Starting phenix.real_space_refine on Wed Apr 10 04:37:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlj_24532/04_2024/7rlj_24532_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlj_24532/04_2024/7rlj_24532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlj_24532/04_2024/7rlj_24532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlj_24532/04_2024/7rlj_24532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlj_24532/04_2024/7rlj_24532_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlj_24532/04_2024/7rlj_24532_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 372 5.16 5 C 43440 2.51 5 N 12180 2.21 5 O 13116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 477": "OE1" <-> "OE2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 477": "OE1" <-> "OE2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 477": "OE1" <-> "OE2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 477": "OE1" <-> "OE2" Residue "F GLU 650": "OE1" <-> "OE2" Residue "F GLU 689": "OE1" <-> "OE2" Residue "L PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 477": "OE1" <-> "OE2" Residue "L GLU 650": "OE1" <-> "OE2" Residue "L GLU 689": "OE1" <-> "OE2" Residue "G PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 477": "OE1" <-> "OE2" Residue "G GLU 650": "OE1" <-> "OE2" Residue "G GLU 689": "OE1" <-> "OE2" Residue "H PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 477": "OE1" <-> "OE2" Residue "H GLU 650": "OE1" <-> "OE2" Residue "H GLU 689": "OE1" <-> "OE2" Residue "I PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 477": "OE1" <-> "OE2" Residue "I GLU 650": "OE1" <-> "OE2" Residue "I GLU 689": "OE1" <-> "OE2" Residue "J PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 477": "OE1" <-> "OE2" Residue "J GLU 650": "OE1" <-> "OE2" Residue "J GLU 689": "OE1" <-> "OE2" Residue "K PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 477": "OE1" <-> "OE2" Residue "K GLU 650": "OE1" <-> "OE2" Residue "K GLU 689": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 69156 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "B" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "C" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "D" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "E" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "F" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "L" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "G" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "H" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "I" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "J" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "K" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 1, 'JDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 25.84, per 1000 atoms: 0.37 Number of scatterers: 69156 At special positions: 0 Unit cell: (172, 179, 183, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 372 16.00 P 36 15.00 Mg 12 11.99 O 13116 8.00 N 12180 7.00 C 43440 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=0, symmetry=0 Time building additional restraints: 19.62 Conformation dependent library (CDL) restraints added in 9.5 seconds 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16296 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 372 helices and 60 sheets defined 34.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.65 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.502A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.582A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 211 through 217 removed outlier: 3.791A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.584A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 232' Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.567A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 374 through 385 removed outlier: 4.312A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.642A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.621A pdb=" N LEU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 483 through 493 removed outlier: 4.237A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.714A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.858A pdb=" N PHE A 563 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A 564 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS A 565 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 568 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 601 through 609 removed outlier: 3.865A pdb=" N ASP A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 660 removed outlier: 3.549A pdb=" N LEU A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.698A pdb=" N ALA A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.623A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.623A pdb=" N ALA A 739 " --> pdb=" O HIS A 735 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.501A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 3.583A pdb=" N ASN B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 211 through 217 removed outlier: 3.791A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.583A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 232' Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 removed outlier: 3.567A pdb=" N ARG B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 374 through 385 removed outlier: 4.311A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.642A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 449 through 456 removed outlier: 3.622A pdb=" N LEU B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 483 through 493 removed outlier: 4.237A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.714A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.858A pdb=" N PHE B 563 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 564 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS B 565 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN B 568 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 586 Processing helix chain 'B' and resid 601 through 609 removed outlier: 3.864A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 660 removed outlier: 3.549A pdb=" N LEU B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.699A pdb=" N ALA B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.623A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.622A pdb=" N ALA B 739 " --> pdb=" O HIS B 735 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 757 Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'C' and resid 43 through 48 removed outlier: 3.502A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.582A pdb=" N ASN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 211 through 217 removed outlier: 3.791A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.583A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 232' Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 333 removed outlier: 3.567A pdb=" N ARG C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 374 through 385 removed outlier: 4.312A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.642A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 449 through 456 removed outlier: 3.621A pdb=" N LEU C 456 " --> pdb=" O PHE C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 483 through 493 removed outlier: 4.237A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.714A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 560 through 568 removed outlier: 3.858A pdb=" N PHE C 563 " --> pdb=" O ARG C 560 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 564 " --> pdb=" O GLU C 561 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS C 565 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN C 568 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 586 Processing helix chain 'C' and resid 601 through 609 removed outlier: 3.865A pdb=" N ASP C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 660 removed outlier: 3.548A pdb=" N LEU C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.699A pdb=" N ALA C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.623A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.622A pdb=" N ALA C 739 " --> pdb=" O HIS C 735 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 757 Processing helix chain 'C' and resid 763 through 765 No H-bonds generated for 'chain 'C' and resid 763 through 765' Processing helix chain 'D' and resid 43 through 48 removed outlier: 3.501A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.582A pdb=" N ASN D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 211 through 217 removed outlier: 3.792A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.585A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 227 through 232' Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.567A pdb=" N ARG D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 374 through 385 removed outlier: 4.312A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 381 " --> pdb=" O ARG D 377 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.642A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 449 through 456 removed outlier: 3.622A pdb=" N LEU D 456 " --> pdb=" O PHE D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 461 No H-bonds generated for 'chain 'D' and resid 459 through 461' Processing helix chain 'D' and resid 483 through 493 removed outlier: 4.237A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D 490 " --> pdb=" O LYS D 486 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 524 through 532 removed outlier: 3.713A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 549 Processing helix chain 'D' and resid 560 through 568 removed outlier: 3.858A pdb=" N PHE D 563 " --> pdb=" O ARG D 560 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 564 " --> pdb=" O GLU D 561 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS D 565 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D 568 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 586 Processing helix chain 'D' and resid 601 through 609 removed outlier: 3.864A pdb=" N ASP D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 660 removed outlier: 3.549A pdb=" N LEU D 657 " --> pdb=" O ARG D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.700A pdb=" N ALA D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.623A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.622A pdb=" N ALA D 739 " --> pdb=" O HIS D 735 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 757 Processing helix chain 'D' and resid 763 through 765 No H-bonds generated for 'chain 'D' and resid 763 through 765' Processing helix chain 'E' and resid 43 through 48 removed outlier: 3.501A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 removed outlier: 3.582A pdb=" N ASN E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 211 through 217 removed outlier: 3.790A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 225 No H-bonds generated for 'chain 'E' and resid 222 through 225' Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.584A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 227 through 232' Processing helix chain 'E' and resid 253 through 260 Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.568A pdb=" N ARG E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 374 through 385 removed outlier: 4.311A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE E 380 " --> pdb=" O GLY E 376 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.642A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 449 through 456 removed outlier: 3.621A pdb=" N LEU E 456 " --> pdb=" O PHE E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 461 No H-bonds generated for 'chain 'E' and resid 459 through 461' Processing helix chain 'E' and resid 483 through 493 removed outlier: 4.236A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN E 490 " --> pdb=" O LYS E 486 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU E 491 " --> pdb=" O ARG E 487 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 524 through 532 removed outlier: 3.713A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 549 Processing helix chain 'E' and resid 560 through 568 removed outlier: 3.858A pdb=" N PHE E 563 " --> pdb=" O ARG E 560 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP E 564 " --> pdb=" O GLU E 561 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS E 565 " --> pdb=" O ILE E 562 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN E 568 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 586 Processing helix chain 'E' and resid 601 through 609 removed outlier: 3.863A pdb=" N ASP E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 660 removed outlier: 3.550A pdb=" N LEU E 657 " --> pdb=" O ARG E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.700A pdb=" N ALA E 676 " --> pdb=" O LEU E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.623A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.622A pdb=" N ALA E 739 " --> pdb=" O HIS E 735 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 757 Processing helix chain 'E' and resid 763 through 765 No H-bonds generated for 'chain 'E' and resid 763 through 765' Processing helix chain 'F' and resid 43 through 48 removed outlier: 3.501A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 removed outlier: 3.582A pdb=" N ASN F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 211 through 217 removed outlier: 3.791A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 225 No H-bonds generated for 'chain 'F' and resid 222 through 225' Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.583A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 227 through 232' Processing helix chain 'F' and resid 253 through 260 Processing helix chain 'F' and resid 272 through 276 Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.567A pdb=" N ARG F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'F' and resid 355 through 357' Processing helix chain 'F' and resid 374 through 385 removed outlier: 4.311A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE F 380 " --> pdb=" O GLY F 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU F 381 " --> pdb=" O ARG F 377 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.643A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 449 through 456 removed outlier: 3.622A pdb=" N LEU F 456 " --> pdb=" O PHE F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 461 No H-bonds generated for 'chain 'F' and resid 459 through 461' Processing helix chain 'F' and resid 483 through 493 removed outlier: 4.238A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN F 490 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU F 491 " --> pdb=" O ARG F 487 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 524 through 532 removed outlier: 3.713A pdb=" N ILE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 549 Processing helix chain 'F' and resid 560 through 568 removed outlier: 3.857A pdb=" N PHE F 563 " --> pdb=" O ARG F 560 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP F 564 " --> pdb=" O GLU F 561 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS F 565 " --> pdb=" O ILE F 562 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN F 568 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 586 Processing helix chain 'F' and resid 601 through 609 removed outlier: 3.864A pdb=" N ASP F 609 " --> pdb=" O LEU F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 660 removed outlier: 3.549A pdb=" N LEU F 657 " --> pdb=" O ARG F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.700A pdb=" N ALA F 676 " --> pdb=" O LEU F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 706 removed outlier: 3.624A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 741 removed outlier: 3.622A pdb=" N ALA F 739 " --> pdb=" O HIS F 735 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 757 Processing helix chain 'F' and resid 763 through 765 No H-bonds generated for 'chain 'F' and resid 763 through 765' Processing helix chain 'L' and resid 43 through 48 removed outlier: 3.501A pdb=" N ASP L 47 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 92 removed outlier: 3.583A pdb=" N ASN L 90 " --> pdb=" O ARG L 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN L 91 " --> pdb=" O VAL L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 139 No H-bonds generated for 'chain 'L' and resid 136 through 139' Processing helix chain 'L' and resid 211 through 217 removed outlier: 3.791A pdb=" N GLN L 215 " --> pdb=" O LYS L 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE L 216 " --> pdb=" O GLN L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 225 No H-bonds generated for 'chain 'L' and resid 222 through 225' Processing helix chain 'L' and resid 227 through 232 removed outlier: 3.584A pdb=" N LYS L 231 " --> pdb=" O PRO L 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA L 232 " --> pdb=" O ALA L 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 227 through 232' Processing helix chain 'L' and resid 253 through 260 Processing helix chain 'L' and resid 272 through 276 Processing helix chain 'L' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS L 295 " --> pdb=" O GLU L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 333 removed outlier: 3.568A pdb=" N ARG L 323 " --> pdb=" O GLU L 319 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE L 324 " --> pdb=" O VAL L 320 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL L 325 " --> pdb=" O GLU L 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'L' and resid 355 through 357' Processing helix chain 'L' and resid 374 through 385 removed outlier: 4.311A pdb=" N GLU L 379 " --> pdb=" O THR L 375 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE L 380 " --> pdb=" O GLY L 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU L 381 " --> pdb=" O ARG L 377 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN L 382 " --> pdb=" O LEU L 378 " (cutoff:3.500A) removed outlier: 3.567A 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: 3.642A pdb=" N LYS L 426 " --> pdb=" O ALA L 422 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU L 429 " --> pdb=" O LYS L 425 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 442 No H-bonds generated for 'chain 'L' and resid 439 through 442' Processing helix chain 'L' and resid 449 through 456 removed outlier: 3.622A pdb=" N LEU L 456 " --> pdb=" O PHE L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 461 No H-bonds generated for 'chain 'L' and resid 459 through 461' Processing helix chain 'L' and resid 