Starting phenix.real_space_refine on Sat Mar 16 08:40:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2o_0610/03_2024/6o2o_0610.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2o_0610/03_2024/6o2o_0610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2o_0610/03_2024/6o2o_0610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2o_0610/03_2024/6o2o_0610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2o_0610/03_2024/6o2o_0610.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2o_0610/03_2024/6o2o_0610.pdb" } resolution = 4.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 45474 2.51 5 N 11801 2.21 5 O 15222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A ASP 465": "OD1" <-> "OD2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 868": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 607": "NH1" <-> "NH2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 740": "OE1" <-> "OE2" Residue "B ASP 758": "OD1" <-> "OD2" Residue "B ARG 868": "NH1" <-> "NH2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ASP 216": "OD1" <-> "OD2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C ASP 362": "OD1" <-> "OD2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 417": "OD1" <-> "OD2" Residue "C PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C ASP 465": "OD1" <-> "OD2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "C TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 868": "NH1" <-> "NH2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D ASP 291": "OD1" <-> "OD2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 417": "OD1" <-> "OD2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 561": "OD1" <-> "OD2" Residue "D TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 582": "OD1" <-> "OD2" Residue "D ARG 607": "NH1" <-> "NH2" Residue "D PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 749": "OD1" <-> "OD2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "D TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 868": "NH1" <-> "NH2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 290": "NH1" <-> "NH2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 458": "NH1" <-> "NH2" Residue "E ASP 471": "OD1" <-> "OD2" Residue "E PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 520": "OD1" <-> "OD2" Residue "E TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 677": "OD1" <-> "OD2" Residue "E GLU 692": "OE1" <-> "OE2" Residue "E GLU 701": "OE1" <-> "OE2" Residue "E ASP 734": "OD1" <-> "OD2" Residue "E PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 868": "NH1" <-> "NH2" Residue "F TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 325": "NH1" <-> "NH2" Residue "F PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 417": "OD1" <-> "OD2" Residue "F ASP 465": "OD1" <-> "OD2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 568": "OD1" <-> "OD2" Residue "F ASP 597": "OD1" <-> "OD2" Residue "F ARG 607": "NH1" <-> "NH2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 749": "OD1" <-> "OD2" Residue "F GLU 760": "OE1" <-> "OE2" Residue "F PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 796": "OE1" <-> "OE2" Residue "F PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 868": "NH1" <-> "NH2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 290": "NH1" <-> "NH2" Residue "G TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 458": "NH1" <-> "NH2" Residue "G ASP 465": "OD1" <-> "OD2" Residue "G ASP 561": "OD1" <-> "OD2" Residue "G GLU 662": "OE1" <-> "OE2" Residue "G PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 758": "OD1" <-> "OD2" Residue "G TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 822": "OD1" <-> "OD2" Residue "G ARG 868": "NH1" <-> "NH2" Residue "G GLU 869": "OE1" <-> "OE2" Residue "H GLU 215": "OE1" <-> "OE2" Residue "H ASP 228": "OD1" <-> "OD2" Residue "H TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 232": "NH1" <-> "NH2" Residue "H TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 290": "NH1" <-> "NH2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 499": "OE1" <-> "OE2" Residue "H ASP 520": "OD1" <-> "OD2" Residue "H GLU 522": "OE1" <-> "OE2" Residue "H PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 572": "OD1" <-> "OD2" Residue "H ARG 607": "NH1" <-> "NH2" Residue "H ASP 624": "OD1" <-> "OD2" Residue "H TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 749": "OD1" <-> "OD2" Residue "H PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 868": "NH1" <-> "NH2" Residue "I ARG 232": "NH1" <-> "NH2" Residue "I PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 263": "OE1" <-> "OE2" Residue "I ARG 290": "NH1" <-> "NH2" Residue "I TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 458": "NH1" <-> "NH2" Residue "I ASP 465": "OD1" <-> "OD2" Residue "I ASP 540": "OD1" <-> "OD2" Residue "I TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 653": "OE1" <-> "OE2" Residue "I TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 868": "NH1" <-> "NH2" Residue "J ASP 216": "OD1" <-> "OD2" Residue "J TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 232": "NH1" <-> "NH2" Residue "J TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 288": "OE1" <-> "OE2" Residue "J ARG 290": "NH1" <-> "NH2" Residue "J ARG 325": "NH1" <-> "NH2" Residue "J TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 511": "OD1" <-> "OD2" Residue "J GLU 522": "OE1" <-> "OE2" Residue "J TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 568": "OD1" <-> "OD2" Residue "J ASP 590": "OD1" <-> "OD2" Residue "J ARG 607": "NH1" <-> "NH2" Residue "J GLU 692": "OE1" <-> "OE2" Residue "J GLU 746": "OE1" <-> "OE2" Residue "J TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 868": "NH1" <-> "NH2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 290": "NH1" <-> "NH2" Residue "K ASP 362": "OD1" <-> "OD2" Residue "K TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 426": "OE1" <-> "OE2" Residue "K ARG 458": "NH1" <-> "NH2" Residue "K ASP 520": "OD1" <-> "OD2" Residue "K TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 527": "OE1" <-> "OE2" Residue "K TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 582": "OD1" <-> "OD2" Residue "K ASP 590": "OD1" <-> "OD2" Residue "K TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 701": "OE1" <-> "OE2" Residue "K GLU 710": "OE1" <-> "OE2" Residue "K ASP 749": "OD1" <-> "OD2" Residue "K ASP 758": "OD1" <-> "OD2" Residue "K TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 868": "NH1" <-> "NH2" Residue "L ASP 216": "OD1" <-> "OD2" Residue "L ARG 232": "NH1" <-> "NH2" Residue "L TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 290": "NH1" <-> "NH2" Residue "L ARG 325": "NH1" <-> "NH2" Residue "L TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 471": "OD1" <-> "OD2" Residue "L PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 607": "NH1" <-> "NH2" Residue "L PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 662": "OE1" <-> "OE2" Residue "L GLU 701": "OE1" <-> "OE2" Residue "L TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 749": "OD1" <-> "OD2" Residue "L TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 868": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ASP 247": "OD1" <-> "OD2" Residue "M PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 290": "NH1" <-> "NH2" Residue "M TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 453": "OD1" <-> "OD2" Residue "M PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 458": "NH1" <-> "NH2" Residue "M ASP 520": "OD1" <-> "OD2" Residue "M GLU 549": "OE1" <-> "OE2" Residue "M TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 572": "OD1" <-> "OD2" Residue "M TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 693": "OE1" <-> "OE2" Residue "M TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 831": "OD1" <-> "OD2" Residue "M TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 868": "NH1" <-> "NH2" Residue "Z ARG 232": "NH1" <-> "NH2" Residue "Z PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 290": "NH1" <-> "NH2" Residue "Z TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 458": "NH1" <-> "NH2" Residue "Z GLU 479": "OE1" <-> "OE2" Residue "Z GLU 499": "OE1" <-> "OE2" Residue "Z TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 573": "OE1" <-> "OE2" Residue "Z TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 641": "OD1" <-> "OD2" Residue "Z TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 701": "OE1" <-> "OE2" Residue "Z TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 712": "OE1" <-> "OE2" Residue "Z ASP 734": "OD1" <-> "OD2" Residue "Z GLU 796": "OE1" <-> "OE2" Residue "Z TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 868": "NH1" <-> "NH2" Residue "Z GLU 869": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 72637 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "B" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "C" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "D" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "E" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "F" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "G" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "H" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "I" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "J" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "K" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "L" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "M" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "Z" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5173 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 27, 'TRANS': 629} Time building chain proxies: 27.45, per 1000 atoms: 0.38 Number of scatterers: 72637 At special positions: 0 Unit cell: (184.15, 182.7, 268.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 15222 8.00 N 11801 7.00 C 45474 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: 19.55 Conformation dependent library (CDL) restraints added in 10.2 seconds 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17288 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 138 sheets defined 11.4% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.592A pdb=" N GLU A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 232' Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.239A pdb=" N ASP A 291 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 502 through 505 removed outlier: 4.122A pdb=" N ASP A 505 " --> pdb=" O SER A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 506 through 512 removed outlier: 3.702A pdb=" N ILE A 510 " --> pdb=" O TYR A 506 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 removed outlier: 3.870A pdb=" N GLU A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 590 removed outlier: 3.542A pdb=" N ALA A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.769A pdb=" N SER B 278 " --> pdb=" O TYR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.674A pdb=" N ARG B 290 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 removed outlier: 4.026A pdb=" N ALA B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 506 through 511 removed outlier: 3.522A pdb=" N ILE B 510 " --> pdb=" O TYR B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 removed outlier: 3.792A pdb=" N GLU B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 591 removed outlier: 3.584A pdb=" N ASP B 590 " --> pdb=" O ASN B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 800 removed outlier: 4.122A pdb=" N ASP B 799 " --> pdb=" O GLU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 333 through 338 removed outlier: 4.723A pdb=" N GLY C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.645A pdb=" N LEU C 379 " --> pdb=" O ASN C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 463 through 472 removed outlier: 3.569A pdb=" N LEU C 467 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 512 removed outlier: 3.646A pdb=" N SER C 512 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 removed outlier: 4.471A pdb=" N GLU C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 593 removed outlier: 3.539A pdb=" N ALA C 585 " --> pdb=" O ASP C 581 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 587 " --> pdb=" O