992 Z= 0.272 Angle : 0.632 12.057 95952 Z= 0.298 Chirality : 0.046 0.333 10704 Planarity : 0.004 0.064 12636 Dihedral : 11.488 158.053 9852 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.49 % Favored : 95.23 % Rotamer: Outliers : 2.04 % Allowed : 24.01 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.09), residues: 8772 helix: -0.27 (0.09), residues: 3636 sheet: -0.30 (0.17), residues: 924 loop : -0.79 (0.10), residues: 4212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 454 HIS 0.004 0.001 HIS E 340 PHE 0.033 0.002 PHE B 516 TYR 0.023 0.002 TYR C 134 ARG 0.005 0.000 ARG D 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17544 Ramachandran restraints generated. 8772 Oldfield, 0 Emsley, 8772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 348 time to evaluate : 5.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8639 (tmtm) cc_final: 0.8323 (tptp) REVERT: A 349 ARG cc_start: 0.8597 (ttm110) cc_final: 0.8383 (ttm-80) REVERT: B 578 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8526 (pt0) REVERT: C 84 MET cc_start: 0.7308 (tpt) cc_final: 0.7002 (tpt) REVERT: C 138 TYR cc_start: 0.7052 (p90) cc_final: 0.6696 (p90) REVERT: C 158 MET cc_start: 0.7729 (tpt) cc_final: 0.6878 (tpt) REVERT: C 550 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8618 (mtm) REVERT: D 45 LYS cc_start: 0.7705 (mmmt) cc_final: 0.7160 (mmmt) REVERT: D 84 MET cc_start: 0.7268 (tpt) cc_final: 0.6917 (tpp) REVERT: D 211 LYS cc_start: 0.8701 (tmtm) cc_final: 0.8378 (tptp) REVERT: E 84 MET cc_start: 0.7999 (tpp) cc_final: 0.7752 (tpt) REVERT: E 420 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8738 (mm) REVERT: E 578 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8528 (pt0) REVERT: F 84 MET cc_start: 0.7168 (tpt) cc_final: 0.6719 (tpt) REVERT: F 139 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: G 211 LYS cc_start: 0.8659 (tmtm) cc_final: 0.8329 (tptp) REVERT: H 84 MET cc_start: 0.7102 (tpt) cc_final: 0.6878 (tpp) REVERT: H 420 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8782 (mm) REVERT: I 158 MET cc_start: 0.7372 (tpp) cc_final: 0.5907 (tpt) REVERT: J 46 MET cc_start: 0.7951 (pmm) cc_final: 0.7644 (pmm) REVERT: J 84 MET cc_start: 0.7189 (tpt) cc_final: 0.6798 (tpp) REVERT: J 138 TYR cc_start: 0.6698 (p90) cc_final: 0.6448 (p90) REVERT: J 158 MET cc_start: 0.6649 (tpt) cc_final: 0.6057 (tpt) REVERT: J 211 LYS cc_start: 0.8668 (tmtm) cc_final: 0.8288 (tptp) REVERT: K 148 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6283 (mmtm) REVERT: K 578 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8521 (pt0) REVERT: L 158 MET cc_start: 0.7580 (tpt) cc_final: 0.7124 (tpt) REVERT: L 550 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8577 (mtm) outliers start: 153 outliers final: 134 residues processed: 488 average time/residue: 0.6519 time to fit residues: 556.0075 Evaluate side-chains 478 residues out of total 7500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 335 time to evaluate : 5.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 139 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 269 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 464 LEU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 611 MET Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 269 ILE Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 382 GLN Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 467 THR Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 300 ILE Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 578 GLU Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 484 ASP Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 382 GLN Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 484 ASP Chi-restraints excluded: chain K residue 578 GLU Chi-restraints excluded: chain L residue 146 ILE Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 221 GLU Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 300 ILE Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 550 MET Chi-restraints excluded: chain L residue 578 GLU Chi-restraints excluded: chain L residue 611 MET Chi-restraints excluded: chain L residue 640 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 552 optimal weight: 8.9990 chunk 740 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 640 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 696 optimal weight: 7.9990 chunk 291 optimal weight: 9.9990 chunk 714 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.114824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070885 restraints weight = 165036.971| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.86 r_work: 0.2816 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 70992 Z= 0.329 Angle : 0.664 12.093 95952 Z= 0.315 Chirality : 0.047 0.328 10704 Planarity : 0.005 0.069 12636 Dihedral : 11.595 164.220 9852 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.66 % Favored : 95.08 % Rotamer: Outliers : 2.11 % Allowed : 23.91 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.86 (0.09), residues: 8772 helix: -0.32 (0.09), residues: 3660 sheet: -0.34 (0.17), residues: 924 loop : -0.74 (0.10), residues: 4188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 454 HIS 0.005 0.001 HIS J 384 PHE 0.036 0.002 PHE B 516 TYR 0.022 0.002 TYR C 134 ARG 0.006 0.000 ARG A 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13148.97 seconds wall clock time: 234 minutes 20.81 seconds (14060.81 seconds total)