483 through 493 removed outlier: 4.237A pdb=" N GLU L 488 " --> pdb=" O ASP L 484 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN L 490 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU L 491 " --> pdb=" O ARG L 487 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU L 492 " --> pdb=" O GLU L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 495 through 498 No H-bonds generated for 'chain 'L' and resid 495 through 498' Processing helix chain 'L' and resid 524 through 532 removed outlier: 3.714A pdb=" N ILE L 531 " --> pdb=" O LEU L 527 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA L 532 " --> pdb=" O ALA L 528 " (cutoff:3.500A) Processing helix chain 'L' and resid 544 through 549 Processing helix chain 'L' and resid 560 through 568 removed outlier: 3.858A pdb=" N PHE L 563 " --> pdb=" O ARG L 560 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP L 564 " --> pdb=" O GLU L 561 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS L 565 " --> pdb=" O ILE L 562 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN L 568 " --> pdb=" O LYS L 565 " (cutoff:3.500A) Processing helix chain 'L' and resid 579 through 586 Processing helix chain 'L' and resid 601 through 609 removed outlier: 3.864A pdb=" N ASP L 609 " --> pdb=" O LEU L 605 " (cutoff:3.500A) Processing helix chain 'L' and resid 650 through 660 removed outlier: 3.549A pdb=" N LEU L 657 " --> pdb=" O ARG L 653 " (cutoff:3.500A) Processing helix chain 'L' and resid 672 through 678 removed outlier: 3.699A pdb=" N ALA L 676 " --> pdb=" O LEU L 672 " (cutoff:3.500A) Processing helix chain 'L' and resid 684 through 706 removed outlier: 3.624A pdb=" N CYS L 691 " --> pdb=" O LEU L 687 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU L 706 " --> pdb=" O SER L 702 " (cutoff:3.500A) Processing helix chain 'L' and resid 733 through 741 removed outlier: 3.622A pdb=" N ALA L 739 " --> pdb=" O HIS L 735 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG L 741 " --> pdb=" O GLU L 737 " (cutoff:3.500A) Processing helix chain 'L' and resid 750 through 757 Processing helix chain 'L' and resid 763 through 765 No H-bonds generated for 'chain 'L' and resid 763 through 765' Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 86 through 92 removed outlier: 3.582A pdb=" N ASN G 90 " --> pdb=" O ARG G 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN G 91 " --> pdb=" O VAL G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 139 No H-bonds generated for 'chain 'G' and resid 136 through 139' Processing helix chain 'G' and resid 211 through 217 removed outlier: 3.791A pdb=" N GLN G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE G 216 " --> pdb=" O GLN G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 225 No H-bonds generated for 'chain 'G' and resid 222 through 225' Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.584A pdb=" N LYS G 231 " --> pdb=" O PRO G 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 227 through 232' Processing helix chain 'G' and resid 253 through 260 Processing helix chain 'G' and resid 272 through 276 Processing helix chain 'G' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA G 293 " --> pdb=" O ALA G 289 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 removed outlier: 3.567A pdb=" N ARG G 323 " --> pdb=" O GLU G 319 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE G 324 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'G' and resid 355 through 357' Processing helix chain 'G' and resid 374 through 385 removed outlier: 4.312A pdb=" N GLU G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE G 380 " --> pdb=" O GLY G 376 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU G 381 " --> pdb=" O ARG G 377 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN G 382 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.643A pdb=" N LYS G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU G 429 " --> pdb=" O LYS G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 442 No H-bonds generated for 'chain 'G' and resid 439 through 442' Processing helix chain 'G' and resid 449 through 456 removed outlier: 3.621A pdb=" N LEU G 456 " --> pdb=" O PHE G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 461 No H-bonds generated for 'chain 'G' and resid 459 through 461' Processing helix chain 'G' and resid 483 through 493 removed outlier: 4.237A pdb=" N GLU G 488 " --> pdb=" O ASP G 484 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN G 490 " --> pdb=" O LYS G 486 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU G 491 " --> pdb=" O ARG G 487 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU G 492 " --> pdb=" O GLU G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 495 through 498 No H-bonds generated for 'chain 'G' and resid 495 through 498' Processing helix chain 'G' and resid 524 through 532 removed outlier: 3.714A pdb=" N ILE G 531 " --> pdb=" O LEU G 527 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA G 532 " --> pdb=" O ALA G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 Processing helix chain 'G' and resid 560 through 568 removed outlier: 3.858A pdb=" N PHE G 563 " --> pdb=" O ARG G 560 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP G 564 " --> pdb=" O GLU G 561 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS G 565 " --> pdb=" O ILE G 562 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN G 568 " --> pdb=" O LYS G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 579 through 586 Processing helix chain 'G' and resid 601 through 609 removed outlier: 3.864A pdb=" N ASP G 609 " --> pdb=" O LEU G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 660 removed outlier: 3.548A pdb=" N LEU G 657 " --> pdb=" O ARG G 653 " (cutoff:3.500A) Processing helix chain 'G' and resid 672 through 678 removed outlier: 3.699A pdb=" N ALA G 676 " --> pdb=" O LEU G 672 " (cutoff:3.500A) Processing helix chain 'G' and resid 684 through 706 removed outlier: 3.623A pdb=" N CYS G 691 " --> pdb=" O LEU G 687 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU G 706 " --> pdb=" O SER G 702 " (cutoff:3.500A) Processing helix chain 'G' and resid 733 through 741 removed outlier: 3.623A pdb=" N ALA G 739 " --> pdb=" O HIS G 735 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG G 741 " --> pdb=" O GLU G 737 " (cutoff:3.500A) Processing helix chain 'G' and resid 750 through 757 Processing helix chain 'G' and resid 763 through 765 No H-bonds generated for 'chain 'G' and resid 763 through 765' Processing helix chain 'H' and resid 43 through 48 removed outlier: 3.500A pdb=" N ASP H 47 " --> pdb=" O GLN H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 92 removed outlier: 3.582A pdb=" N ASN H 90 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN H 91 " --> pdb=" O VAL H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 139 No H-bonds generated for 'chain 'H' and resid 136 through 139' Processing helix chain 'H' and resid 211 through 217 removed outlier: 3.792A pdb=" N GLN H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE H 216 " --> pdb=" O GLN H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 225 No H-bonds generated for 'chain 'H' and resid 222 through 225' Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.584A pdb=" N LYS H 231 " --> pdb=" O PRO H 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA H 232 " --> pdb=" O ALA H 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 227 through 232' Processing helix chain 'H' and resid 253 through 260 Processing helix chain 'H' and resid 272 through 276 Processing helix chain 'H' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA H 293 " --> pdb=" O ALA H 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS H 295 " --> pdb=" O GLU H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 333 removed outlier: 3.568A pdb=" N ARG H 323 " --> pdb=" O GLU H 319 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE H 324 " --> pdb=" O VAL H 320 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'H' and resid 355 through 357' Processing helix chain 'H' and resid 374 through 385 removed outlier: 4.311A pdb=" N GLU H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE H 380 " --> pdb=" O GLY H 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU H 381 " --> pdb=" O ARG H 377 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN H 382 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 3.567A 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: 3.643A pdb=" N LYS H 426 " --> pdb=" O ALA H 422 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU H 429 " --> pdb=" O LYS H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 442 No H-bonds generated for 'chain 'H' and resid 439 through 442' Processing helix chain 'H' and resid 449 through 456 removed outlier: 3.621A pdb=" N LEU H 456 " --> pdb=" O PHE H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 461 No H-bonds generated for 'chain 'H' and resid 459 through 461' Processing helix chain 'H' and resid 483 through 493 removed outlier: 4.237A pdb=" N GLU H 488 " --> pdb=" O ASP H 484 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN H 490 " --> pdb=" O LYS H 486 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU H 491 " --> pdb=" O ARG H 487 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU H 492 " --> pdb=" O GLU H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 498 No H-bonds generated for 'chain 'H' and resid 495 through 498' Processing helix chain 'H' and resid 524 through 532 removed outlier: 3.714A pdb=" N ILE H 531 " --> pdb=" O LEU H 527 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H 532 " --> pdb=" O ALA H 528 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 549 Processing helix chain 'H' and resid 560 through 568 removed outlier: 3.857A pdb=" N PHE H 563 " --> pdb=" O ARG H 560 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP H 564 " --> pdb=" O GLU H 561 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS H 565 " --> pdb=" O ILE H 562 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN H 568 " --> pdb=" O LYS H 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 579 through 586 Processing helix chain 'H' and resid 601 through 609 removed outlier: 3.864A pdb=" N ASP H 609 " --> pdb=" O LEU H 605 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 660 removed outlier: 3.547A pdb=" N LEU H 657 " --> pdb=" O ARG H 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 672 through 678 removed outlier: 3.700A pdb=" N ALA H 676 " --> pdb=" O LEU H 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 684 through 706 removed outlier: 3.624A pdb=" N CYS H 691 " --> pdb=" O LEU H 687 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU H 706 " --> pdb=" O SER H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 733 through 741 removed outlier: 3.623A pdb=" N ALA H 739 " --> pdb=" O HIS H 735 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG H 741 " --> pdb=" O GLU H 737 " (cutoff:3.500A) Processing helix chain 'H' and resid 750 through 757 Processing helix chain 'H' and resid 763 through 765 No H-bonds generated for 'chain 'H' and resid 763 through 765' Processing helix chain 'I' and resid 43 through 48 removed outlier: 3.502A pdb=" N ASP I 47 " --> pdb=" O GLN I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 removed outlier: 3.583A pdb=" N ASN I 90 " --> pdb=" O ARG I 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN I 91 " --> pdb=" O VAL I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 139 No H-bonds generated for 'chain 'I' and resid 136 through 139' Processing helix chain 'I' and resid 211 through 217 removed outlier: 3.791A pdb=" N GLN I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE I 216 " --> pdb=" O GLN I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 225 No H-bonds generated for 'chain 'I' and resid 222 through 225' Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.584A pdb=" N LYS I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA I 232 " --> pdb=" O ALA I 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 227 through 232' Processing helix chain 'I' and resid 253 through 260 Processing helix chain 'I' and resid 272 through 276 Processing helix chain 'I' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA I 293 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS I 295 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 333 removed outlier: 3.567A pdb=" N ARG I 323 " --> pdb=" O GLU I 319 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE I 324 " --> pdb=" O VAL I 320 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'I' and resid 355 through 357' Processing helix chain 'I' and resid 374 through 385 removed outlier: 4.312A pdb=" N GLU I 379 " --> pdb=" O THR I 375 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE I 380 " --> pdb=" O GLY I 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU I 381 " --> pdb=" O ARG I 377 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN I 382 " --> pdb=" O LEU I 378 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.642A pdb=" N LYS I 426 " --> pdb=" O ALA I 422 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU I 429 " --> pdb=" O LYS I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 439 through 442 No H-bonds generated for 'chain 'I' and resid 439 through 442' Processing helix chain 'I' and resid 449 through 456 removed outlier: 3.621A pdb=" N LEU I 456 " --> pdb=" O PHE I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 461 No H-bonds generated for 'chain 'I' and resid 459 through 461' Processing helix chain 'I' and resid 483 through 493 removed outlier: 4.237A pdb=" N GLU I 488 " --> pdb=" O ASP I 484 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN I 490 " --> pdb=" O LYS I 486 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU I 491 " --> pdb=" O ARG I 487 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU I 492 " --> pdb=" O GLU I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 498 No H-bonds generated for 'chain 'I' and resid 495 through 498' Processing helix chain 'I' and resid 524 through 532 removed outlier: 3.713A pdb=" N ILE I 531 " --> pdb=" O LEU I 527 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 532 " --> pdb=" O ALA I 528 " (cutoff:3.500A) Processing helix chain 'I' and resid 544 through 549 Processing helix chain 'I' and resid 560 through 568 removed outlier: 3.858A pdb=" N PHE I 563 " --> pdb=" O ARG I 560 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP I 564 " --> pdb=" O GLU I 561 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS I 565 " --> pdb=" O ILE I 562 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN I 568 " --> pdb=" O LYS I 565 " (cutoff:3.500A) Processing helix chain 'I' and resid 579 through 586 Processing helix chain 'I' and resid 601 through 609 removed outlier: 3.864A pdb=" N ASP I 609 " --> pdb=" O LEU I 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 650 through 660 removed outlier: 3.549A pdb=" N LEU I 657 " --> pdb=" O ARG I 653 " (cutoff:3.500A) Processing helix chain 'I' and resid 672 through 678 removed outlier: 3.700A pdb=" N ALA I 676 " --> pdb=" O LEU I 672 " (cutoff:3.500A) Processing helix chain 'I' and resid 684 through 706 removed outlier: 3.623A pdb=" N CYS I 691 " --> pdb=" O LEU I 687 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU I 706 " --> pdb=" O SER I 702 " (cutoff:3.500A) Processing helix chain 'I' and resid 733 through 741 removed outlier: 3.623A pdb=" N ALA I 739 " --> pdb=" O HIS I 735 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG I 741 " --> pdb=" O GLU I 737 " (cutoff:3.500A) Processing helix chain 'I' and resid 750 through 757 Processing helix chain 'I' and resid 763 through 765 No H-bonds generated for 'chain 'I' and resid 763 through 765' Processing helix chain 'J' and resid 43 through 48 removed outlier: 3.502A pdb=" N ASP J 47 " --> pdb=" O GLN J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 92 removed outlier: 3.582A pdb=" N ASN J 90 " --> pdb=" O ARG J 86 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN J 91 " --> pdb=" O VAL J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 139 No H-bonds generated for 'chain 'J' and resid 136 through 139' Processing helix chain 'J' and resid 211 through 217 removed outlier: 3.792A pdb=" N GLN J 215 " --> pdb=" O LYS J 211 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE J 216 " --> pdb=" O GLN J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 225 No H-bonds generated for 'chain 'J' and resid 222 through 225' Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.584A pdb=" N LYS J 231 " --> pdb=" O PRO J 227 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA J 232 " --> pdb=" O ALA J 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 227 through 232' Processing helix chain 'J' and resid 253 through 260 Processing helix chain 'J' and resid 272 through 276 Processing helix chain 'J' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA J 293 " --> pdb=" O ALA J 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS J 295 " --> pdb=" O GLU J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 333 removed outlier: 3.567A pdb=" N ARG J 323 " --> pdb=" O GLU J 319 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE J 324 " --> pdb=" O VAL J 320 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL J 325 " --> pdb=" O GLU J 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'J' and resid 355 through 357' Processing helix chain 'J' and resid 374 through 385 removed outlier: 4.311A pdb=" N GLU J 379 " --> pdb=" O THR J 375 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE J 380 " --> pdb=" O GLY J 376 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU J 381 " --> pdb=" O ARG J 377 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN J 382 " --> pdb=" O LEU J 378 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.643A pdb=" N LYS J 426 " --> pdb=" O ALA J 422 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU J 429 " --> pdb=" O LYS J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 439 through 442 No H-bonds generated for 'chain 'J' and resid 439 through 442' Processing helix chain 'J' and resid 449 through 456 removed outlier: 3.621A pdb=" N LEU J 456 " --> pdb=" O PHE J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 461 No H-bonds generated for 'chain 'J' and resid 459 through 461' Processing helix chain 'J' and resid 483 through 493 removed outlier: 4.237A pdb=" N GLU J 488 " --> pdb=" O ASP J 484 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN J 490 " --> pdb=" O LYS J 486 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU J 491 " --> pdb=" O ARG J 487 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU J 492 " --> pdb=" O GLU J 488 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 498 No H-bonds generated for 'chain 'J' and resid 495 through 498' Processing helix chain 'J' and resid 524 through 532 removed outlier: 3.714A pdb=" N ILE J 531 " --> pdb=" O LEU J 527 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA J 532 " --> pdb=" O ALA J 528 " (cutoff:3.500A) Processing helix chain 'J' and resid 544 through 549 Processing helix chain 'J' and resid 560 through 568 removed outlier: 3.858A pdb=" N PHE J 563 " --> pdb=" O ARG J 560 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP J 564 " --> pdb=" O GLU J 561 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS J 565 " --> pdb=" O ILE J 562 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN J 568 " --> pdb=" O LYS J 565 " (cutoff:3.500A) Processing helix chain 'J' and resid 579 through 586 Processing helix chain 'J' and resid 601 through 609 removed outlier: 3.865A pdb=" N ASP J 609 " --> pdb=" O LEU J 605 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 660 removed outlier: 3.549A pdb=" N LEU J 657 " --> pdb=" O ARG J 653 " (cutoff:3.500A) Processing helix chain 'J' and resid 672 through 678 removed outlier: 3.699A pdb=" N ALA J 676 " --> pdb=" O LEU J 672 " (cutoff:3.500A) Processing helix chain 'J' and resid 684 through 706 removed outlier: 3.622A pdb=" N CYS J 691 " --> pdb=" O LEU J 687 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU J 706 " --> pdb=" O SER J 702 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.622A pdb=" N ALA J 739 " --> pdb=" O HIS J 735 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG J 741 " --> pdb=" O GLU J 737 " (cutoff:3.500A) Processing helix chain 'J' and resid 750 through 757 Processing helix chain 'J' and resid 763 through 765 No H-bonds generated for 'chain 'J' and resid 763 through 765' Processing helix chain 'K' and resid 43 through 48 removed outlier: 3.501A pdb=" N ASP K 47 " --> pdb=" O GLN K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 92 removed outlier: 3.583A pdb=" N ASN K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN K 91 " --> pdb=" O VAL K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 139 No H-bonds generated for 'chain 'K' and resid 136 through 139' Processing helix chain 'K' and resid 211 through 217 removed outlier: 3.791A pdb=" N GLN K 215 " --> pdb=" O LYS K 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE K 216 " --> pdb=" O GLN K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 225 No H-bonds generated for 'chain 'K' and resid 222 through 225' Processing helix chain 'K' and resid 227 through 232 removed outlier: 3.584A pdb=" N LYS K 231 " --> pdb=" O PRO K 227 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 227 through 232' Processing helix chain 'K' and resid 253 through 260 Processing helix chain 'K' and resid 272 through 276 Processing helix chain 'K' and resid 281 through 295 removed outlier: 3.974A pdb=" N ALA K 293 " --> pdb=" O ALA K 289 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 333 removed outlier: 3.568A pdb=" N ARG K 323 " --> pdb=" O GLU K 319 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE K 324 " --> pdb=" O VAL K 320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL K 325 " --> pdb=" O GLU K 321 " (cutoff:3.500A) 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 357 No H-bonds generated for 'chain 'K' and resid 355 through 357' Processing helix chain 'K' and resid 374 through 385 removed outlier: 4.312A pdb=" N GLU K 379 " --> pdb=" O THR K 375 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE K 380 " --> pdb=" O GLY K 376 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU K 381 " --> pdb=" O ARG K 377 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN K 382 " --> pdb=" O LEU K 378 " (cutoff:3.500A) removed outlier: 3.567A 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: 3.642A pdb=" N LYS K 426 " --> pdb=" O ALA K 422 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU K 429 " --> pdb=" O LYS K 425 " (cutoff:3.500A) Processing helix chain 'K' and resid 439 through 442 No H-bonds generated for 'chain 'K' and resid 439 through 442' Processing helix chain 'K' and resid 449 through 456 removed outlier: 3.621A pdb=" N LEU K 456 " --> pdb=" O PHE K 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 461 No H-bonds generated for 'chain 'K' and resid 459 through 461' Processing helix chain 'K' and resid 483 through 493 removed outlier: 4.237A pdb=" N GLU K 488 " --> pdb=" O ASP K 484 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN K 490 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU K 491 " --> pdb=" O ARG K 487 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 492 " --> pdb=" O GLU K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 498 No H-bonds generated for 'chain 'K' and resid 495 through 498' Processing helix chain 'K' and resid 524 through 532 removed outlier: 3.713A pdb=" N ILE K 531 " --> pdb=" O LEU K 527 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA K 532 " --> pdb=" O ALA K 528 " (cutoff:3.500A) Processing helix chain 'K' and resid 544 through 549 Processing helix chain 'K' and resid 560 through 568 removed outlier: 3.859A pdb=" N PHE K 563 " --> pdb=" O ARG K 560 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP K 564 " --> pdb=" O GLU K 561 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS K 565 " --> pdb=" O ILE K 562 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN K 568 " --> pdb=" O LYS K 565 " (cutoff:3.500A) Processing helix chain 'K' and resid 579 through 586 Processing helix chain 'K' and resid 601 through 609 removed outlier: 3.865A pdb=" N ASP K 609 " --> pdb=" O LEU K 605 " (cutoff:3.500A) Processing helix chain 'K' and resid 650 through 660 removed outlier: 3.549A pdb=" N LEU K 657 " --> pdb=" O ARG K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 672 through 678 removed outlier: 3.700A pdb=" N ALA K 676 " --> pdb=" O LEU K 672 " (cutoff:3.500A) Processing helix chain 'K' and resid 684 through 706 removed outlier: 3.623A pdb=" N CYS K 691 " --> pdb=" O LEU K 687 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU K 706 " --> pdb=" O SER K 702 " (cutoff:3.500A) Processing helix chain 'K' and resid 733 through 741 removed outlier: 3.623A pdb=" N ALA K 739 " --> pdb=" O HIS K 735 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG K 741 " --> pdb=" O GLU K 737 " (cutoff:3.500A) Processing helix chain 'K' and resid 750 through 757 Processing helix chain 'K' and resid 763 through 765 No H-bonds generated for 'chain 'K' and resid 763 through 765' Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 removed outlier: 3.820A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 67 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= C, first strand: chain 'A' and resid 153 through 155 removed outlier: 3.550A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 240 through 242 removed outlier: 8.697A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 641 through 645 removed outlier: 4.324A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 515 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 643 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 517 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.820A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B 57 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 67 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 39 through 41 Processing sheet with id= H, first strand: chain 'B' and resid 153 through 155 removed outlier: 3.549A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 240 through 242 removed outlier: 8.697A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 641 through 645 removed outlier: 4.324A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 515 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 643 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B 517 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.820A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL C 57 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 67 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= M, first strand: chain 'C' and resid 153 through 155 removed outlier: 3.549A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 240 through 242 removed outlier: 8.697A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 641 through 645 removed outlier: 4.323A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 515 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 643 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR C 517 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.820A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL D 57 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 67 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 39 through 41 Processing sheet with id= R, first strand: chain 'D' and resid 153 through 155 removed outlier: 3.551A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 240 through 242 removed outlier: 8.697A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 641 through 645 removed outlier: 4.323A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 515 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE D 643 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR D 517 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 25 through 27 removed outlier: 3.819A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA E 67 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 39 through 41 Processing sheet with id= W, first strand: chain 'E' and resid 153 through 155 removed outlier: 3.550A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 240 through 242 removed outlier: 8.696A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 645 removed outlier: 4.324A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU E 515 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 643 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR E 517 " --> pdb=" O ILE E 643 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 25 through 27 removed outlier: 3.821A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA F 67 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 39 through 41 Processing sheet with id= AB, first strand: chain 'F' and resid 153 through 155 removed outlier: 3.550A pdb=" N VAL F 161 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 240 through 242 removed outlier: 8.697A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 641 through 645 removed outlier: 4.324A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 515 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.820A pdb=" N SER L 101 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL L 57 " --> pdb=" O CYS L 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS L 69 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA L 67 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 39 through 41 Processing sheet with id= AG, first strand: chain 'L' and resid 153 through 155 removed outlier: 3.551A pdb=" N VAL L 161 " --> pdb=" O VAL L 154 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 240 through 242 removed outlier: 8.696A pdb=" N ILE L 241 " --> pdb=" O VAL L 341 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL L 343 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA L 299 " --> pdb=" O ILE L 342 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N MET L 344 " --> pdb=" O ALA L 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE L 301 " --> pdb=" O MET L 344 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE L 265 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE L 302 " --> pdb=" O PHE L 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE L 267 " --> pdb=" O PHE L 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'L' and resid 641 through 645 removed outlier: 4.325A pdb=" N GLN L 641 " --> pdb=" O GLY L 513 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU L 515 " --> pdb=" O GLN L 641 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE L 643 " --> pdb=" O LEU L 515 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR L 517 " --> pdb=" O ILE L 643 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE L 619 " --> pdb=" O VAL L 514 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE L 516 " --> pdb=" O ILE L 619 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY L 621 " --> pdb=" O PHE L 516 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY L 518 " --> pdb=" O GLY L 621 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN L 538 " --> pdb=" O VAL L 573 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE L 575 " --> pdb=" O ASN L 538 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE L 540 " --> pdb=" O PHE L 575 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 25 through 27 removed outlier: 3.820A pdb=" N SER G 101 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL G 57 " --> pdb=" O CYS G 69 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS G 69 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA G 67 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 39 through 41 Processing sheet with id= AL, first strand: chain 'G' and resid 153 through 155 removed outlier: 3.550A pdb=" N VAL G 161 " --> pdb=" O VAL G 154 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 240 through 242 removed outlier: 8.697A pdb=" N ILE G 241 " --> pdb=" O VAL G 341 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL G 343 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA G 299 " --> pdb=" O ILE G 342 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N MET G 344 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE G 301 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE G 265 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE G 302 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE G 267 " --> pdb=" O PHE G 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'G' and resid 641 through 645 removed outlier: 4.325A pdb=" N GLN G 641 " --> pdb=" O GLY G 513 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU G 515 " --> pdb=" O GLN G 641 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 643 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR G 517 " --> pdb=" O ILE G 643 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE G 619 " --> pdb=" O VAL G 514 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE G 516 " --> pdb=" O ILE G 619 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY G 621 " --> pdb=" O PHE G 516 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY G 518 " --> pdb=" O GLY G 621 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN G 538 " --> pdb=" O VAL G 573 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE G 575 " --> pdb=" O ASN G 538 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE G 540 " --> pdb=" O PHE G 575 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.821A pdb=" N SER H 101 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL H 57 " --> pdb=" O CYS H 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS H 69 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA H 67 " --> pdb=" O LEU H 59 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 39 through 41 Processing sheet with id= AQ, first strand: chain 'H' and resid 153 through 155 removed outlier: 3.550A pdb=" N VAL H 161 " --> pdb=" O VAL H 154 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 240 through 242 removed outlier: 8.697A pdb=" N ILE H 241 " --> pdb=" O VAL H 341 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL H 343 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA H 299 " --> pdb=" O ILE H 342 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N MET H 344 " --> pdb=" O ALA H 299 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE H 301 " --> pdb=" O MET H 344 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE H 265 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE H 302 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE H 267 " --> pdb=" O PHE H 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'H' and resid 641 through 645 removed outlier: 4.324A pdb=" N GLN H 641 " --> pdb=" O GLY H 513 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 515 " --> pdb=" O GLN H 641 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 643 " --> pdb=" O LEU H 515 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR H 517 " --> pdb=" O ILE H 643 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE H 619 " --> pdb=" O VAL H 514 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N PHE H 516 " --> pdb=" O ILE H 619 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY H 621 " --> pdb=" O PHE H 516 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY H 518 " --> pdb=" O GLY H 621 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN H 538 " --> pdb=" O VAL H 573 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE H 575 " --> pdb=" O ASN H 538 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE H 540 " --> pdb=" O PHE H 575 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'I' and resid 25 through 27 removed outlier: 3.820A pdb=" N SER I 101 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL I 57 " --> pdb=" O CYS I 69 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS I 69 " --> pdb=" O VAL I 57 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA I 67 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 39 through 41 Processing sheet with id= AV, first strand: chain 'I' and resid 153 through 155 removed outlier: 3.550A pdb=" N VAL I 161 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'I' and resid 240 through 242 removed outlier: 8.697A pdb=" N ILE I 241 " --> pdb=" O VAL I 341 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL I 343 " --> pdb=" O ILE I 241 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA I 299 " --> pdb=" O ILE I 342 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N MET I 344 " --> pdb=" O ALA I 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE I 301 " --> pdb=" O MET I 344 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE I 265 " --> pdb=" O ILE I 300 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE I 302 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE I 267 " --> pdb=" O PHE I 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'I' and