ASN C 583 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 764 Processing helix chain 'C' and resid 843 through 845 No H-bonds generated for 'chain 'C' and resid 843 through 845' Processing helix chain 'D' and resid 226 through 230 Processing helix chain 'D' and resid 272 through 278 removed outlier: 3.600A pdb=" N SER D 278 " --> pdb=" O TYR D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 removed outlier: 4.042A pdb=" N ARG D 290 " --> pdb=" O THR D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 503 through 505 No H-bonds generated for 'chain 'D' and resid 503 through 505' Processing helix chain 'D' and resid 506 through 512 removed outlier: 3.836A pdb=" N ILE D 510 " --> pdb=" O TYR D 506 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 512 " --> pdb=" O SER D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 removed outlier: 3.687A pdb=" N GLU D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 590 removed outlier: 3.576A pdb=" N ASP D 590 " --> pdb=" O ASN D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.578A pdb=" N THR D 594 " --> pdb=" O SER D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 831 No H-bonds generated for 'chain 'D' and resid 829 through 831' Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.598A pdb=" N ILE E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 506 through 511 Processing helix chain 'E' and resid 546 through 555 Processing helix chain 'E' and resid 581 through 593 removed outlier: 3.621A pdb=" N LYS E 587 " --> pdb=" O ASN E 583 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP E 590 " --> pdb=" O ASN E 586 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER E 591 " --> pdb=" O LYS E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 removed outlier: 3.655A pdb=" N VAL E 603 " --> pdb=" O ILE E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 760 through 764 Processing helix chain 'E' and resid 797 through 801 removed outlier: 3.604A pdb=" N TYR E 800 " --> pdb=" O ALA E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 831 No H-bonds generated for 'chain 'E' and resid 829 through 831' Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.520A pdb=" N ARG F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 251 Processing helix chain 'F' and resid 272 through 278 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 471 Processing helix chain 'F' and resid 503 through 505 No H-bonds generated for 'chain 'F' and resid 503 through 505' Processing helix chain 'F' and resid 506 through 512 removed outlier: 3.715A pdb=" N ILE F 510 " --> pdb=" O TYR F 506 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER F 512 " --> pdb=" O SER F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 555 removed outlier: 4.120A pdb=" N GLU F 552 " --> pdb=" O GLY F 548 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE F 555 " --> pdb=" O ILE F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 591 Processing helix chain 'F' and resid 661 through 663 No H-bonds generated for 'chain 'F' and resid 661 through 663' Processing helix chain 'F' and resid 796 through 800 removed outlier: 3.794A pdb=" N ASP F 799 " --> pdb=" O GLU F 796 " (cutoff:3.500A) Processing helix chain 'F' and resid 827 through 831 removed outlier: 3.848A pdb=" N GLY F 830 " --> pdb=" O ASN F 827 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.761A pdb=" N ASN G 233 " --> pdb=" O SER G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.798A pdb=" N ARG G 290 " --> pdb=" O THR G 287 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 339 removed outlier: 4.048A pdb=" N GLY G 338 " --> pdb=" O ASN G 335 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL G 339 " --> pdb=" O THR G 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 335 through 339' Processing helix chain 'G' and resid 374 through 378 removed outlier: 3.642A pdb=" N THR G 377 " --> pdb=" O SER G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.641A pdb=" N GLN G 428 " --> pdb=" O GLN G 425 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 463 through 471 Processing helix chain 'G' and resid 506 through 512 removed outlier: 3.746A pdb=" N ILE G 510 " --> pdb=" O TYR G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 555 removed outlier: 3.673A pdb=" N GLU G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 593 removed outlier: 3.704A pdb=" N ALA G 585 " --> pdb=" O ASP G 581 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN G 586 " --> pdb=" O ASP G 582 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS G 587 " --> pdb=" O ASN G 583 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER G 591 " --> pdb=" O LYS G 587 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 removed outlier: 3.675A pdb=" N ASN G 602 " --> pdb=" O LYS G 599 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL G 603 " --> pdb=" O ILE G 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 599 through 603' Processing helix chain 'G' and resid 760 through 764 removed outlier: 3.823A pdb=" N ASP G 763 " --> pdb=" O GLU G 760 " (cutoff:3.500A) Processing helix chain 'G' and resid 829 through 831 No H-bonds generated for 'chain 'G' and resid 829 through 831' Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.503A pdb=" N GLU H 231 " --> pdb=" O PRO H 227 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 227 through 232' Processing helix chain 'H' and resid 246 through 251 Processing helix chain 'H' and resid 272 through 278 Processing helix chain 'H' and resid 286 through 290 Processing helix chain 'H' and resid 463 through 472 removed outlier: 3.729A pdb=" N ALA H 472 " --> pdb=" O LYS H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 505 No H-bonds generated for 'chain 'H' and resid 503 through 505' Processing helix chain 'H' and resid 506 through 511 Processing helix chain 'H' and resid 546 through 555 removed outlier: 3.833A pdb=" N PHE H 555 " --> pdb=" O ILE H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 591 removed outlier: 3.535A pdb=" N ALA H 585 " --> pdb=" O ASP H 581 " (cutoff:3.500A) Processing helix chain 'H' and resid 796 through 800 Processing