resid 641 through 645 removed outlier: 4.323A pdb=" N GLN I 641 " --> pdb=" O GLY I 513 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU I 515 " --> pdb=" O GLN I 641 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 643 " --> pdb=" O LEU I 515 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR I 517 " --> pdb=" O ILE I 643 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE I 619 " --> pdb=" O VAL I 514 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE I 516 " --> pdb=" O ILE I 619 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY I 621 " --> pdb=" O PHE I 516 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLY I 518 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN I 538 " --> pdb=" O VAL I 573 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE I 575 " --> pdb=" O ASN I 538 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE I 540 " --> pdb=" O PHE I 575 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'J' and resid 25 through 27 removed outlier: 3.820A pdb=" N SER J 101 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL J 57 " --> pdb=" O CYS J 69 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS J 69 " --> pdb=" O VAL J 57 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA J 67 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'J' and resid 39 through 41 Processing sheet with id= BA, first strand: chain 'J' and resid 153 through 155 removed outlier: 3.550A pdb=" N VAL J 161 " --> pdb=" O VAL J 154 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'J' and resid 240 through 242 removed outlier: 8.697A pdb=" N ILE J 241 " --> pdb=" O VAL J 341 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL J 343 " --> pdb=" O ILE J 241 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA J 299 " --> pdb=" O ILE J 342 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N MET J 344 " --> pdb=" O ALA J 299 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE J 301 " --> pdb=" O MET J 344 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE J 265 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE J 302 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE J 267 " --> pdb=" O PHE J 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= BB Processing sheet with id= BC, first strand: chain 'J' and resid 641 through 645 removed outlier: 4.324A pdb=" N GLN J 641 " --> pdb=" O GLY J 513 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU J 515 " --> pdb=" O GLN J 641 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 643 " --> pdb=" O LEU J 515 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR J 517 " --> pdb=" O ILE J 643 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE J 619 " --> pdb=" O VAL J 514 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE J 516 " --> pdb=" O ILE J 619 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY J 621 " --> pdb=" O PHE J 516 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLY J 518 " --> pdb=" O GLY J 621 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN J 538 " --> pdb=" O VAL J 573 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE J 575 " --> pdb=" O ASN J 538 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE J 540 " --> pdb=" O PHE J 575 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'K' and resid 25 through 27 removed outlier: 3.821A pdb=" N SER K 101 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL K 57 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS K 69 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA K 67 " --> pdb=" O LEU K 59 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'K' and resid 39 through 41 Processing sheet with id= BF, first strand: chain 'K' and resid 153 through 155 removed outlier: 3.550A pdb=" N VAL K 161 " --> pdb=" O VAL K 154 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'K' and resid 240 through 242 removed outlier: 8.697A pdb=" N ILE K 241 " --> pdb=" O VAL K 341 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL K 343 " --> pdb=" O ILE K 241 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA K 299 " --> pdb=" O ILE K 342 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N MET K 344 " --> pdb=" O ALA K 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE K 301 " --> pdb=" O MET K 344 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE K 265 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE K 302 " --> pdb=" O PHE K 265 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE K 267 " --> pdb=" O PHE K 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= BG Processing sheet with id= BH, first strand: chain 'K' and resid 641 through 645 removed outlier: 4.324A pdb=" N GLN K 641 " --> pdb=" O GLY K 513 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU K 515 " --> pdb=" O GLN K 641 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE K 643 " --> pdb=" O LEU K 515 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR K 517 " --> pdb=" O ILE K 643 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE K 619 " --> pdb=" O VAL K 514 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE K 516 " --> pdb=" O ILE K 619 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY K 621 " --> pdb=" O PHE K 516 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLY K 518 " --> pdb=" O GLY K 621 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN K 538 " --> pdb=" O VAL K 573 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE K 575 " --> pdb=" O ASN K 538 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE K 540 " --> pdb=" O PHE K 575 " (cutoff:3.500A) 1369 hydrogen bonds defined for protein. 3819 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: 24.74 Time building geometry restraints manager: 21.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 22557 1.34 - 1.49: 16344 1.49 - 1.64: 30843 1.64 - 1.80: 238 1.80 - 1.95: 350 Bond restraints: 70332 Sorted by residual: bond pdb=" C15 JDP A 803 " pdb=" N16 JDP A 803 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C15 JDP G 803 " pdb=" N16 JDP G 803 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C15 JDP J 803 " pdb=" N16 JDP J 803 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C15 JDP B 803 " pdb=" N16 JDP B 803 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C15 JDP F 803 " pdb=" N16 JDP F 803 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 70327 not shown) Histogram of bond angle deviations from ideal: 96.75 - 107.70: 2790 107.70 - 118.64: 54190 118.64 - 129.58: 37808 129.58 - 140.53: 288 140.53 - 151.47: 12 Bond angle restraints: 95088 Sorted by residual: angle pdb=" C11 JDP G 803 " pdb=" C10 JDP G 803 " pdb=" N12 JDP G 803 " ideal model delta sigma weight residual 124.18 151.47 -27.29 3.00e+00 1.11e-01 8.27e+01 angle pdb=" C11 JDP B 803 " pdb=" C10 JDP B 803 " pdb=" N12 JDP B 803 " ideal model delta sigma weight residual 124.18 151.46 -27.28 3.00e+00 1.11e-01 8.27e+01 angle pdb=" C11 JDP H 803 " pdb=" C10 JDP H 803 " pdb=" N12 JDP H 803 " ideal model delta sigma weight residual 124.18 151.46 -27.28 3.00e+00 1.11e-01 8.27e+01 angle pdb=" C11 JDP I 803 " pdb=" C10 JDP I 803 " pdb=" N12 JDP I 803 " ideal model delta sigma weight residual 124.18 151.44 -27.26 3.00e+00 1.11e-01 8.26e+01 angle pdb=" C11 JDP J 803 " pdb=" C10 JDP J 803 " pdb=" N12 JDP J 803 " ideal model delta sigma weight residual 124.18 151.44 -27.26 3.00e+00 1.11e-01 8.25e+01 ... (remaining 95083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.17: 40678 24.17 - 48.34: 2582 48.34 - 72.52: 180 72.52 - 96.69: 108 96.69 - 120.86: 24 Dihedral angle restraints: 43572 sinusoidal: 18432 harmonic: 25140 Sorted by residual: dihedral pdb=" CA ASN I 270 " pdb=" C ASN I 270 " pdb=" N GLY I 271 " pdb=" CA GLY I 271 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASN C 270 " pdb=" C ASN C 270 " pdb=" N GLY C 271 " pdb=" CA GLY C 271 " ideal model delta harmonic sigma weight residual 180.00 156.20 23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASN J 270 " pdb=" C ASN J 270 " pdb=" N GLY J 271 " pdb=" CA GLY J 271 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 43569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 7387 0.043 - 0.085: 2393 0.085 - 0.128: 822 0.128 - 0.171: 42 0.171 - 0.213: 12 Chirality restraints: 10656 Sorted by residual: chirality pdb=" CA ASN E 460 " pdb=" N ASN E 460 " pdb=" C ASN E 460 " pdb=" CB ASN E 460 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASN J 460 " pdb=" N ASN J 460 " pdb=" C ASN J 460 " pdb=" CB ASN J 460 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ASN D 460 " pdb=" N ASN D 460 " pdb=" C ASN D 460 " pdb=" CB ASN D 460 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 10653 not shown) Planarity restraints: 12504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 635 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO A 636 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 636 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 636 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 635 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO H 636 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO H 636 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 636 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 635 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.90e+00 pdb=" N PRO F 636 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO F 636 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 636 " -0.038 5.00e-02 4.00e+02 ... (remaining 12501 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 1183 2.63 - 3.20: 63618 3.20 - 3.77: 106063 3.77 - 4.33: 143642 4.33 - 4.90: 222847 Nonbonded interactions: 537353 Sorted by model distance: nonbonded pdb=" O3G AGS B 801 " pdb="MG MG B 802 " model vdw 2.067 2.170 nonbonded pdb=" O3G AGS H 801 " pdb="MG MG H 802 " model vdw 2.068 2.170 nonbonded pdb=" O3G AGS J 801 " pdb="MG MG J 802 " model vdw 2.068 2.170 nonbonded pdb=" O3G AGS K 801 " pdb="MG MG K 802 " model vdw 2.068 2.170 nonbonded pdb=" O3G AGS G 801 " pdb="MG MG G 802 " model vdw 2.068 2.170 ... (remaining 537348 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 0.050 Extract box with map and model: 9.220 Check model and map are aligned: 0.760 Set scattering table: 0.450 Process input model: 138.440 Find NCS groups from input model: 4.110 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.004 0.108 70332 Z= 0.281 Angle : 0.918 27.289 95088 Z= 0.460 Chirality : 0.045 0.213 10656 Planarity : 0.005 0.073 12504 Dihedral : 15.195 120.862 27276 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.23 % Favored : 93.22 % Rotamer: Outliers : 0.01 % Allowed : 0.73 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.09), residues: 8688 helix: -1.78 (0.09), residues: 2736 sheet: -0.73 (0.16), residues: 1044 loop : -2.04 (0.09), residues: 4908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 454 HIS 0.003 0.001 HIS D 384 PHE 0.025 0.001 PHE J 674 TYR 0.019 0.001 TYR I 517 ARG 0.019 0.001 ARG I 625 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 874 time to evaluate : 5.730 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: A 378 LEU cc_start: 0.8977 (mt) cc_final: 0.8754 (mt) REVERT: A 427 MET cc_start: 0.8526 (tpp) cc_final: 0.8224 (tpt) REVERT: A 477 GLU cc_start: 0.8786 (pm20) cc_final: 0.8556 (pm20) REVERT: A 508 MET cc_start: 0.8337 (ppp) cc_final: 0.7963 (ppp) REVERT: A 578 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 378 LEU cc_start: 0.8834 (mt) cc_final: 0.8631 (mt) REVERT: B 427 MET cc_start: 0.8394 (tpp) cc_final: 0.8112 (tpp) REVERT: B 508 MET cc_start: 0.8430 (ppp) cc_final: 0.8175 (ppp) REVERT: B 578 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 275 MET cc_start: 0.8816 (mpp) cc_final: 0.8355 (mpp) REVERT: C 427 MET cc_start: 0.8543 (tpp) cc_final: 0.8298 (tpt) REVERT: C 508 MET cc_start: 0.8341 (ppp) cc_final: 0.8082 (ppp) REVERT: C 578 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8270 (tm-30) REVERT: D 275 MET cc_start: 0.8706 (mpp) cc_final: 0.8449 (mpp) REVERT: D 378 LEU cc_start: 0.9087 (mt) cc_final: 0.8880 (mt) REVERT: D 427 MET cc_start: 0.8399 (tpp) cc_final: 0.8130 (tpt) REVERT: D 508 MET cc_start: 0.8355 (ppp) cc_final: 0.7997 (ppp) REVERT: D 578 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8392 (tm-30) REVERT: E 378 LEU cc_start: 0.9035 (mt) cc_final: 0.8802 (mt) REVERT: E 427 MET cc_start: 0.8226 (tpp) cc_final: 0.7949 (tpp) REVERT: E 483 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8689 (mm-30) REVERT: E 550 MET cc_start: 0.8444 (ppp) cc_final: 0.8178 (ppp) REVERT: F 578 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8161 (tm-30) REVERT: L 378 LEU cc_start: 0.9086 (mt) cc_final: 0.8857 (mt) REVERT: L 578 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8560 (tm-30) REVERT: L 608 MET cc_start: 0.9308 (ptm) cc_final: 0.9066 (ptm) REVERT: L 633 ILE cc_start: 0.8708 (pt) cc_final: 0.8408 (pt) REVERT: G 378 LEU cc_start: 0.9103 (mt) cc_final: 0.8890 (mt) REVERT: G 427 MET cc_start: 0.8424 (tpp) cc_final: 0.8134 (tpt) REVERT: G 508 MET cc_start: 0.8305 (ppp) cc_final: 0.8074 (ppp) REVERT: G 578 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8279 (tm-30) REVERT: H 275 MET cc_start: 0.8821 (mpp) cc_final: 0.8215 (mpp) REVERT: H 508 MET cc_start: 0.8087 (ppp) cc_final: 0.7851 (ppp) REVERT: H 578 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8240 (tm-30) REVERT: I 508 MET cc_start: 0.8337 (ppp) cc_final: 0.8102 (ppp) REVERT: I 578 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8302 (tm-30) REVERT: J 378 LEU cc_start: 0.8903 (mt) cc_final: 0.8691 (mt) REVERT: J 427 MET cc_start: 0.8450 (tpp) cc_final: 0.8235 (tpp) REVERT: J 477 GLU cc_start: 0.8766 (pm20) cc_final: 0.8538 (pm20) REVERT: J 508 MET cc_start: 0.8160 (ppp) cc_final: 0.7769 (ppp) REVERT: J 578 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8230 (tm-30) REVERT: K 578 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8220 (tm-30) outliers start: 1 outliers final: 0 residues processed: 875 average time/residue: 0.6410 time to fit residues: 950.3836 Evaluate side-chains 635 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 635 time to evaluate : 5.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 729 optimal weight: 30.0000 chunk 654 optimal weight: 50.0000 chunk 363 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 441 optimal weight: 0.9980 chunk 349 optimal weight: 0.0010 chunk 677 optimal weight: 7.9990 chunk 262 optimal weight: 9.9990 chunk 411 optimal weight: 9.9990 chunk 504 optimal weight: 30.0000 chunk 784 optimal weight: 10.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 115 HIS A 348 ASN A 538 ASN B 36 ASN B 215 GLN B 348 ASN B 384 HIS B 603 GLN C 36 ASN C 115 HIS C 348 ASN D 36 ASN D 115 HIS D 348 ASN D 538 ASN E 36 ASN E 115 HIS E 215 GLN E 348 ASN E 384 HIS E 603 GLN F 36 ASN F 115 HIS F 215 GLN F 348 ASN F 384 HIS L 36 ASN L 115 HIS L 348 ASN L 490 GLN L 538 ASN L 603 GLN G 36 ASN G 115 HIS H 36 ASN H 115 HIS H 348 ASN I 36 ASN I 115 HIS I 348 ASN I 384 HIS J 36 ASN J 115 HIS J 348 ASN J 490 GLN J 538 ASN K 36 ASN K 215 GLN K 348 ASN K 603 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 70332 Z= 0.416 Angle : 0.787 11.080 95088 Z= 0.399 Chirality : 0.048 0.186 10656 Planarity : 0.005 0.078 12504 Dihedral : 8.727 83.964 9864 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.69 % Favored : 93.69 % Rotamer: Outliers : 1.74 % Allowed : 10.41 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.09), residues: 8688 helix: -1.51 (0.09), residues: 2880 sheet: -0.34 (0.16), residues: 1176 loop : -1.50 (0.09), residues: 4632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 551 HIS 0.005 0.001 HIS E 404 PHE 0.039 0.002 PHE E 674 TYR 0.025 0.003 TYR J 173 ARG 0.009 0.001 ARG L 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 622 time to evaluate : 5.836 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 275 MET cc_start: 0.8952 (mpp) cc_final: 0.8691 (mpp) REVERT: A 427 MET cc_start: 0.8536 (tpp) cc_final: 0.8315 (tpp) REVERT: A 477 GLU cc_start: 0.8994 (pm20) cc_final: 0.8744 (pm20) REVERT: A 508 MET cc_start: 0.8786 (ppp) cc_final: 0.8380 (ppp) REVERT: A 517 TYR cc_start: 0.9145 (p90) cc_final: 0.8537 (p90) REVERT: A 546 GLU cc_start: 0.9119 (pp20) cc_final: 0.8863 (pp20) REVERT: A 578 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8356 (tm-30) REVERT: A 608 MET cc_start: 0.9676 (ptm) cc_final: 0.9397 (ptm) REVERT: B 427 MET cc_start: 0.8308 (tpp) cc_final: 0.8058 (tpt) REVERT: B 508 MET cc_start: 0.8819 (ppp) cc_final: 0.8500 (ppp) REVERT: B 578 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8423 (tm-30) REVERT: C 275 MET cc_start: 0.8940 (mpp) cc_final: 0.8654 (mpp) REVERT: C 427 MET cc_start: 0.8547 (tpp) cc_final: 0.8270 (tpt) REVERT: C 470 GLU cc_start: 0.7798 (pm20) cc_final: 0.7454 (pm20) REVERT: C 508 MET cc_start: 0.8768 (ppp) cc_final: 0.8414 (ppp) REVERT: C 517 TYR cc_start: 0.9098 (p90) cc_final: 0.8818 (p90) REVERT: C 578 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8168 (tm-30) REVERT: D 83 ARG cc_start: 0.6875 (mpt180) cc_final: 0.6552 (mpt180) REVERT: D 219 MET cc_start: 0.8979 (ptp) cc_final: 0.8769 (ptp) REVERT: D 275 MET cc_start: 0.9091 (mpp) cc_final: 0.8823 (mpp) REVERT: D 427 MET cc_start: 0.8466 (tpp) cc_final: 0.8202 (tpt) REVERT: D 508 MET cc_start: 0.8850 (ppp) cc_final: 0.8517 (ppp) REVERT: D 578 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8210 (tm-30) REVERT: D 608 MET cc_start: 0.9717 (ptm) cc_final: 0.9424 (ptm) REVERT: E 275 MET cc_start: 0.8843 (mpp) cc_final: 0.8639 (mpp) REVERT: E 427 MET cc_start: 0.8153 (tpp) cc_final: 0.7903 (tpp) REVERT: E 536 GLN cc_start: 0.8955 (mp10) cc_final: 0.8753 (mp10) REVERT: E 641 GLN cc_start: 0.8660 (mp10) cc_final: 0.8408 (mp10) REVERT: F 427 MET cc_start: 0.7808 (tpp) cc_final: 0.7456 (tpp) REVERT: F 517 TYR cc_start: 0.9216 (p90) cc_final: 0.8695 (p90) REVERT: F 578 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8306 (tm-30) REVERT: F 608 MET cc_start: 0.9797 (ptm) cc_final: 0.9421 (ptt) REVERT: L 470 GLU cc_start: 0.7631 (pm20) cc_final: 0.7384 (pm20) REVERT: L 578 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8300 (tm-30) REVERT: L 678 MET cc_start: 0.8662 (mpp) cc_final: 0.8448 (mpp) REVERT: G 83 ARG cc_start: 0.7029 (mpt180) cc_final: 0.6689 (mpp80) REVERT: G 427 MET cc_start: 0.8401 (tpp) cc_final: 0.8033 (tpt) REVERT: G 508 MET cc_start: 0.8739 (ppp) cc_final: 0.8524 (ppp) REVERT: G 517 TYR cc_start: 0.9120 (p90) cc_final: 0.8644 (p90) REVERT: G 578 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8371 (tm-30) REVERT: H 427 MET cc_start: 0.7892 (tpp) cc_final: 0.7541 (tpp) REVERT: H 508 MET cc_start: 0.8713 (ppp) cc_final: 0.8425 (ppp) REVERT: H 578 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8369 (tm-30) REVERT: H 608 MET cc_start: 0.9606 (ptm) cc_final: 0.9374 (ptt) REVERT: I 470 GLU cc_start: 0.7797 (pm20) cc_final: 0.7496 (pm20) REVERT: I 508 MET cc_start: 0.8781 (ppp) cc_final: 0.8426 (ppp) REVERT: I 517 TYR cc_start: 0.9073 (p90) cc_final: 0.8831 (p90) REVERT: I 546 GLU cc_start: 0.9158 (pp20) cc_final: 0.8954 (pp20) REVERT: I 577 ASP cc_start: 0.8636 (t0) cc_final: 0.8423 (t0) REVERT: I 578 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8297 (tm-30) REVERT: I 678 MET cc_start: 0.8542 (mpp) cc_final: 0.8039 (mpp) REVERT: J 427 MET cc_start: 0.8411 (tpp) cc_final: 0.8177 (tpp) REVERT: J 477 GLU cc_start: 0.8965 (pm20) cc_final: 0.8729 (pm20) REVERT: J 508 MET cc_start: 0.8737 (ppp) cc_final: 0.8317 (ppp) REVERT: J 517 TYR cc_start: 0.9178 (p90) cc_final: 0.8716 (p90) REVERT: J 546 GLU cc_start: 0.9098 (pp20) cc_final: 0.8873 (pp20) REVERT: J 578 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8346 (tm-30) REVERT: J 608 MET cc_start: 0.9703 (ptm) cc_final: 0.9202 (ptp) REVERT: K 83 ARG cc_start: 0.6923 (mpt180) cc_final: 0.6558 (mpt180) REVERT: K 427 MET cc_start: 0.7921 (tpp) cc_final: 0.7574 (tpp) REVERT: K 578 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8195 (tm-30) outliers start: 129 outliers final: 87 residues processed: 686 average time/residue: 0.6292 time to fit residues: 744.8359 Evaluate side-chains 628 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 541 time to evaluate : 5.