helix chain 'H' and resid 829 through 831 No H-bonds generated for 'chain 'H' and resid 829 through 831' Processing helix chain 'I' and resid 227 through 233 Processing helix chain 'I' and resid 272 through 279 removed outlier: 3.868A pdb=" N GLY I 279 " --> pdb=" O GLU I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 291 removed outlier: 3.518A pdb=" N ALA I 289 " --> pdb=" O LYS I 286 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP I 291 " --> pdb=" O GLU I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.694A pdb=" N ILE I 429 " --> pdb=" O GLU I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 472 Processing helix chain 'I' and resid 506 through 512 Processing helix chain 'I' and resid 546 through 555 removed outlier: 4.260A pdb=" N GLU I 552 " --> pdb=" O GLY I 548 " (cutoff:3.500A) Processing helix chain 'I' and resid 581 through 593 removed outlier: 3.638A pdb=" N ALA I 585 " --> pdb=" O ASP I 581 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN I 586 " --> pdb=" O ASP I 582 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS I 587 " --> pdb=" O ASN I 583 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER I 591 " --> pdb=" O LYS I 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU I 592 " --> pdb=" O ILE I 588 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS I 593 " --> pdb=" O LYS I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 603 removed outlier: 3.640A pdb=" N ASN I 602 " --> pdb=" O LYS I 599 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL I 603 " --> pdb=" O ILE I 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 599 through 603' Processing helix chain 'I' and resid 829 through 831 No H-bonds generated for 'chain 'I' and resid 829 through 831' Processing helix chain 'J' and resid 227 through 232 removed outlier: 4.223A pdb=" N ARG J 232 " --> pdb=" O ASP J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 251 removed outlier: 3.771A pdb=" N PHE J 249 " --> pdb=" O GLU J 246 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA J 250 " --> pdb=" O ASP J 247 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU J 251 " --> pdb=" O SER J 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 246 through 251' Processing helix chain 'J' and resid 273 through 278 Processing helix chain 'J' and resid 463 through 472 Processing helix chain 'J' and resid 506 through 512 removed outlier: 4.091A pdb=" N ILE J 510 " --> pdb=" O TYR J 506 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 555 removed outlier: 3.915A pdb=" N GLU J 552 " --> pdb=" O GLY J 548 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 591 removed outlier: 3.963A pdb=" N ASP J 590 " --> pdb=" O ASN J 586 " (cutoff:3.500A) Processing helix chain 'J' and resid 796 through 800 Processing helix chain 'J' and resid 829 through 831 No H-bonds generated for 'chain 'J' and resid 829 through 831' Processing helix chain 'K' and resid 227 through 233 removed outlier: 3.636A pdb=" N ASN K 233 " --> pdb=" O SER K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 279 removed outlier: 3.589A pdb=" N LYS K 276 " --> pdb=" O THR K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 290 removed outlier: 3.950A pdb=" N ARG K 290 " --> pdb=" O THR K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 379 Processing helix chain 'K' and resid 425 through 429 removed outlier: 3.689A pdb=" N ILE K 429 " --> pdb=" O GLU K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 472 Processing helix chain 'K' and resid 506 through 512 removed outlier: 3.561A pdb=" N SER K 512 " --> pdb=" O SER K 508 " (cutoff:3.500A) Processing helix chain 'K' and resid 546 through 555 removed outlier: 4.069A pdb=" N GLU K 552 " --> pdb=" O GLY K 548 " (cutoff:3.500A) Processing helix chain 'K' and resid 581 through 593 removed outlier: 4.066A pdb=" N ALA K 585 " --> pdb=" O ASP K 581 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS K 587 " --> pdb=" O ASN K 583 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP K 590 " --> pdb=" O ASN K 586 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER K 591 " --> pdb=" O LYS K 587 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS K 593 " --> pdb=" O LYS K 589 " (cutoff:3.500A) Processing helix chain 'K' and resid 599 through 603 removed outlier: 3.519A pdb=" N VAL K 603 " --> pdb=" O ILE K 600 " (cutoff:3.500A) Processing helix chain 'K' and resid 760 through 764 removed outlier: 4.118A pdb=" N ASP K 763 " --> pdb=" O GLU K 760 " (cutoff:3.500A) Processing helix chain 'K' and resid 797 through 801 Processing helix chain 'K' and resid 843 through 845 No H-bonds generated for 'chain 'K' and resid 843 through 845' Processing helix chain 'L' and resid 227 through 232 removed outlier: 4.065A pdb=" N GLU L 231 " --> pdb=" O PRO L 227 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG L 232 " --> pdb=" O ASP L 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 227 through 232' Processing helix chain 'L' and resid 248 through 253 removed outlier: 3.868A pdb=" N GLU L 251 " --> pdb=" O SER L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 278 Processing helix chain 'L' and resid 286 through 290 removed outlier: 3.804A pdb=" N ARG L 290 " --> pdb=" O THR L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 463 through 472 removed outlier: 3.797A pdb=" N ALA L 472 " --> pdb=" O LYS L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 503 through 506 Processing helix chain 'L' and resid 507 through 512 Processing helix chain 'L' and resid 546 through 555 Processing helix chain 'L' and resid 581 through 591 Processing helix chain 'L' and resid 796 through 801 Processing helix chain 'L' and resid 829 through 831 No H-bonds generated for 'chain 'L' and resid 829 through 831' Processing helix chain 'M' and resid 227 through 233 removed outlier: 4.220A pdb=" N ASN M 233 " --> pdb=" O SER M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 279 removed outlier: 3.923A pdb=" N GLY M 279 " --> pdb=" O GLU M 275 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 291 removed outlier: 3.703A pdb=" N ARG M 290 " --> pdb=" O THR M 287 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP M 291 " --> pdb=" O GLU M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 379 removed outlier: 3.697A pdb=" N GLY M 378 " --> pdb=" O SER M 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 463 through 471 Processing helix chain 'M' and resid 506 through 512 removed outlier: 3.655A pdb=" N ILE M 510 " --> pdb=" O TYR M 506 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER M 512 " --> pdb=" O SER M 508 " (cutoff:3.500A) Processing helix chain 'M' and resid 546 through 555 removed outlier: 3.667A pdb=" N GLU M 552 " --> pdb=" O GLY M 548 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE M 555 " --> pdb=" O ILE M 551 " (cutoff:3.500A) Processing helix chain 'M' and resid 581 through 590 removed outlier: 3.505A pdb=" N ASN M 586 " --> pdb=" O ASP M 582 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS M 587 " --> pdb=" O ASN M 583 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 603 removed outlier: 3.854A pdb=" N ASN M 602 " --> pdb=" O LYS M 599 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL M 603 " --> pdb=" O ILE M 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 599 through 603' Processing helix chain 'M' and resid 760 through 764 Processing helix chain 'M' and resid 829 through 831 No H-bonds generated for 'chain 'M' and resid 829 through 831' Processing helix chain 'Z' and resid 227 through 233 removed outlier: 3.978A pdb=" N ASN Z 233 " --> pdb=" O SER Z 229 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 279 Processing helix chain 'Z' and resid 286 through 291 removed outlier: 4.328A pdb=" N ASP Z 291 " --> pdb=" O GLU Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 425 through 429 removed outlier: 3.603A pdb=" N ILE Z 429 " --> pdb=" O GLU Z 426 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 472 Processing helix chain 'Z' and resid 506 through 511 Processing helix chain 'Z' and resid 546 through 555 removed outlier: 3.811A pdb=" N GLU Z 552 " --> pdb=" O GLY Z 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 581 through 593 removed outlier: 3.715A pdb=" N ASP Z 590 " --> pdb=" O ASN Z 586 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER Z 591 " --> pdb=" O LYS Z 587 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS Z 593 " --> pdb=" O LYS Z 589 " (cutoff:3.500A) Processing helix chain 'Z' and resid 599 through 603 removed outlier: 3.903A pdb=" N ASN Z 602 " --> pdb=" O LYS Z 599 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL Z 603 " --> pdb=" O ILE Z 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 599 through 603' Processing helix chain 'Z' and resid 760 through 764 removed outlier: 3.741A pdb=" N ASP Z 763 " --> pdb=" O GLU Z 760 " (cutoff:3.500A) Processing helix chain 'Z' and resid 796 through 800 Processing helix chain 'Z' and resid 829 through 831 No H-bonds generated for 'chain 'Z' and resid 829 through 831' Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 311 removed outlier: 3.769A pdb=" N GLY A 301 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 311 removed outlier: 3.769A pdb=" N GLY A 301 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 345 removed outlier: 3.567A pdb=" N HIS A 359 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 337 " --> pdb=" O HIS A 359 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 335 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 363 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 333 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 331 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 327 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 323 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 321 " --> pdb=" O TRP A 375 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 351 " --> pdb=" O TYR D 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 369 " --> pdb=" O THR D 327 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRP B 375 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR D 317 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 315 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA D 351 " --> pdb=" O TYR F 345 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 353 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL F 343 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR D 357 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 337 " --> pdb=" O HIS D 359 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D 365 " --> pdb=" O LYS F 331 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS F 331 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN H 329 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG H 325 " --> pdb=" O ASN F 371 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL H 323 " --> pdb=" O GLU F 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS H 321 " --> pdb=" O TRP F 375 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR F 377 " --> pdb=" O GLN H 319 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN H 319 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR H 317 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA H 351 " --> pdb=" O TYR J 345 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS H 359 " --> pdb=" O ALA J 337 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN H 363 " --> pdb=" O GLU J 333 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU J 333 " --> pdb=" O ASN H 363 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR J 327 " --> pdb=" O ASP H 369 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN J 319 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA J 351 " --> pdb=" O TYR L 345 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR L 345 " --> pdb=" O ALA J 351 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN J 363 " --> pdb=" O GLU L 333 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU L 333 " --> pdb=" O ASN J 363 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP J 369 " --> pdb=" O THR L 327 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL L 323 " --> pdb=" O GLU J 373 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP J 375 " --> pdb=" O LYS L 321 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN L 319 " --> pdb=" O THR J 377 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA L 351 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 341 " --> pdb=" O THR L 355 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR L 357 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 339 " --> pdb=" O TYR L 357 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS L 359 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 337 " --> pdb=" O HIS L 359 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN L 363 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 325 " --> pdb=" O ASN L 371 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 319 " --> pdb=" O THR L 377 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 317 " --> pdb=" O LEU L 379 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 421 through 423 removed outlier: 6.749A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 481 " --> pdb=" O THR A 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 525 through 531 removed outlier: 9.464A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 618 through 619 removed outlier: 3.735A pdb=" N TYR A 618 " --> pdb=" O ILE A 738 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 651 through 659 Processing sheet with id=AA9, first strand: chain 'A' and resid 768 through 774 removed outlier: 6.366A pdb=" N PHE A 769 " --> pdb=" O MET A 786 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N MET A 786 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP A 771 " --> pdb=" O ASN A 784 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN A 838 " --> pdb=" O PHE A 788 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 817 through 822 removed outlier: 4.916A pdb=" N GLY A 819 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 806 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS A 803 " --> pdb=" O TYR A 861 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 856 " --> pdb=" O VAL A 872 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 872 " --> pdb=" O LYS A 856 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE A 860 " --> pdb=" O ARG A 868 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ARG A 868 " --> pdb=" O ILE A 860 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 236 through 237 Processing sheet with id=AB3, first strand: chain 'B' and resid 298 through 311 removed outlier: 3.535A pdb=" N ILE B 299 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 303 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 394 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 438 through 439 Processing sheet with id=AB5, first strand: chain 'B' and resid 420 through 423 removed outlier: 3.800A pdb=" N SER B 420 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN B 431 " --> pdb=" O LYS B 405 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 420 through 423 removed outlier: 3.800A pdb=" N SER B 420 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR B 481 " --> pdb=" O THR B 409 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 490 removed outlier: 3.830A pdb=" N THR B 489 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 525 through 530 removed outlier: 6.593A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 558 through 559 removed outlier: 3.816A pdb=" N THR B 558 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 618 through 619 removed outlier: 3.572A pdb=" N TYR B 618 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 738 " --> pdb=" O TYR B 618 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 652 through 659 Processing sheet with id=AC3, first strand: chain 'B' and resid 768 through 773 removed outlier: 6.112A pdb=" N PHE B 769 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET B 786 " --> pdb=" O PHE B 769 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP B 771 " --> pdb=" O ASN B 784 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN B 838 " --> pdb=" O PHE B 788 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 816 through 822 removed outlier: 5.606A pdb=" N ASP B 817 " --> pdb=" O ALA B 808 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA B 808 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY B 819 " --> pdb=" O VAL B 806 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL B 806 " --> pdb=" O GLY B 819 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS B 803 " --> pdb=" O TYR B 861 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS B 856 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU B 871 " --> pdb=" O LYS B 856 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 858 " --> pdb=" O GLU B 869 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC6, first strand: chain 'C' and resid 323 through 326 removed outlier: 3.648A pdb=" N GLY C 301 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN C 392 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA C 391 " --> pdb=" O LEU C 449 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C 393 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 323 through 326 removed outlier: 3.648A pdb=" N GLY C 301 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN C 392 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE C 460 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 352 through 353 removed outlier: 6.385A pdb=" N ASN C 352 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP C 520 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 363 through 364 removed outlier: 3.576A pdb=" N SER C 420 " --> pdb=" O LEU C 412 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AD2, first strand: chain 'C' and resid 618 through 620 removed outlier: 6.419A pdb=" N ARG C 668 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 654 through 659 Processing sheet with id=AD4, first strand: chain 'C' and resid 768 through 771 removed outlier: 3.656A pdb=" N MET C 786 " --> pdb=" O VAL C 840 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE C 788 " --> pdb=" O ASN C 838 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASN C 838 " --> pdb=" O