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 756 GLU Chi-restraints excluded: chain F residue 758 PHE Chi-restraints excluded: chain L residue 344 MET Chi-restraints excluded: chain L residue 420 LEU Chi-restraints excluded: chain L residue 527 LEU Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 619 ILE Chi-restraints excluded: chain L residue 697 LEU Chi-restraints excluded: chain L residue 756 GLU Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 564 ASP Chi-restraints excluded: chain G residue 619 ILE Chi-restraints excluded: chain G residue 756 GLU Chi-restraints excluded: chain G residue 758 PHE Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 375 THR Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 564 ASP Chi-restraints excluded: chain H residue 619 ILE Chi-restraints excluded: chain H residue 756 GLU Chi-restraints excluded: chain H residue 758 PHE Chi-restraints excluded: chain I residue 344 MET Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 527 LEU Chi-restraints excluded: chain I residue 564 ASP Chi-restraints excluded: chain I residue 619 ILE Chi-restraints excluded: chain I residue 675 LEU Chi-restraints excluded: chain I residue 756 GLU Chi-restraints excluded: chain I residue 758 PHE Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 564 ASP Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain K residue 344 MET Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 564 ASP Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 750 ASN Chi-restraints excluded: chain K residue 756 GLU Chi-restraints excluded: chain K residue 758 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 436 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 653 optimal weight: 9.9990 chunk 534 optimal weight: 0.9990 chunk 216 optimal weight: 30.0000 chunk 786 optimal weight: 1.9990 chunk 849 optimal weight: 40.0000 chunk 700 optimal weight: 0.0170 chunk 779 optimal weight: 0.5980 chunk 267 optimal weight: 5.9990 chunk 630 optimal weight: 0.7980 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS B 215 GLN B 568 GLN C 115 HIS C 568 GLN D 115 HIS ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 GLN F 115 HIS F 215 GLN F 568 GLN L 115 HIS G 115 HIS ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 HIS I 568 GLN J 115 HIS K 215 GLN K 568 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 70332 Z= 0.153 Angle : 0.571 8.155 95088 Z= 0.281 Chirality : 0.045 0.161 10656 Planarity : 0.004 0.059 12504 Dihedral : 8.345 88.967 9864 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.82 % Favored : 93.90 % Rotamer: Outliers : 1.97 % Allowed : 13.15 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.09), residues: 8688 helix: -0.95 (0.09), residues: 2868 sheet: -0.10 (0.16), residues: 1140 loop : -1.68 (0.09), residues: 4680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 476 HIS 0.003 0.001 HIS B 406 PHE 0.055 0.001 PHE J 758 TYR 0.013 0.001 TYR F 134 ARG 0.006 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 591 time to evaluate : 6.022 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: A 36 ASN cc_start: 0.5776 (OUTLIER) cc_final: 0.5564 (t0) REVERT: A 397 GLU cc_start: 0.8984 (tp30) cc_final: 0.8778 (tp30) REVERT: A 477 GLU cc_start: 0.8845 (pm20) cc_final: 0.8604 (pm20) REVERT: A 508 MET cc_start: 0.8707 (ppp) cc_final: 0.8181 (ppp) REVERT: A 546 GLU cc_start: 0.9117 (pp20) cc_final: 0.8865 (pp20) REVERT: A 578 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8336 (tm-30) REVERT: B 36 ASN cc_start: 0.5579 (OUTLIER) cc_final: 0.5324 (t0) REVERT: B 275 MET cc_start: 0.8743 (mpp) cc_final: 0.8480 (mpp) REVERT: B 427 MET cc_start: 0.8301 (tpp) cc_final: 0.8093 (tpt) REVERT: B 508 MET cc_start: 0.8770 (ppp) cc_final: 0.8358 (ppp) REVERT: B 578 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8357 (tm-30) REVERT: B 678 MET cc_start: 0.8523 (mpp) cc_final: 0.7868 (mpp) REVERT: B 757 MET cc_start: 0.9100 (ppp) cc_final: 0.8784 (ppp) REVERT: C 275 MET cc_start: 0.8819 (mpp) cc_final: 0.8585 (mpp) REVERT: C 427 MET cc_start: 0.8567 (tpp) cc_final: 0.8296 (tpt) REVERT: C 470 GLU cc_start: 0.7578 (pm20) cc_final: 0.7248 (pm20) REVERT: C 508 MET cc_start: 0.8739 (ppp) cc_final: 0.8307 (ppp) REVERT: C 517 TYR cc_start: 0.8953 (p90) cc_final: 0.8521 (p90) REVERT: C 578 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8101 (tm-30) REVERT: D 36 ASN cc_start: 0.6119 (OUTLIER) cc_final: 0.5841 (t0) REVERT: D 83 ARG cc_start: 0.6819 (mpt180) cc_final: 0.6499 (mpt180) REVERT: D 219 MET cc_start: 0.8990 (ptp) cc_final: 0.8789 (ptp) REVERT: D 427 MET cc_start: 0.8466 (tpp) cc_final: 0.8245 (tpt) REVERT: D 508 MET cc_start: 0.8746 (ppp) cc_final: 0.8248 (ppp) REVERT: D 578 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8166 (tm-30) REVERT: D 757 MET cc_start: 0.9091 (ppp) cc_final: 0.8818 (ppp) REVERT: E 36 ASN cc_start: 0.5910 (OUTLIER) cc_final: 0.5386 (t0) REVERT: E 275 MET cc_start: 0.8637 (mpp) cc_final: 0.8346 (mpp) REVERT: E 536 GLN cc_start: 0.8845 (mp10) cc_final: 0.8641 (mp10) REVERT: E 578 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8361 (tm-30) REVERT: F 36 ASN cc_start: 0.6008 (OUTLIER) cc_final: 0.5646 (t0) REVERT: F 397 GLU cc_start: 0.8828 (tp30) cc_final: 0.8623 (tp30) REVERT: F 427 MET cc_start: 0.7875 (tpp) cc_final: 0.7518 (tpt) REVERT: F 578 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8272 (tm-30) REVERT: L 36 ASN cc_start: 0.5911 (OUTLIER) cc_final: 0.5614 (t0) REVERT: L 449 MET cc_start: 0.7790 (mmp) cc_final: 0.7345 (mmp) REVERT: L 466 GLU cc_start: 0.8313 (pm20) cc_final: 0.7931 (mp0) REVERT: L 470 GLU cc_start: 0.7566 (pm20) cc_final: 0.7282 (pm20) REVERT: L 517 TYR cc_start: 0.8981 (p90) cc_final: 0.8415 (p90) REVERT: L 578 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8301 (tm-30) REVERT: G 36 ASN cc_start: 0.5958 (OUTLIER) cc_final: 0.5716 (t0) REVERT: G 427 MET cc_start: 0.8425 (tpp) cc_final: 0.8135 (tpt) REVERT: G 508 MET cc_start: 0.8745 (ppp) cc_final: 0.8381 (ppp) REVERT: G 578 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8307 (tm-30) REVERT: G 757 MET cc_start: 0.9057 (ppp) cc_final: 0.8852 (ppp) REVERT: H 36 ASN cc_start: 0.6001 (OUTLIER) cc_final: 0.5672 (t0) REVERT: H 397 GLU cc_start: 0.8897 (tp30) cc_final: 0.8672 (tp30) REVERT: H 427 MET cc_start: 0.7927 (tpp) cc_final: 0.7543 (tpp) REVERT: H 508 MET cc_start: 0.8608 (ppp) cc_final: 0.8168 (ppp) REVERT: H 578 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8292 (tm-30) REVERT: H 757 MET cc_start: 0.9126 (ppp) cc_final: 0.8841 (ppp) REVERT: I 470 GLU cc_start: 0.7721 (pm20) cc_final: 0.7404 (pm20) REVERT: I 508 MET cc_start: 0.8719 (ppp) cc_final: 0.8287 (ppp) REVERT: I 517 TYR cc_start: 0.8913 (p90) cc_final: 0.8408 (p90) REVERT: I 546 GLU cc_start: 0.9239 (pp20) cc_final: 0.8990 (pp20) REVERT: I 578 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8182 (tm-30) REVERT: I 608 MET cc_start: 0.9739 (ptm) cc_final: 0.9390 (ptt) REVERT: J 36 ASN cc_start: 0.5745 (OUTLIER) cc_final: 0.5519 (t0) REVERT: J 397 GLU cc_start: 0.8917 (tp30) cc_final: 0.8717 (tp30) REVERT: J 477 GLU cc_start: 0.8832 (pm20) cc_final: 0.8586 (pm20) REVERT: J 508 MET cc_start: 0.8654 (ppp) cc_final: 0.8119 (ppp) REVERT: J 517 TYR cc_start: 0.8961 (p90) cc_final: 0.8365 (p90) REVERT: J 546 GLU cc_start: 0.9134 (pp20) cc_final: 0.8878 (pp20) REVERT: J 578 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8260 (tm-30) REVERT: K 36 ASN cc_start: 0.5856 (OUTLIER) cc_final: 0.5554 (t0) REVERT: K 397 GLU cc_start: 0.8763 (tp30) cc_final: 0.8526 (tp30) REVERT: K 427 MET cc_start: 0.8000 (tpp) cc_final: 0.7641 (tpp) REVERT: K 578 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8123 (tm-30) outliers start: 146 outliers final: 87 residues processed: 670 average time/residue: 0.6164 time to fit residues: 724.7369 Evaluate side-chains 639 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 542 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 568 GLN Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 568 GLN Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 568 GLN Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 758 PHE Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 394 VAL Chi-restraints excluded: chain L residue 420 LEU Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 619 ILE Chi-restraints excluded: chain L residue 647 LEU Chi-restraints excluded: chain L residue 697 LEU Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 351 ASN Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 564 ASP Chi-restraints excluded: chain G residue 619 ILE Chi-restraints excluded: chain G residue 758 PHE Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 564 ASP Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain H residue 619 ILE Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 758 PHE Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 468 VAL Chi-restraints excluded: chain I residue 564 ASP Chi-restraints excluded: chain I residue 568 GLN Chi-restraints excluded: chain I residue 619 ILE Chi-restraints excluded: chain I residue 758 PHE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 564 ASP Chi-restraints excluded: chain J residue 611 MET Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 351 ASN Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 564 ASP Chi-restraints excluded: chain K residue 568 GLN Chi-restraints excluded: chain K residue 611 MET Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 758 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 776 optimal weight: 9.9990 chunk 590 optimal weight: 8.9990 chunk 407 optimal weight: 0.9980 chunk 87 optimal weight: 30.0000 chunk 375 optimal weight: 2.9990 chunk 527 optimal weight: 0.0570 chunk 788 optimal weight: 10.0000 chunk 835 optimal weight: 9.9990 chunk 412 optimal weight: 8.9990 chunk 747 optimal weight: 5.9990 chunk 225 optimal weight: 30.0000 overall best weight: 3.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS C 36 ASN C 115 HIS C 215 GLN C 603 GLN D 115 HIS ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS F 215 GLN L 115 HIS G 115 HIS ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 70332 Z= 0.276 Angle : 0.603 8.310 95088 Z= 0.303 Chirality : 0.045 0.170 10656 Planarity : 0.004 0.061 12504 Dihedral : 8.368 86.926 9864 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.87 % Favored : 93.90 % Rotamer: Outliers : 2.68 % Allowed : 13.48 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.67 (0.09), residues: 8688 helix: -0.85 (0.09), residues: 3084 sheet: -0.05 (0.16), residues: 1140 loop : -1.57 (0.10), residues: 4464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 476 HIS 0.005 0.001 HIS B 406 PHE 0.037 0.001 PHE J 758 TYR 0.017 0.001 TYR H 173 ARG 0.009 0.001 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 537 time to evaluate : 5.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 508 MET cc_start: 0.8887 (ppp) cc_final: 0.8362 (ppp) REVERT: A 546 GLU cc_start: 0.9178 (pp20) cc_final: 0.8888 (pp20) REVERT: A 578 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 757 MET cc_start: 0.9087 (ppp) cc_final: 0.8837 (ppp) REVERT: B 427 MET cc_start: 0.8222 (tpp) cc_final: 0.7981 (tpt) REVERT: B 508 MET cc_start: 0.8912 (ppp) cc_final: 0.8492 (ppp) REVERT: B 578 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8338 (tm-30) REVERT: B 756 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8518 (pm20) REVERT: B 757 MET cc_start: 0.9188 (ppp) cc_final: 0.8931 (ppp) REVERT: C 275 MET cc_start: 0.8939 (mpp) cc_final: 0.8641 (mpp) REVERT: C 427 MET cc_start: 0.8530 (tpp) cc_final: 0.8286 (tpt) REVERT: C 470 GLU cc_start: 0.7857 (pm20) cc_final: 0.7425 (pm20) REVERT: C 508 MET cc_start: 0.8893 (ppp) cc_final: 0.8465 (ppp) REVERT: C 517 TYR cc_start: 0.9192 (p90) cc_final: 0.8696 (p90) REVERT: C 578 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8150 (tm-30) REVERT: D 36 ASN cc_start: 0.6190 (OUTLIER) cc_final: 0.5918 (t0) REVERT: D 83 ARG cc_start: 0.6956 (mpt180) cc_final: 0.6621 (mpt180) REVERT: D 211 LYS cc_start: 0.9294 (ptmm) cc_final: 0.9051 (ptmm) REVERT: D 427 MET cc_start: 0.8473 (tpp) cc_final: 0.8238 (tpt) REVERT: D 449 MET cc_start: 0.8470 (mmt) cc_final: 0.7921 (tmm) REVERT: D 508 MET cc_start: 0.8881 (ppp) cc_final: 0.8376 (ppp) REVERT: D 517 TYR cc_start: 0.9180 (p90) cc_final: 0.8433 (p90) REVERT: D 578 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8288 (tm-30) REVERT: D 757 MET cc_start: 0.9180 (ppp) cc_final: 0.8840 (ppp) REVERT: E 36 ASN cc_start: 0.6000 (OUTLIER) cc_final: 0.5522 (t0) REVERT: E 442 MET cc_start: 0.8931 (pmm) cc_final: 0.8716 (pmm) REVERT: E 578 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8371 (tm-30) REVERT: F 36 ASN cc_start: 0.6085 (OUTLIER) cc_final: 0.5721 (t0) REVERT: F 578 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8295 (tm-30) REVERT: L 36 ASN cc_start: 0.6027 (OUTLIER) cc_final: 0.5757 (t0) REVERT: L 470 GLU cc_start: 0.7790 (pm20) cc_final: 0.7469 (pm20) REVERT: L 517 TYR cc_start: 0.9150 (p90) cc_final: 0.8487 (p90) REVERT: L 578 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8344 (tm-30) REVERT: G 36 ASN cc_start: 0.5949 (OUTLIER) cc_final: 0.5710 (t0) REVERT: G 427 MET cc_start: 0.8400 (tpp) cc_final: 0.8077 (tpt) REVERT: G 449 MET cc_start: 0.8378 (mmp) cc_final: 0.7815 (tmm) REVERT: G 508 MET cc_start: 0.8842 (ppp) cc_final: 0.8420 (ppp) REVERT: G 517 TYR cc_start: 0.9213 (p90) cc_final: 0.8553 (p90) REVERT: G 578 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8255 (tm-30) REVERT: G 756 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8573 (pm20) REVERT: G 757 MET cc_start: 0.9139 (ppp) cc_final: 0.8925 (ppp) REVERT: H 36 ASN cc_start: 0.6106 (OUTLIER) cc_final: 0.5781 (t0) REVERT: H 378 LEU cc_start: 0.9596 (tp) cc_final: 0.9385 (tt) REVERT: H 427 MET cc_start: 0.8004 (tpp) cc_final: 0.7659 (tpp) REVERT: H 508 MET cc_start: 0.8847 (ppp) cc_final: 0.8410 (ppp) REVERT: H 578 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8312 (tm-30) REVERT: H 756 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8576 (pm20) REVERT: H 757 MET cc_start: 0.9189 (ppp) cc_final: 0.8909 (ppp) REVERT: I 470 GLU cc_start: 0.7951 (pm20) cc_final: 0.7577 (pm20) REVERT: I 508 MET cc_start: 0.8871 (ppp) cc_final: 0.8443 (ppp) REVERT: I 517 TYR cc_start: 0.9228 (p90) cc_final: 0.8724 (p90) REVERT: I 546 GLU cc_start: 0.9271 (pp20) cc_final: 0.8973 (pp20) REVERT: I 578 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8210 (tm-30) REVERT: J 508 MET cc_start: 0.8884 (ppp) cc_final: 0.8352 (ppp) REVERT: J 546 GLU cc_start: 0.9198 (pp20) cc_final: 0.8924 (pp20) REVERT: J 578 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8218 (tm-30) REVERT: J 757 MET cc_start: 0.9128 (ppp) cc_final: 0.8868 (ppp) REVERT: K 36 ASN cc_start: 0.5873 (OUTLIER) cc_final: 0.5560 (t0) REVERT: K 83 ARG cc_start: 0.7030 (mpt180) cc_final: 0.6801 (mpp80) REVERT: K 378 LEU cc_start: 0.9565 (tp) cc_final: 0.9354 (tt) REVERT: K 427 MET cc_start: 0.8083 (tpp) cc_final: 0.7744 (tpp) REVERT: K 578 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8253 (tm-30) outliers start: 199 outliers final: 118 residues processed: 663 average time/residue: 0.6073 time to fit residues: 704.6371 Evaluate side-chains 629 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 501 time to evaluate : 5.