PHE C 788 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 816 through 818 removed outlier: 3.917A pdb=" N VAL C 806 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS C 856 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU C 871 " --> pdb=" O LYS C 856 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU C 858 " --> pdb=" O GLU C 869 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 236 through 238 Processing sheet with id=AD7, first strand: chain 'D' and resid 298 through 311 removed outlier: 3.849A pdb=" N GLY D 301 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 394 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 421 through 423 removed outlier: 6.818A pdb=" N LYS D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY D 485 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 407 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL D 483 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 525 through 531 removed outlier: 9.656A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 618 through 619 removed outlier: 3.642A pdb=" N TYR D 618 " --> pdb=" O ILE D 738 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 711 " --> pdb=" O TYR D 669 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 654 through 658 Processing sheet with id=AE3, first strand: chain 'D' and resid 768 through 774 removed outlier: 6.537A pdb=" N PHE D 769 " --> pdb=" O MET D 786 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N MET D 786 " --> pdb=" O PHE D 769 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP D 771 " --> pdb=" O ASN D 784 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 816 through 822 removed outlier: 4.083A pdb=" N LYS D 816 " --> pdb=" O ALA D 808 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA D 808 " --> pdb=" O LYS D 816 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 818 " --> pdb=" O VAL D 806 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL D 806 " --> pdb=" O ILE D 818 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR D 820 " --> pdb=" O TYR D 804 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR D 804 " --> pdb=" O THR D 820 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS D 803 " --> pdb=" O TYR D 861 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR D 855 " --> pdb=" O THR D 809 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS D 856 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU D 871 " --> pdb=" O LYS D 856 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU D 858 " --> pdb=" O GLU D 869 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AE6, first strand: chain 'E' and resid 236 through 238 Processing sheet with id=AE7, first strand: chain 'E' and resid 366 through 367 removed outlier: 5.695A pdb=" N GLU E 305 " --> pdb=" O THR E 327 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN E 392 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE E 460 " --> pdb=" O ILE E 389 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 352 through 353 removed outlier: 6.160A pdb=" N ASN E 352 " --> pdb=" O PHE E 580 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 362 through 364 removed outlier: 4.278A pdb=" N SER E 420 " --> pdb=" O LEU E 412 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 564 through 565 removed outlier: 3.551A pdb=" N LEU E 564 " --> pdb=" O ILE E 571 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 618 through 620 removed outlier: 6.485A pdb=" N ARG E 668 " --> pdb=" O LEU E 741 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 653 through 658 removed outlier: 3.535A pdb=" N SER E 683 " --> pdb=" O THR E 695 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 768 through 771 removed outlier: 3.655A pdb=" N MET E 786 " --> pdb=" O VAL E 840 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE E 788 " --> pdb=" O ASN E 838 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN E 838 " --> pdb=" O PHE E 788 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 816 through 822 removed outlier: 3.806A pdb=" N ALA E 808 " --> pdb=" O LYS E 816 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 806 " --> pdb=" O ILE E 818 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR E 820 " --> pdb=" O TYR E 804 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR E 804 " --> pdb=" O THR E 820 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS E 803 " --> pdb=" O TYR E 861 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS E 856 " --> pdb=" O LEU E 871 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU E 871 " --> pdb=" O LYS E 856 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU E 858 " --> pdb=" O GLU E 869 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AF7, first strand: chain 'F' and resid 300 through 311 removed outlier: 6.711A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 418 through 423 removed outlier: 4.268A pdb=" N SER F 420 " --> pdb=" O LEU F 412 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR F 481 " --> pdb=" O THR F 409 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AG1, first strand: chain 'F' and resid 525 through 531 Processing sheet with id=AG2, first strand: chain 'F' and resid 618 through 619 removed outlier: 3.995A pdb=" N TYR F 618 " --> pdb=" O ILE F 738 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE F 738 " --> pdb=" O TYR F 618 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 652 through 659 Processing sheet with id=AG4, first strand: chain 'F' and resid 770 through 775 removed outlier: 5.851A pdb=" N ASN F 773 " --> pdb=" O ILE F 783 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE F 783 " --> pdb=" O ASN F 773 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN F 775 " --> pdb=" O THR F 781 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR F 781 " --> pdb=" O ASN F 775 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET F 786 " --> pdb=" O VAL F 840 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL F 840 " --> pdb=" O MET F 786 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN F 838 " --> pdb=" O PHE F 788 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 