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 756 GLU Chi-restraints excluded: chain F residue 758 PHE Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 344 MET Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 394 VAL Chi-restraints excluded: chain L residue 527 LEU Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 619 ILE Chi-restraints excluded: chain L residue 697 LEU Chi-restraints excluded: chain L residue 756 GLU Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 351 ASN Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 468 VAL Chi-restraints excluded: chain G residue 564 ASP Chi-restraints excluded: chain G residue 617 VAL Chi-restraints excluded: chain G residue 619 ILE Chi-restraints excluded: chain G residue 756 GLU Chi-restraints excluded: chain G residue 758 PHE Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 375 THR Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 564 ASP Chi-restraints excluded: chain H residue 619 ILE Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 756 GLU Chi-restraints excluded: chain I residue 344 MET Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 468 VAL Chi-restraints excluded: chain I residue 527 LEU Chi-restraints excluded: chain I residue 564 ASP Chi-restraints excluded: chain I residue 611 MET Chi-restraints excluded: chain I residue 619 ILE Chi-restraints excluded: chain I residue 756 GLU Chi-restraints excluded: chain I residue 758 PHE Chi-restraints excluded: chain J residue 344 MET Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 449 MET Chi-restraints excluded: chain J residue 564 ASP Chi-restraints excluded: chain J residue 617 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 344 MET Chi-restraints excluded: chain K residue 351 ASN Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 564 ASP Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 687 LEU Chi-restraints excluded: chain K residue 758 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 695 optimal weight: 7.9990 chunk 474 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 621 optimal weight: 0.7980 chunk 344 optimal weight: 10.0000 chunk 712 optimal weight: 10.0000 chunk 577 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 426 optimal weight: 5.9990 chunk 749 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS B 36 ASN C 115 HIS C 398 GLN D 115 HIS D 384 HIS D 603 GLN F 115 HIS F 603 GLN L 115 HIS G 115 HIS G 603 GLN H 115 HIS H 603 GLN I 36 ASN I 115 HIS I 603 GLN J 115 HIS ** J 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 70332 Z= 0.284 Angle : 0.617 10.099 95088 Z= 0.313 Chirality : 0.046 0.206 10656 Planarity : 0.004 0.063 12504 Dihedral : 8.425 89.602 9864 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.60 % Favored : 93.17 % Rotamer: Outliers : 3.22 % Allowed : 14.94 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.52 (0.09), residues: 8688 helix: -0.65 (0.10), residues: 3108 sheet: 0.05 (0.15), residues: 1140 loop : -1.54 (0.10), residues: 4440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 454 HIS 0.008 0.001 HIS B 406 PHE 0.029 0.001 PHE J 758 TYR 0.017 0.001 TYR F 495 ARG 0.008 0.001 ARG K 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 529 time to evaluate : 6.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.9119 (ttp) cc_final: 0.8901 (ttt) REVERT: A 508 MET cc_start: 0.8938 (ppp) cc_final: 0.8453 (ppp) REVERT: A 517 TYR cc_start: 0.9294 (p90) cc_final: 0.8740 (p90) REVERT: A 578 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8293 (tm-30) REVERT: B 427 MET cc_start: 0.8220 (tpp) cc_final: 0.7982 (tpt) REVERT: B 508 MET cc_start: 0.8989 (ppp) cc_final: 0.8588 (ppp) REVERT: B 578 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 756 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8566 (pm20) REVERT: B 757 MET cc_start: 0.9214 (ppp) cc_final: 0.8810 (ppp) REVERT: C 275 MET cc_start: 0.8969 (mpp) cc_final: 0.8727 (mpp) REVERT: C 316 THR cc_start: 0.4889 (OUTLIER) cc_final: 0.4589 (p) REVERT: C 427 MET cc_start: 0.8399 (tpp) cc_final: 0.8154 (tpt) REVERT: C 470 GLU cc_start: 0.8089 (pm20) cc_final: 0.7584 (pm20) REVERT: C 508 MET cc_start: 0.8977 (ppp) cc_final: 0.8598 (ppp) REVERT: C 517 TYR cc_start: 0.9271 (p90) cc_final: 0.8575 (p90) REVERT: C 578 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8212 (tm-30) REVERT: C 608 MET cc_start: 0.9779 (ptm) cc_final: 0.9519 (ppp) REVERT: D 36 ASN cc_start: 0.6203 (OUTLIER) cc_final: 0.5904 (t0) REVERT: D 83 ARG cc_start: 0.6999 (mpt180) cc_final: 0.6700 (mpt180) REVERT: D 211 LYS cc_start: 0.9366 (ptmm) cc_final: 0.9120 (ptmm) REVERT: D 427 MET cc_start: 0.8381 (tpp) cc_final: 0.8105 (tpt) REVERT: D 442 MET cc_start: 0.9008 (pmm) cc_final: 0.8529 (pmm) REVERT: D 449 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8099 (tmm) REVERT: D 508 MET cc_start: 0.8973 (ppp) cc_final: 0.8498 (ppp) REVERT: D 549 THR cc_start: 0.8678 (t) cc_final: 0.8478 (p) REVERT: D 578 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8313 (tm-30) REVERT: D 757 MET cc_start: 0.9205 (ppp) cc_final: 0.8820 (ppp) REVERT: E 36 ASN cc_start: 0.6105 (OUTLIER) cc_final: 0.5604 (t0) REVERT: E 388 MET cc_start: 0.6406 (tmm) cc_final: 0.6171 (tmm) REVERT: E 442 MET cc_start: 0.8947 (pmm) cc_final: 0.8733 (pmm) REVERT: E 578 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8373 (tm-30) REVERT: E 678 MET cc_start: 0.8547 (mpp) cc_final: 0.8234 (mpp) REVERT: F 36 ASN cc_start: 0.6104 (OUTLIER) cc_final: 0.5785 (t0) REVERT: F 211 LYS cc_start: 0.9567 (ptmm) cc_final: 0.9339 (ptmm) REVERT: F 449 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7829 (mmp) REVERT: F 578 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8249 (tm-30) REVERT: L 36 ASN cc_start: 0.5998 (OUTLIER) cc_final: 0.5707 (t0) REVERT: L 211 LYS cc_start: 0.9528 (ptmm) cc_final: 0.9214 (ptmm) REVERT: L 470 GLU cc_start: 0.8035 (pm20) cc_final: 0.7674 (pm20) REVERT: L 578 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8331 (tm-30) REVERT: G 36 ASN cc_start: 0.5988 (OUTLIER) cc_final: 0.5730 (t0) REVERT: G 427 MET cc_start: 0.8378 (tpp) cc_final: 0.8053 (tpt) REVERT: G 449 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8026 (tmm) REVERT: G 508 MET cc_start: 0.8977 (ppp) cc_final: 0.8535 (ppp) REVERT: G 517 TYR cc_start: 0.9280 (p90) cc_final: 0.8647 (p90) REVERT: G 578 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8297 (tm-30) REVERT: G 757 MET cc_start: 0.9210 (ppp) cc_final: 0.8950 (ppp) REVERT: H 36 ASN cc_start: 0.6175 (OUTLIER) cc_final: 0.5867 (t0) REVERT: H 304 ASP cc_start: 0.8000 (t70) cc_final: 0.7773 (t0) REVERT: H 393 ASP cc_start: 0.7547 (p0) cc_final: 0.7169 (p0) REVERT: H 427 MET cc_start: 0.8088 (tpp) cc_final: 0.7745 (tpp) REVERT: H 470 GLU cc_start: 0.8058 (pm20) cc_final: 0.7844 (pm20) REVERT: H 508 MET cc_start: 0.8956 (ppp) cc_final: 0.8537 (ppp) REVERT: H 517 TYR cc_start: 0.9299 (p90) cc_final: 0.8610 (p90) REVERT: H 578 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8368 (tm-30) REVERT: H 757 MET cc_start: 0.9207 (ppp) cc_final: 0.8855 (ppp) REVERT: I 449 MET cc_start: 0.8430 (mmt) cc_final: 0.8225 (tmm) REVERT: I 470 GLU cc_start: 0.8250 (pm20) cc_final: 0.7778 (pm20) REVERT: I 508 MET cc_start: 0.8940 (ppp) cc_final: 0.8561 (ppp) REVERT: I 517 TYR cc_start: 0.9283 (p90) cc_final: 0.8627 (p90) REVERT: I 546 GLU cc_start: 0.9339 (pp20) cc_final: 0.9126 (pp20) REVERT: I 578 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8220 (tm-30) REVERT: J 470 GLU cc_start: 0.8123 (pm20) cc_final: 0.7919 (pm20) REVERT: J 508 MET cc_start: 0.8948 (ppp) cc_final: 0.8471 (ppp) REVERT: J 578 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8257 (tm-30) REVERT: K 36 ASN cc_start: 0.5881 (OUTLIER) cc_final: 0.5605 (t0) REVERT: K 83 ARG cc_start: 0.7145 (mpt180) cc_final: 0.6923 (mpp80) REVERT: K 275 MET cc_start: 0.8977 (mpp) cc_final: 0.8623 (mpp) REVERT: K 427 MET cc_start: 0.8064 (tpp) cc_final: 0.7726 (tpp) REVERT: K 470 GLU cc_start: 0.7990 (pm20) cc_final: 0.7790 (pm20) REVERT: K 517 TYR cc_start: 0.9292 (p90) cc_final: 0.8752 (p90) REVERT: K 578 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8353 (tm-30) outliers start: 239 outliers final: 138 residues processed: 693 average time/residue: 0.6386 time to fit residues: 775.2569 Evaluate side-chains 635 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 485 time to evaluate : 5.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 398 GLN Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 449 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 756 GLU Chi-restraints excluded: chain F residue 758 PHE Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 344 MET Chi-restraints excluded: chain L residue 349 ARG Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 394 VAL Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain L residue 420 LEU Chi-restraints excluded: chain L residue 527 LEU Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 619 ILE Chi-restraints excluded: chain L residue 697 LEU Chi-restraints excluded: chain L residue 756 GLU Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 449 MET Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 468 VAL Chi-restraints excluded: chain G residue 564 ASP Chi-restraints excluded: chain G residue 617 VAL Chi-restraints excluded: chain G residue 619 ILE Chi-restraints excluded: chain G residue 756 GLU Chi-restraints excluded: chain G residue 758 PHE Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 215 GLN Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 344 MET Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 403 THR Chi-restraints excluded: chain H residue 415 CYS Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 564 ASP Chi-restraints excluded: chain H residue 619 ILE Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain I residue 344 MET Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 468 VAL Chi-restraints excluded: chain I residue 527 LEU Chi-restraints excluded: chain I residue 564 ASP Chi-restraints excluded: chain I residue 619 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 756 GLU Chi-restraints excluded: chain I residue 758 PHE Chi-restraints excluded: chain J residue 344 MET Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 449 MET Chi-restraints excluded: chain J residue 460 ASN Chi-restraints excluded: chain J residue 564 ASP Chi-restraints excluded: chain J residue 617 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 344 MET Chi-restraints excluded: chain K residue 351 ASN Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 415 CYS Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 564 ASP Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 687 LEU Chi-restraints excluded: chain K residue 750 ASN Chi-restraints excluded: chain K residue 758 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 280 optimal weight: 3.9990 chunk 752 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 490 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 835 optimal weight: 4.9990 chunk 693 optimal weight: 0.7980 chunk 387 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 438 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 115 HIS ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS L 115 HIS L 398 GLN G 115 HIS ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN J 115 HIS J 603 GLN ** K 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 70332 Z= 0.235 Angle : 0.587 8.705 95088 Z= 0.294 Chirality : 0.045 0.199 10656 Planarity : 0.004 0.065 12504 Dihedral : 8.354 89.292 9864 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.12 % Favored : 93.69 % Rotamer: Outliers : 2.77 % Allowed : 16.57 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.39 (0.09), residues: 8688 helix: -0.53 (0.10), residues: 3072 sheet: 0.06 (0.15), residues: 1140 loop : -1.45 (0.10), residues: 4476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 454 HIS 0.007 0.001 HIS B 406 PHE 0.025 0.001 PHE J 758 TYR 0.014 0.001 TYR F 134 ARG 0.010 0.000 ARG H 453 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 522 time to evaluate : 6.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.8943 (ppp) cc_final: 0.8466 (ppp) REVERT: A 517 TYR cc_start: 0.9289 (p90) cc_final: 0.8658 (p90) REVERT: A 578 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 427 MET cc_start: 0.8197 (tpp) cc_final: 0.7925 (tpt) REVERT: B 508 MET cc_start: 0.8997 (ppp) cc_final: 0.8599 (ppp) REVERT: B 578 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 756 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: B 757 MET cc_start: 0.9130 (ppp) cc_final: 0.8681 (ppp) REVERT: C 211 LYS cc_start: 0.9509 (ptmm) cc_final: 0.9247 (ptmm) REVERT: C 275 MET cc_start: 0.8957 (mpp) cc_final: 0.8723 (mpp) REVERT: C 316 THR cc_start: 0.5018 (OUTLIER) cc_final: 0.4694 (p) REVERT: C 427 MET cc_start: 0.8407 (tpp) cc_final: 0.8172 (tpt) REVERT: C 470 GLU cc_start: 0.8159 (pm20) cc_final: 0.7638 (pm20) REVERT: C 508 MET cc_start: 0.8981 (ppp) cc_final: 0.8608 (ppp) REVERT: C 578 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8098 (tm-30) REVERT: D 36 ASN cc_start: 0.6062 (OUTLIER) cc_final: 0.5769 (t0) REVERT: D 83 ARG cc_start: 0.6937 (mpt180) cc_final: 0.6595 (mpt180) REVERT: D 211 LYS cc_start: 0.9372 (ptmm) cc_final: 0.9117 (ptmm) REVERT: D 275 MET cc_start: 0.9062 (mpp) cc_final: 0.8858 (mpp) REVERT: D 427 MET cc_start: 0.8352 (tpp) cc_final: 0.8081 (tpt) REVERT: D 442 MET cc_start: 0.9022 (pmm) cc_final: 0.8600 (pmm) REVERT: D 449 MET cc_start: 0.8431 (mmt) cc_final: 0.8204 (tmm) REVERT: D 508 MET cc_start: 0.8979 (ppp) cc_final: 0.8510 (ppp) REVERT: D 517 TYR cc_start: 0.9234 (p90) cc_final: 0.8486 (p90) REVERT: D 549 THR cc_start: 0.8728 (t) cc_final: 0.8519 (p) REVERT: D 578 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8320 (tm-30) REVERT: D 757 MET cc_start: 0.9189 (ppp) cc_final: 0.8790 (ppp) REVERT: E 36 ASN cc_start: 0.6116 (OUTLIER) cc_final: 0.5604 (t0) REVERT: E 388 MET cc_start: 0.6455 (tmm) cc_final: 0.6222 (tmm) REVERT: E 427 MET cc_start: 0.7120 (tpp) cc_final: 0.6823 (tpp) REVERT: E 442 MET cc_start: 0.8913 (pmm) cc_final: 0.8705 (pmm) REVERT: E 578 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8333 (tm-30) REVERT: E 678 MET cc_start: 0.8570 (mpp) cc_final: 0.8227 (mpp) REVERT: F 36 ASN cc_start: 0.6150 (OUTLIER) cc_final: 0.5813 (t0) REVERT: F 83 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6747 (mpp80) REVERT: F 211 LYS cc_start: 0.9563 (ptmm) cc_final: 0.9326 (ptmm) REVERT: F 578 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8256 (tm-30) REVERT: L 36 ASN cc_start: 0.5964 (OUTLIER) cc_final: 0.5691 (t0) REVERT: L 211 LYS cc_start: 0.9514 (ptmm) cc_final: 0.9218 (ptmm) REVERT: L 470 GLU cc_start: 0.8055 (pm20) cc_final: 0.7681 (pm20) REVERT: L 578 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8313 (tm-30) REVERT: G 36 ASN cc_start: 0.5965 (OUTLIER) cc_final: 0.5707 (t0) REVERT: G 427 MET cc_start: 0.8364 (tpp) cc_final: 0.8058 (tpt) REVERT: G 449 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8210 (tmm) REVERT: G 508 MET cc_start: 0.8978 (ppp) cc_final: 0.8522 (ppp) REVERT: G 578 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8234 (tm-30) REVERT: G 757 MET cc_start: 0.9203 (ppp) cc_final: 0.8909 (ppp) REVERT: H 87 VAL cc_start: 0.9273 (m) cc_final: 0.9050 (p) REVERT: H 304 ASP cc_start: 0.7929 (t70) cc_final: 0.7723 (t0) REVERT: H 427 MET cc_start: 0.8095 (tpp) cc_final: 0.7762 (tpp) REVERT: H 470 GLU cc_start: 0.8147 (pm20) cc_final: 0.7916 (pm20) REVERT: H 508 MET cc_start: 0.8966 (ppp) cc_final: 0.8546 (ppp) REVERT: H 517 TYR cc_start: 0.9299 (p90) cc_final: 0.8644 (p90) REVERT: H 549 THR cc_start: 0.8701 (t) cc_final: 0.8342 (p) REVERT: H 578 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8311 (tm-30) REVERT: I 449 MET cc_start: 0.8340 (mmt) cc_final: 0.8077 (tmm) REVERT: I 470 GLU cc_start: 0.8338 (pm20) cc_final: 0.7831 (pm20) REVERT: I 508 MET cc_start: 0.8966 (ppp) cc_final: 0.8599 (ppp) REVERT: I 578 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8205 (tm-30) REVERT: J 470 GLU cc_start: 0.8130 (pm20) cc_final: 0.7914 (pm20) REVERT: J 508 MET cc_start: 0.8945 (ppp) cc_final: 0.8475 (ppp) REVERT: J 578 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8243 (tm-30) REVERT: J 757 MET cc_start: 0.9108 (ppp) cc_final: 0.8840 (ppp) REVERT: K 36 ASN cc_start: 0.5923 (OUTLIER) cc_final: 0.5641 (t0) REVERT: K 83 ARG cc_start: 0.7208 (mpt180) cc_final: 0.6939 (mpp80) REVERT: K 275 MET cc_start: 0.8996 (mpp) cc_final: 0.8638 (mpp) REVERT: K 427 MET cc_start: 0.8095 (tpp) cc_final: 0.7766 (tpp) REVERT: K 449 MET cc_start: 0.8346 (mmp) cc_final: 0.8074 (tmm) REVERT: K 470 GLU cc_start: 0.8081 (pm20) cc_final: 0.7850 (pm20) REVERT: K 578 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8355 (tm-30) outliers start: 206 outliers final: 129 residues processed: 667 average time/residue: 0.5953 time to fit residues: 696.4348 Evaluate side-chains 636 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 497 time to evaluate : 5.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 415 CYS Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 756 GLU Chi-restraints excluded: chain F residue 758 PHE Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 344 MET Chi-restraints excluded: chain L residue 349 ARG Chi-restraints excluded: chain L residue 351 ASN Chi-restraints excluded: chain L residue 364 ASP Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 394 VAL Chi-restraints excluded: chain L residue 398 GLN Chi-restraints excluded: chain L residue 420 LEU Chi-restraints excluded: chain L residue 619 ILE Chi-restraints excluded: chain L residue 697 LEU Chi-restraints excluded: chain L residue 756 GLU Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 449 MET Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 468 VAL Chi-restraints excluded: chain G residue 617 VAL Chi-restraints excluded: chain G residue 619 ILE Chi-restraints excluded: chain G residue 756 GLU Chi-restraints excluded: chain G residue 758 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 375 THR Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 403 THR Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 460 ASN Chi-restraints excluded: chain H residue 467 THR Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 562 ILE Chi-restraints excluded: chain H residue 619 ILE Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain I residue 344 MET Chi-restraints excluded: chain I residue 351 ASN Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 460 ASN Chi-restraints excluded: chain I residue 468 VAL Chi-restraints excluded: chain I residue 619 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 756 GLU Chi-restraints excluded: chain I residue 758 PHE Chi-restraints excluded: chain J residue 344 MET Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 449 MET Chi-restraints excluded: chain J residue 460 ASN Chi-restraints excluded: chain J residue 614 LYS Chi-restraints excluded: chain J residue 617 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 351 ASN Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 460 ASN Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 562 ILE Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 687 LEU Chi-restraints excluded: chain K residue 750 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 805 optimal weight: 30.0000 chunk 94 optimal weight: 7.9990 chunk 476 optimal weight: 10.0000 chunk 610 optimal weight: 6.9990 chunk 472 optimal weight: 20.0000 chunk 703 optimal weight: 2.9990 chunk 466 optimal weight: 0.0570 chunk 832 optimal weight: 9.9990 chunk 521 optimal weight: 0.1980 chunk 507 optimal weight: 30.0000 chunk 384 optimal weight: 7.9990 overall best weight: 3.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS C 115 HIS C 398 GLN D 115 HIS F 115 HIS L 115 HIS L 398 GLN G 115 HIS ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 HIS J 115 HIS ** K 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 70332 Z= 0.266 Angle : 0.603 10.037 95088 Z= 0.304 Chirality : 0.045 0.191 10656 Planarity : 0.004 0.067 12504 Dihedral : 8.411 89.714 9864 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.01 % Favored : 92.76 % Rotamer: Outliers : 2.91 % Allowed : 17.41 % Favored : 79.68 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 7.69 % 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: -1.33 (0.09), residues: 8688 helix: -0.51 (0.10), residues: 3120 sheet: 0.09 (0.16), residues: 1140 loop : -1.39 (0.10), residues: 4428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 454 HIS 0.006 0.001 HIS B 406 PHE 0.076 0.001 PHE K 758 TYR 0.017 0.001 TYR F 134 ARG 0.005 0.000 ARG K 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 530 time to evaluate : 5.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.9472 (ptmm) cc_final: 0.9143 (ptmm) REVERT: A 508 MET cc_start: 0.8999 (ppp) cc_final: 0.8540 (ppp) REVERT: A 517 TYR cc_start: 0.9340 (p90) cc_final: 0.8731 (p90) REVERT: A 578 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8281 (tm-30) REVERT: B 427 MET cc_start: 0.8178 (tpp) cc_final: 0.7914 (tpt) REVERT: B 508 MET cc_start: 0.9022 (ppp) cc_final: 0.8623 (ppp) REVERT: B 578 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8324 (tm-30) REVERT: B 678 MET cc_start: 0.8604 (mpp) cc_final: 0.8302 (mpp) REVERT: B 757 MET cc_start: 0.9153 (ppp) cc_final: 0.8718 (ppp) REVERT: C 211 LYS cc_start: 0.9524 (ptmm) cc_final: 0.9252 (ptmm) REVERT: C 275 MET cc_start: 0.8975 (mpp) cc_final: 0.8766 (mpp) REVERT: C 316 THR cc_start: 0.4759 (OUTLIER) cc_final: 0.4397 (p) REVERT: C 427 MET cc_start: 0.8407 (tpp) cc_final: 0.8176 (tpt) REVERT: C 470 GLU cc_start: 0.8347 (pm20) cc_final: 0.7812 (pm20) REVERT: C 508 MET cc_start: 0.9039 (ppp) cc_final: 0.8686 (ppp) REVERT: C 578 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8099 (tm-30) REVERT: C 678 MET cc_start: 0.8720 (mpp) cc_final: 0.8356 (mpp) REVERT: D 36 ASN cc_start: 0.6022 (OUTLIER) cc_final: 0.5719 (t0) REVERT: D 83 ARG cc_start: 0.7073 (mpt180) cc_final: 0.6732 (mpt180) REVERT: D 211 LYS cc_start: 0.9393 (ptmm) cc_final: 0.9156 (ptmm) REVERT: D 275 MET cc_start: 0.9121 (mpp) cc_final: 0.8795 (mpp) REVERT: D 427 MET cc_start: 0.8370 (tpp) cc_final: 0.8143 (tpp) REVERT: D 442 MET cc_start: 0.9100 (pmm) cc_final: 0.8727 (pmm) REVERT: D 508 MET cc_start: 0.9016 (ppp) cc_final: 0.8550 (ppp) REVERT: D 517 TYR cc_start: 0.9299 (p90) cc_final: 0.8633 (p90) REVERT: D 549 THR cc_start: 0.8722 (t) cc_final: 0.8469 (p) REVERT: D 550 MET cc_start: 0.7947 (ppp) cc_final: 0.7228 (ppp) REVERT: D 578 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8271 (tm-30) REVERT: D 757 MET cc_start: 0.9189 (ppp) cc_final: 0.8780 (ppp) REVERT: E 388 MET cc_start: 0.6668 (tmm) cc_final: 0.6410 (tmm) REVERT: E 442 MET cc_start: 0.8915 (pmm) cc_final: 0.8713 (pmm) REVERT: E 578 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8330 (tm-30) REVERT: E 580 ASP cc_start: 0.8757 (t0) cc_final: 0.8478 (t0) REVERT: E 678 MET cc_start: 0.8638 (mpp) cc_final: 0.8289 (mpp) REVERT: F 36 ASN cc_start: 0.6193 (OUTLIER) cc_final: 0.5859 (t0) REVERT: F 211 LYS cc_start: 0.9569 (ptmm) cc_final: 0.9327 (ptmm) REVERT: F 393 ASP cc_start: 0.7749 (p0) cc_final: 0.7415 (p0) REVERT: F 578 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8250 (tm-30) REVERT: F 678 MET cc_start: 0.8681 (mpp) cc_final: 0.8324 (mpp) REVERT: L 36 ASN cc_start: 0.5957 (OUTLIER) cc_final: 0.5702 (t0) REVERT: L 211 LYS cc_start: 0.9528 (ptmm) cc_final: 0.9210 (ptmm) REVERT: L 453 ARG cc_start: 0.9251 (mpt180) cc_final: 0.8944 (mmp80) REVERT: L 470 GLU cc_start: 0.8199 (pm20) cc_final: 0.7918 (pm20) REVERT: L 517 TYR cc_start: 0.9244 (p90) cc_final: 0.8521 (p90) REVERT: L 578 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8340 (tm-30) REVERT: L 678 MET cc_start: 0.8739 (mpp) cc_final: 0.8397 (mpp) REVERT: G 36 ASN cc_start: 0.5969 (OUTLIER) cc_final: 0.5758 (t0) REVERT: G 427 MET cc_start: 0.8362 (tpp) cc_final: 0.8066 (tpt) REVERT: G 442 MET cc_start: 0.9073 (pmm) cc_final: 0.8747 (pmm) REVERT: G 508 MET cc_start: 0.9010 (ppp) cc_final: 0.8559 (ppp) REVERT: G 517 TYR cc_start: 0.9238 (p90) cc_final: 0.8583 (p90) REVERT: G 549 THR cc_start: 0.8790 (t) cc_final: 0.8560 (p) REVERT: G 578 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8261 (tm-30) REVERT: G 608 MET cc_start: 0.9751 (ptm) cc_final: 0.9540 (ppp) REVERT: G 757 MET cc_start: 0.9218 (ppp) cc_final: 0.8923 (ppp) REVERT: H 87 VAL cc_start: 0.9247 (m) cc_final: 0.9036 (p) REVERT: H 275 MET cc_start: 0.9099 (mpp) cc_final: 0.8809 (mpp) REVERT: H 393 ASP cc_start: 0.7456 (p0) cc_final: 0.6987 (p0) REVERT: H 427 MET cc_start: 0.8164 (tpp) cc_final: 0.7955 (tpp) REVERT: H 508 MET cc_start: 0.9004 (ppp) cc_final: 0.8601 (ppp) REVERT: H 517 TYR cc_start: 0.9334 (p90) cc_final: 0.8590 (p90) REVERT: H 578 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8400 (tm-30) REVERT: I 470 GLU cc_start: 0.8383 (pm20) cc_final: 0.7881 (pm20) REVERT: I 508 MET cc_start: 0.9008 (ppp) cc_final: 0.8675 (ppp) REVERT: I 546 GLU cc_start: 0.9322 (tm-30) cc_final: 0.9100 (pt0) REVERT: I 578 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8185 (tm-30) REVERT: J 211 LYS cc_start: 0.9492 (ptmm) cc_final: 0.9176 (ptmm) REVERT: J 470 GLU cc_start: 0.8178 (pm20) cc_final: 0.7947 (pm20) REVERT: J 508 MET cc_start: 0.9015 (ppp) cc_final: 0.8551 (ppp) REVERT: J 549 THR cc_start: 0.8791 (t) cc_final: 0.8567 (p) REVERT: J 578 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8254 (tm-30) REVERT: K 36 ASN cc_start: 0.5895 (OUTLIER) cc_final: 0.5642 (t0) REVERT: K 83 ARG cc_start: 0.7151 (mpt180) cc_final: 0.6880 (mpp80) REVERT: K 275 MET cc_start: 0.8992 (mpp) cc_final: 0.8584 (mpp) REVERT: K 427 MET cc_start: 0.8112 (tpp) cc_final: 0.7891 (tpp) REVERT: K 449 MET cc_start: 0.8343 (mmp) cc_final: 0.8119 (tmm) REVERT: K 470 GLU cc_start: 0.8197 (pm20) cc_final: 0.7945 (pm20) REVERT: K 578 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8314 (tm-30) outliers start: 216 outliers final: 149 residues processed: 676 average time/residue: 0.6138 time to fit residues: 725.4503 Evaluate side-chains 663 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 508 time to evaluate : 5.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 351 ASN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 415 CYS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 756 GLU Chi-restraints excluded: chain F residue 758 PHE Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 344 MET Chi-restraints excluded: chain L residue 351 ASN Chi-restraints excluded: chain L residue 364 ASP Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 394 VAL Chi-restraints excluded: chain L residue 415 CYS Chi-restraints excluded: chain L residue 420 LEU Chi-restraints excluded: chain L residue 619 ILE Chi-restraints excluded: chain L residue 697 LEU Chi-restraints excluded: chain L residue 756 GLU Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 415 CYS Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 468 VAL Chi-restraints excluded: chain G residue 564 ASP Chi-restraints excluded: chain G residue 617 VAL Chi-restraints excluded: chain G residue 619 ILE Chi-restraints excluded: chain G residue 756 GLU Chi-restraints excluded: chain G residue 758 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 269 ILE Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 375 THR Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 403 THR Chi-restraints excluded: chain H residue 415 CYS Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 460 ASN Chi-restraints excluded: chain H residue 467 THR Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 562 ILE Chi-restraints excluded: chain H residue 619 ILE Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain I residue 344 MET Chi-restraints excluded: chain I residue 351 ASN Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 415 CYS Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 460 ASN Chi-restraints excluded: chain I residue 468 VAL Chi-restraints excluded: chain I residue 619 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 756 GLU Chi-restraints excluded: chain I residue 758 PHE Chi-restraints excluded: chain J residue 344 MET Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 449 MET Chi-restraints excluded: chain J residue 460 ASN Chi-restraints excluded: chain J residue 564 ASP Chi-restraints excluded: chain J residue 614 LYS Chi-restraints excluded: chain J residue 617 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 657 LEU Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 344 MET Chi-restraints excluded: chain K residue 351 ASN Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 415 CYS Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 460 ASN Chi-restraints excluded: chain K residue 467 THR Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 562 ILE Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 687 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 515 optimal weight: 0.0270 chunk 332 optimal weight: 9.9990 chunk 497 optimal weight: 0.8980 chunk 250 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 161 optimal weight: 30.0000 chunk 529 optimal weight: 7.9990 chunk 567 optimal weight: 9.9990 chunk 411 optimal weight: 7.9990 chunk 77 optimal weight: 40.0000 chunk 654 optimal weight: 8.9990 overall best weight: 3.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS C 115 HIS D 115 HIS F 115 HIS L 115 HIS G 115 HIS ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 HIS J 115 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 70332 Z= 0.258 Angle : 0.612 11.501 95088 Z= 0.305 Chirality : 0.045 0.212 10656 Planarity : 0.004 0.068 12504 Dihedral : 8.429 89.918 9864 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.51 % Favored : 93.26 % Rotamer: Outliers : 2.72 % Allowed : 18.19 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.09), residues: 8688 helix: -0.54 (0.09), residues: 3204 sheet: 0.12 (0.16), residues: 1140 loop : -1.30 (0.10), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 454 HIS 0.006 0.001 HIS E 406 PHE 0.020 0.001 PHE J 758 TYR 0.018 0.001 TYR F 134 ARG 0.015 0.000 ARG H 453 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 534 time to evaluate : 5.846 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: A 508 MET cc_start: 0.8985 (ppp) cc_final: 0.8538 (ppp) REVERT: A 517 TYR cc_start: 0.9338 (p90) cc_final: 0.8663 (p90) REVERT: A 549 THR cc_start: 0.8648 (t) cc_final: 0.8447 (p) REVERT: A 578 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8265 (tm-30) REVERT: B 427 MET cc_start: 0.8214 (tpp) cc_final: 0.7943 (tpt) REVERT: B 508 MET cc_start: 0.9030 (ppp) cc_final: 0.8645 (ppp) REVERT: B 578 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8360 (tm-30) REVERT: B 678 MET cc_start: 0.8611 (mpp) cc_final: 0.8318 (mpp) REVERT: C 211 LYS cc_start: 0.9537 (ptmm) cc_final: 0.9256 (ptmm) REVERT: C 275 MET cc_start: 0.8960 (mpp) cc_final: 0.8753 (mpp) REVERT: C 316 THR cc_start: 0.4968 (OUTLIER) cc_final: 0.4614 (p) REVERT: C 470 GLU cc_start: 0.8387 (pm20) cc_final: 0.7836 (pm20) REVERT: C 508 MET cc_start: 0.9049 (ppp) cc_final: 0.8699 (ppp) REVERT: C 578 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8101 (tm-30) REVERT: C 678 MET cc_start: 0.8720 (mpp) cc_final: 0.8386 (mpp) REVERT: D 36 ASN cc_start: 0.6059 (OUTLIER) cc_final: 0.5775 (t0) REVERT: D 83 ARG cc_start: 0.7034 (mpt180) cc_final: 0.6732 (mpt180) REVERT: D 158 MET cc_start: 0.6677 (mmp) cc_final: 0.6275 (mmp) REVERT: D 211 LYS cc_start: 0.9400 (ptmm) cc_final: 0.9156 (ptmm) REVERT: D 275 MET cc_start: 0.9130 (mpp) cc_final: 0.8749 (mpp) REVERT: D 427 MET cc_start: 0.8386 (tpp) cc_final: 0.8157 (tpp) REVERT: D 442 MET cc_start: 0.9074 (pmm) cc_final: 0.8707 (pmm) REVERT: D 508 MET cc_start: 0.9018 (ppp) cc_final: 0.8571 (ppp) REVERT: D 549 THR cc_start: 0.8722 (t) cc_final: 0.8462 (p) REVERT: D 550 MET cc_start: 0.7939 (ppp) cc_final: 0.7218 (ppp) REVERT: D 578 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8277 (tm-30) REVERT: D 757 MET cc_start: 0.9180 (ppp) cc_final: 0.8770 (ppp) REVERT: E 442 MET cc_start: 0.8969 (pmm) cc_final: 0.8752 (pmm) REVERT: E 508 MET cc_start: 0.9245 (tmm) cc_final: 0.9029 (tmm) REVERT: E 578 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8347 (tm-30) REVERT: E 678 MET cc_start: 0.8678 (mpp) cc_final: 0.8334 (mpp) REVERT: E 757 MET cc_start: 0.8902 (ppp) cc_final: 0.8519 (ppp) REVERT: F 36 ASN cc_start: 0.6183 (OUTLIER) cc_final: 0.5864 (t0) REVERT: F 211 LYS cc_start: 0.9577 (ptmm) cc_final: 0.9339 (ptmm) REVERT: F 393 ASP cc_start: 0.7490 (p0) cc_final: 0.7274 (p0) REVERT: F 578 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8234 (tm-30) REVERT: F 678 MET cc_start: 0.8728 (mpp) cc_final: 0.8385 (mpp) REVERT: L 36 ASN cc_start: 0.5979 (OUTLIER) cc_final: 0.5715 (t0) REVERT: L 211 LYS cc_start: 0.9524 (ptmm) cc_final: 0.9218 (ptmm) REVERT: L 470 GLU cc_start: 0.8208 (pm20) cc_final: 0.7920 (pm20) REVERT: L 578 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8329 (tm-30) REVERT: L 678 MET cc_start: 0.8721 (mpp) cc_final: 0.8403 (mpp) REVERT: G 36 ASN cc_start: 0.5939 (OUTLIER) cc_final: 0.5729 (t0) REVERT: G 427 MET cc_start: 0.8376 (tpp) cc_final: 0.8104 (tpp) REVERT: G 442 MET cc_start: 0.9107 (pmm) cc_final: 0.8743 (pmm) REVERT: G 508 MET cc_start: 0.9038 (ppp) cc_final: 0.8590 (ppp) REVERT: G 549 THR cc_start: 0.8825 (t) cc_final: 0.8594 (p) REVERT: G 578 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8254 (tm-30) REVERT: G 608 MET cc_start: 0.9762 (ptm) cc_final: 0.9537 (ppp) REVERT: G 757 MET cc_start: 0.9199 (ppp) cc_final: 0.8895 (ppp) REVERT: H 87 VAL cc_start: 0.9238 (m) cc_final: 0.9032 (p) REVERT: H 275 MET cc_start: 0.9092 (mpp) cc_final: 0.8750 (mpp) REVERT: H 427 MET cc_start: 0.8162 (tpp) cc_final: 0.7953 (tpp) REVERT: H 508 MET cc_start: 0.9033 (ppp) cc_final: 0.8632 (ppp) REVERT: H 517 TYR cc_start: 0.9358 (p90) cc_final: 0.8613 (p90) REVERT: H 578 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8394 (tm-30) REVERT: H 657 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9454 (mm) REVERT: I 470 GLU cc_start: 0.8362 (pm20) cc_final: 0.7862 (pm20) REVERT: I 508 MET cc_start: 0.9027 (ppp) cc_final: 0.8691 (ppp) REVERT: I 546 GLU cc_start: 0.9262 (tm-30) cc_final: 0.9060 (pt0) REVERT: I 578 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8131 (tm-30) REVERT: I 678 MET cc_start: 0.8713 (mpp) cc_final: 0.8364 (mpp) REVERT: J 470 GLU cc_start: 0.8250 (pm20) cc_final: 0.8020 (pm20) REVERT: J 508 MET cc_start: 0.9015 (ppp) cc_final: 0.8561 (ppp) REVERT: J 549 THR cc_start: 0.8807 (t) cc_final: 0.8575 (p) REVERT: J 578 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8304 (tm-30) REVERT: K 36 ASN cc_start: 0.5882 (OUTLIER) cc_final: 0.5628 (t0) REVERT: K 83 ARG cc_start: 0.7152 (mpt180) cc_final: 0.6827 (mpt180) REVERT: K 427 MET cc_start: 0.8160 (tpp) cc_final: 0.7935 (tpp) REVERT: K 470 GLU cc_start: 0.8251 (pm20) cc_final: 0.8030 (pm20) REVERT: K 578 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8319 (tm-30) REVERT: K 657 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9465 (mm) outliers start: 202 outliers final: 155 residues processed: 672 average time/residue: 0.6108 time to fit residues: 721.4659 Evaluate side-chains 677 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 514 time to evaluate : 5.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 351 ASN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 415 CYS Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 756 GLU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 344 MET Chi-restraints excluded: chain L residue 349 ARG Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 394 VAL Chi-restraints excluded: chain L residue 415 CYS Chi-restraints excluded: chain L residue 420 LEU Chi-restraints excluded: chain L residue 619 ILE Chi-restraints excluded: chain L residue 697 LEU Chi-restraints excluded: chain L residue 756 GLU Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 415 CYS Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 468 VAL Chi-restraints excluded: chain G residue 617 VAL Chi-restraints excluded: chain G residue 619 ILE Chi-restraints excluded: chain G residue 756 GLU Chi-restraints excluded: chain G residue 758 PHE Chi-restraints excluded: chain H residue 215 GLN Chi-restraints excluded: chain H residue 269 ILE Chi-restraints excluded: chain H residue 351 ASN Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 403 THR Chi-restraints excluded: chain H residue 415 CYS Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 460 ASN Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 562 ILE Chi-restraints excluded: chain H residue 619 ILE Chi-restraints excluded: chain H residue 657 LEU Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 751 ASP Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 344 MET Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 415 CYS Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 460 ASN Chi-restraints excluded: chain I residue 468 VAL Chi-restraints excluded: chain I residue 619 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 756 GLU Chi-restraints excluded: chain I residue 758 PHE Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 344 MET Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 415 CYS Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 460 ASN Chi-restraints excluded: chain J residue 614 LYS Chi-restraints excluded: chain J residue 617 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 351 ASN Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 415 CYS Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 460 ASN Chi-restraints excluded: chain K residue 467 THR Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 562 ILE Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 657 LEU Chi-restraints excluded: chain K residue 687 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 757 optimal weight: 10.0000 chunk 797 optimal weight: 40.0000 chunk 727 optimal weight: 1.9990 chunk 776 optimal weight: 20.0000 chunk 467 optimal weight: 7.9990 chunk 338 optimal weight: 9.9990 chunk 609 optimal weight: 10.0000 chunk 238 optimal weight: 0.8980 chunk 701 optimal weight: 20.0000 chunk 733 optimal weight: 50.0000 chunk 773 optimal weight: 20.0000 overall best weight: 6.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 384 HIS A 401 ASN A 494 GLN A 603 GLN B 494 GLN C 115 HIS C 384 HIS C 494 GLN D 115 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN F 115 HIS L 115 HIS L 384 HIS L 494 GLN G 115 HIS G 384 HIS ** G 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 384 HIS H 401 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 GLN J 115 HIS J 384 HIS ** K 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 384 HIS ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 70332 Z= 0.409 Angle : 0.711 11.126 95088 Z= 0.361 Chirality : 0.047 0.260 10656 Planarity : 0.005 0.069 12504 Dihedral : 8.797 88.367 9864 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.32 % Favored : 91.45 % Rotamer: Outliers : 2.93 % Allowed : 18.36 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.09), residues: 8688 helix: -0.83 (0.09), residues: 3264 sheet: -0.34 (0.14), residues: 1296 loop : -1.24 (0.10), residues: 4128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 454 HIS 0.009 0.002 HIS B 406 PHE 0.030 0.002 PHE F 758 TYR 0.029 0.002 TYR A 244 ARG 0.011 0.001 ARG F 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 515 time to evaluate : 6.936 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: A 508 MET cc_start: 0.9046 (ppp) cc_final: 0.8657 (ppp) REVERT: A 578 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 757 MET cc_start: 0.9048 (ppp) cc_final: 0.8764 (ppp) REVERT: B 427 MET cc_start: 0.8168 (tpp) cc_final: 0.7866 (tpt) REVERT: B 508 MET cc_start: 0.9123 (ppp) cc_final: 0.8802 (ppp) REVERT: B 578 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8436 (tm-30) REVERT: B 678 MET cc_start: 0.8685 (mpp) cc_final: 0.8455 (mpp) REVERT: C 83 ARG cc_start: 0.7045 (mpt180) cc_final: 0.6815 (mpt180) REVERT: C 211 LYS cc_start: 0.9540 (ptmm) cc_final: 0.9259 (ptmm) REVERT: C 275 MET cc_start: 0.9004 (mpp) cc_final: 0.8683 (mpp) REVERT: C 316 THR cc_start: 0.5096 (OUTLIER) cc_final: 0.4831 (p) REVERT: C 470 GLU cc_start: 0.8479 (pm20) cc_final: 0.8093 (pm20) REVERT: C 508 MET cc_start: 0.9132 (ppp) cc_final: 0.8789 (ppp) REVERT: C 578 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8123 (tm-30) REVERT: C 678 MET cc_start: 0.8747 (mpp) cc_final: 0.8493 (mpp) REVERT: D 36 ASN cc_start: 0.6172 (OUTLIER) cc_final: 0.5874 (t0) REVERT: D 158 MET cc_start: 0.7181 (mmp) cc_final: 0.6844 (mmp) REVERT: D 275 MET cc_start: 0.9167 (mpp) cc_final: 0.8675 (mpp) REVERT: D 427 MET cc_start: 0.8388 (tpp) cc_final: 0.8132 (tpp) REVERT: D 442 MET cc_start: 0.9095 (pmm) cc_final: 0.8767 (pmm) REVERT: D 508 MET cc_start: 0.9039 (ppp) cc_final: 0.8639 (ppp) REVERT: D 550 MET cc_start: 0.7844 (ppp) cc_final: 0.7314 (ppp) REVERT: D 578 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8191 (tm-30) REVERT: D 757 MET cc_start: 0.9195 (ppp) cc_final: 0.8839 (ppp) REVERT: E 508 MET cc_start: 0.9207 (tmm) cc_final: 0.8954 (tmm) REVERT: E 578 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8378 (tm-30) REVERT: E 678 MET cc_start: 0.8834 (mpp) cc_final: 0.8591 (mpp) REVERT: E 757 MET cc_start: 0.8869 (ppp) cc_final: 0.8604 (ppp) REVERT: F 36 ASN cc_start: 0.6215 (OUTLIER) cc_final: 0.5960 (t0) REVERT: F 211 LYS cc_start: 0.9564 (ptmm) cc_final: 0.9306 (ptmm) REVERT: F 549 THR cc_start: 0.8814 (t) cc_final: 0.8509 (p) REVERT: F 550 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.6877 (ppp) REVERT: F 578 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8206 (tm-30) REVERT: F 678 MET cc_start: 0.8825 (mpp) cc_final: 0.8577 (mpp) REVERT: L 36 ASN cc_start: 0.6059 (OUTLIER) cc_final: 0.5855 (t0) REVERT: L 211 LYS cc_start: 0.9515 (ptmm) cc_final: 0.9191 (ptmm) REVERT: L 470 GLU cc_start: 0.8436 (pm20) cc_final: 0.8153 (pm20) REVERT: L 578 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8363 (tm-30) REVERT: L 678 MET cc_start: 0.8786 (mpp) cc_final: 0.8551 (mpp) REVERT: G 36 ASN cc_start: 0.6134 (OUTLIER) cc_final: 0.5917 (t0) REVERT: G 427 MET cc_start: 0.8279 (tpp) cc_final: 0.7967 (tpp) REVERT: G 442 MET cc_start: 0.9163 (pmm) cc_final: 0.8774 (pmm) REVERT: G 508 MET cc_start: 0.9076 (ppp) cc_final: 0.8691 (ppp) REVERT: G 549 THR cc_start: 0.8803 (t) cc_final: 0.8585 (p) REVERT: G 578 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8258 (tm-30) REVERT: G 608 MET cc_start: 0.9759 (ptm) cc_final: 0.9513 (ppp) REVERT: G 757 MET cc_start: 0.9181 (ppp) cc_final: 0.8903 (ppp) REVERT: H 275 MET cc_start: 0.9104 (mpp) cc_final: 0.8658 (mpp) REVERT: H 393 ASP cc_start: 0.8150 (p0) cc_final: 0.7798 (p0) REVERT: H 427 MET cc_start: 0.8091 (tpp) cc_final: 0.7872 (tpp) REVERT: H 508 MET cc_start: 0.9109 (ppp) cc_final: 0.8748 (ppp) REVERT: H 578 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8419 (tm-30) REVERT: H 657 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9467 (mm) REVERT: H 678 MET cc_start: 0.8665 (mpp) cc_final: 0.8441 (mpp) REVERT: I 470 GLU cc_start: 0.8509 (pm20) cc_final: 0.8195 (pm20) REVERT: I 508 MET cc_start: 0.9080 (ppp) cc_final: 0.8724 (ppp) REVERT: I 578 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8190 (tm-30) REVERT: I 678 MET cc_start: 0.8800 (mpp) cc_final: 0.8589 (mpp) REVERT: J 470 GLU cc_start: 0.8320 (pm20) cc_final: 0.8086 (pm20) REVERT: J 508 MET cc_start: 0.9086 (ppp) cc_final: 0.8665 (ppp) REVERT: J 578 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8291 (tm-30) REVERT: K 36 ASN cc_start: 0.5889 (OUTLIER) cc_final: 0.5659 (t0) REVERT: K 83 ARG cc_start: 0.7179 (mpt180) cc_final: 0.6882 (mpt180) REVERT: K 275 MET cc_start: 0.9021 (mpp) cc_final: 0.8565 (mpp) REVERT: K 427 MET cc_start: 0.8151 (tpp) cc_final: 0.7926 (tpp) REVERT: K 470 GLU cc_start: 0.8439 (pm20) cc_final: 0.8222 (pm20) REVERT: K 578 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8320 (tm-30) REVERT: K 657 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9488 (mm) outliers start: 218 outliers final: 158 residues processed: 658 average time/residue: 0.6584 time to fit residues: 764.5634 Evaluate side-chains 673 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 506 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 351 ASN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 344 MET Chi-restraints excluded: chain L residue 349 ARG Chi-restraints excluded: chain L residue 364 ASP Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 394 VAL Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain L residue 415 CYS Chi-restraints excluded: chain L residue 420 LEU Chi-restraints excluded: chain L residue 460 ASN Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 619 ILE Chi-restraints excluded: chain L residue 697 LEU Chi-restraints excluded: chain L residue 756 GLU Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 351 ASN Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 415 CYS Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 468 VAL Chi-restraints excluded: chain G residue 564 ASP Chi-restraints excluded: chain G residue 617 VAL Chi-restraints excluded: chain G residue 619 ILE Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 215 GLN Chi-restraints excluded: chain H residue 269 ILE Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 351 ASN Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 403 THR Chi-restraints excluded: chain H residue 415 CYS Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 460 ASN Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 562 ILE Chi-restraints excluded: chain H residue 564 ASP Chi-restraints excluded: chain H residue 619 ILE Chi-restraints excluded: chain H residue 657 LEU Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain I residue 344 MET Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 415 CYS Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 460 ASN Chi-restraints excluded: chain I residue 468 VAL Chi-restraints excluded: chain I residue 564 ASP Chi-restraints excluded: chain I residue 619 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain J residue 344 MET Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 460 ASN Chi-restraints excluded: chain J residue 564 ASP Chi-restraints excluded: chain J residue 614 LYS Chi-restraints excluded: chain J residue 617 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 351 ASN Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 404 HIS Chi-restraints excluded: chain K residue 415 CYS Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 460 ASN Chi-restraints excluded: chain K residue 467 THR Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 562 ILE Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 657 LEU Chi-restraints excluded: chain K residue 687 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 509 optimal weight: 5.9990 chunk 820 optimal weight: 2.9990 chunk 500 optimal weight: 2.9990 chunk 389 optimal weight: 7.9990 chunk 570 optimal weight: 2.9990 chunk 860 optimal weight: 1.9990 chunk 792 optimal weight: 0.8980 chunk 685 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 529 optimal weight: 1.9990 chunk 420 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 494 GLN B 494 GLN C 115 HIS C 494 GLN D 115 HIS ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS L 115 HIS L 494 GLN G 115 HIS ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 HIS J 115 HIS ** K 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 70332 Z= 0.191 Angle : 0.625 11.900 95088 Z= 0.310 Chirality : 0.046 0.180 10656 Planarity : 0.004 0.070 12504 Dihedral : 8.576 89.770 9864 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.33 % Favored : 93.44 % Rotamer: Outliers : 2.03 % Allowed : 19.39 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.09), residues: 8688 helix: -0.58 (0.09), residues: 3204 sheet: -0.18 (0.15), residues: 1212 loop : -1.29 (0.10), residues: 4272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 454 HIS 0.005 0.001 HIS E 406 PHE 0.039 0.001 PHE G 758 TYR 0.020 0.001 TYR L 134 ARG 0.006 0.000 ARG D 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17376 Ramachandran restraints generated. 8688 Oldfield, 0 Emsley, 8688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 552 time to evaluate : 5.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8833 (tm-30) REVERT: A 508 MET cc_start: 0.8989 (ppp) cc_final: 0.8555 (ppp) REVERT: A 578 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8170 (tm-30) REVERT: A 678 MET cc_start: 0.8801 (mpp) cc_final: 0.8302 (mpp) REVERT: A 757 MET cc_start: 0.8989 (ppp) cc_final: 0.8698 (ppp) REVERT: B 427 MET cc_start: 0.8235 (tpp) cc_final: 0.7974 (tpt) REVERT: B 508 MET cc_start: 0.9033 (ppp) cc_final: 0.8649 (ppp) REVERT: B 578 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8341 (tm-30) REVERT: B 678 MET cc_start: 0.8670 (mpp) cc_final: 0.8450 (mpp) REVERT: C 211 LYS cc_start: 0.9510 (ptmm) cc_final: 0.9242 (ptmm) REVERT: C 275 MET cc_start: 0.8897 (mpp) cc_final: 0.8689 (mpp) REVERT: C 470 GLU cc_start: 0.8516 (pm20) cc_final: 0.8002 (pm20) REVERT: C 508 MET cc_start: 0.9049 (ppp) cc_final: 0.8707 (ppp) REVERT: C 578 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8079 (tm-30) REVERT: C 678 MET cc_start: 0.8753 (mpp) cc_final: 0.8416 (mpp) REVERT: D 36 ASN cc_start: 0.6029 (OUTLIER) cc_final: 0.5734 (t0) REVERT: D 158 MET cc_start: 0.6809 (mmp) cc_final: 0.6542 (mmp) REVERT: D 275 MET cc_start: 0.9077 (mpp) cc_final: 0.8700 (mpp) REVERT: D 427 MET cc_start: 0.8426 (tpp) cc_final: 0.8180 (tpp) REVERT: D 442 MET cc_start: 0.9021 (pmm) cc_final: 0.8699 (pmm) REVERT: D 508 MET cc_start: 0.8995 (ppp) cc_final: 0.8567 (ppp) REVERT: D 578 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 678 MET cc_start: 0.8777 (mpp) cc_final: 0.8298 (mpp) REVERT: D 757 MET cc_start: 0.9121 (ppp) cc_final: 0.8689 (ppp) REVERT: E 442 MET cc_start: 0.8981 (pmm) cc_final: 0.8754 (pmm) REVERT: E 578 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8329 (tm-30) REVERT: E 678 MET cc_start: 0.8765 (mpp) cc_final: 0.8481 (mpp) REVERT: E 757 MET cc_start: 0.8856 (ppp) cc_final: 0.8587 (ppp) REVERT: F 36 ASN cc_start: 0.6147 (OUTLIER) cc_final: 0.5850 (t0) REVERT: F 211 LYS cc_start: 0.9538 (ptmm) cc_final: 0.9285 (ptmm) REVERT: F 332 MET cc_start: 0.9093 (ttp) cc_final: 0.8887 (ttp) REVERT: F 578 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8097 (tm-30) REVERT: F 678 MET cc_start: 0.8780 (mpp) cc_final: 0.8475 (mpp) REVERT: L 36 ASN cc_start: 0.5954 (OUTLIER) cc_final: 0.5727 (t0) REVERT: L 211 LYS cc_start: 0.9484 (ptmm) cc_final: 0.9166 (ptmm) REVERT: L 470 GLU cc_start: 0.8434 (pm20) cc_final: 0.8150 (pm20) REVERT: L 578 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8274 (tm-30) REVERT: L 608 MET cc_start: 0.9762 (ptm) cc_final: 0.9545 (ppp) REVERT: L 678 MET cc_start: 0.8743 (mpp) cc_final: 0.8519 (mpp) REVERT: G 36 ASN cc_start: 0.6056 (OUTLIER) cc_final: 0.5854 (t0) REVERT: G 427 MET cc_start: 0.8357 (tpp) cc_final: 0.8092 (tpp) REVERT: G 442 MET cc_start: 0.9069 (pmm) cc_final: 0.8711 (pmm) REVERT: G 508 MET cc_start: 0.9031 (ppp) cc_final: 0.8577 (ppp) REVERT: G 549 THR cc_start: 0.8752 (t) cc_final: 0.8545 (p) REVERT: G 578 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8188 (tm-30) REVERT: G 678 MET cc_start: 0.8768 (mpp) cc_final: 0.8277 (mpp) REVERT: G 757 MET cc_start: 0.9076 (ppp) cc_final: 0.8758 (ppp) REVERT: H 427 MET cc_start: 0.8114 (tpp) cc_final: 0.7910 (tpp) REVERT: H 508 MET cc_start: 0.9036 (ppp) cc_final: 0.8635 (ppp) REVERT: H 578 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8347 (tm-30) REVERT: H 657 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9391 (mm) REVERT: H 678 MET cc_start: 0.8629 (mpp) cc_final: 0.8391 (mpp) REVERT: I 508 MET cc_start: 0.9016 (ppp) cc_final: 0.8682 (ppp) REVERT: I 578 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8071 (tm-30) REVERT: I 678 MET cc_start: 0.8741 (mpp) cc_final: 0.8442 (mpp) REVERT: J 322 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7345 (ptp90) REVERT: J 470 GLU cc_start: 0.8344 (pm20) cc_final: 0.8105 (pm20) REVERT: J 508 MET cc_start: 0.9042 (ppp) cc_final: 0.8597 (ppp) REVERT: J 517 TYR cc_start: 0.9382 (p90) cc_final: 0.8850 (p90) REVERT: J 550 MET cc_start: 0.7882 (ppp) cc_final: 0.7569 (ppp) REVERT: J 578 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8139 (tm-30) REVERT: J 757 MET cc_start: 0.9020 (ppp) cc_final: 0.8756 (ppp) REVERT: K 36 ASN cc_start: 0.5918 (OUTLIER) cc_final: 0.5679 (t0) REVERT: K 83 ARG cc_start: 0.7120 (mpt180) cc_final: 0.6817 (mpt180) REVERT: K 304 ASP cc_start: 0.8081 (t70) cc_final: 0.7874 (t0) REVERT: K 427 MET cc_start: 0.8173 (tpp) cc_final: 0.7963 (tpp) REVERT: K 470 GLU cc_start: 0.8412 (pm20) cc_final: 0.8181 (pm20) REVERT: K 578 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8325 (tp30) REVERT: K 657 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9392 (mm) outliers start: 151 outliers final: 119 residues processed: 652 average time/residue: 0.6171 time to fit residues: 700.8305 Evaluate side-chains 646 residues out of total 7428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 519 time to evaluate : 5.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 351 ASN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 351 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 349 ARG Chi-restraints excluded: chain L residue 364 ASP Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 394 VAL Chi-restraints excluded: chain L residue 415 CYS Chi-restraints excluded: chain L residue 420 LEU Chi-restraints excluded: chain L residue 619 ILE Chi-restraints excluded: chain L residue 697 LEU Chi-restraints excluded: chain L residue 756 GLU Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 415 CYS Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 617 VAL Chi-restraints excluded: chain G residue 619 ILE Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain H residue 215 GLN Chi-restraints excluded: chain H residue 269 ILE Chi-restraints excluded: chain H residue 351 ASN Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 403 THR Chi-restraints excluded: chain H residue 415 CYS Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 460 ASN Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 562 ILE Chi-restraints excluded: chain H residue 619 ILE Chi-restraints excluded: chain H residue 657 LEU Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 415 CYS Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 460 ASN Chi-restraints excluded: chain I residue 468 VAL Chi-restraints excluded: chain I residue 619 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 415 CYS Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 460 ASN Chi-restraints excluded: chain J residue 617 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 269 ILE Chi-restraints excluded: chain K residue 351 ASN Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 404 HIS Chi-restraints excluded: chain K residue 415 CYS Chi-restraints excluded: chain K residue 420 LEU Chi-restraints excluded: chain K residue 460 ASN Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 562 ILE Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 657 LEU Chi-restraints excluded: chain K residue 687 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 544 optimal weight: 9.9990 chunk 730 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 632 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 686 optimal weight: 10.0000 chunk 287 optimal weight: 0.9990 chunk 704 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS C 115 HIS C 494 GLN D 115 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 HIS L 494 GLN G 115 HIS G 401 ASN ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 HIS J 115 HIS ** K 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.114743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.076365 restraints weight = 208229.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.077561 restraints weight = 138616.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078046 restraints weight = 109286.263| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 70332 Z= 0.318 Angle : 0.665 12.148 95088 Z= 0.334 Chirality : 0.046 0.224 10656 Planarity : 0.004 0.075 12504 Dihedral : 8.709 89.191 9864 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.88 % Favored : 91.89 % Rotamer: Outliers : 2.19 % Allowed : 19.43 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.09), residues: 8688 helix: -0.61 (0.09), residues: 3204 sheet: -0.20 (0.15), residues: 1224 loop : -1.24 (0.10), residues: 4260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 454 HIS 0.007 0.001 HIS A 406 PHE 0.036 0.002 PHE G 758 TYR 0.019 0.001 TYR F 134 ARG 0.012 0.001 ARG H 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12672.74 seconds wall clock time: 224 minutes 57.28 seconds (13497.28 seconds total)