816 through 822 removed outlier: 5.769A pdb=" N ASP F 817 " --> pdb=" O ALA F 808 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ALA F 808 " --> pdb=" O ASP F 817 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLY F 819 " --> pdb=" O VAL F 806 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL F 806 " --> pdb=" O GLY F 819 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS F 821 " --> pdb=" O TYR F 804 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS F 803 " --> pdb=" O TYR F 861 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR F 809 " --> pdb=" O TYR F 855 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR F 855 " --> pdb=" O THR F 809 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AG7, first strand: chain 'G' and resid 418 through 421 removed outlier: 6.884A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE G 476 " --> pdb=" O THR G 365 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER G 364 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER G 330 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA G 366 " --> pdb=" O THR G 328 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLU G 305 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASN G 329 " --> pdb=" O GLY G 303 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N GLY G 303 " --> pdb=" O ASN G 329 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL G 302 " --> pdb=" O TYR G 396 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR G 396 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N MET G 304 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG G 394 " --> pdb=" O MET G 304 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS G 306 " --> pdb=" O ASN G 392 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN G 392 " --> pdb=" O LYS G 306 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE G 460 " --> pdb=" O ILE G 389 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 352 through 353 removed outlier: 6.219A pdb=" N ASN G 352 " --> pdb=" O PHE G 580 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 489 through 490 removed outlier: 3.654A pdb=" N THR G 489 " --> pdb=" O VAL G 497 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL G 497 " --> pdb=" O THR G 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'G' and resid 618 through 621 removed outlier: 4.920A pdb=" N ASN G 735 " --> pdb=" O TYR G 674 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR G 674 " --> pdb=" O ASN G 735 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG G 668 " --> pdb=" O LEU G 741 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 654 through 659 Processing sheet with id=AH3, first strand: chain 'G' and resid 768 through 771 removed outlier: 3.704A pdb=" N MET G 786 " --> pdb=" O VAL G 840 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN G 838 " --> pdb=" O PHE G 788 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 816 through 822 removed outlier: 3.890A pdb=" N VAL G 806 " --> pdb=" O ILE G 818 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR G 820 " --> pdb=" O TYR G 804 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR G 804 " --> pdb=" O THR G 820 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS G 856 " --> pdb=" O LEU G 871 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU G 871 " --> pdb=" O LYS G 856 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU G 858 " --> pdb=" O GLU G 869 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 235 through 238 Processing sheet with id=AH6, first strand: chain 'H' and resid 298 through 311 removed outlier: 3.931A pdb=" N GLY H 301 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN H 392 " --> pdb=" O GLU H 305 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU H 307 " --> pdb=" O ASN H 390 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN H 390 " --> pdb=" O LEU H 307 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE H 309 " --> pdb=" O TYR H 388 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR H 388 " --> pdb=" O ILE H 309 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 418 through 423 removed outlier: 4.225A pdb=" N SER H 420 " --> pdb=" O LEU H 412 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 418 through 423 removed outlier: 4.225A pdb=" N SER H 420 " --> pdb=" O LEU H 412 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL H 406 " --> pdb=" O SER H 484 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER H 484 " --> pdb=" O VAL H 406 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 489 through 490 removed outlier: 3.690A pdb=" N THR H 489 " --> pdb=" O VAL H 497 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 525 through 530 Processing sheet with id=AI2, first strand: chain 'H' and resid 564 through 565 removed outlier: 4.133A pdb=" N LEU H 564 " --> pdb=" O ILE H 571 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 618 through 619 Processing sheet with id=AI4, first strand: chain 'H' and resid 652 through 659 Processing sheet with id=AI5, first strand: chain 'H' and resid 770 through 774 removed outlier: 6.114A pdb=" N ASN H 773 " --> pdb=" O ILE H 783 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE H 783 " --> pdb=" O ASN H 773 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 816 through 822 removed outlier: 3.555A pdb=" N ALA H 808 " --> pdb=" O LYS H 816 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL H 806 " --> pdb=" O ILE H 818 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR H 820 " --> pdb=" O TYR H 804 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR H 804 " --> pdb=" O THR H 820 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS H 803 " --> pdb=" O TYR H 861 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU H 858 " --> pdb=" O GLU H 869 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 826 through 827 removed outlier: 3.847A pdb=" N ARG H 826 " --> pdb=" O THR H 837 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'I' and resid 236 through 238 Processing sheet with id=AI9, first strand: chain 'I' and resid 302 through 304 Processing sheet with id=AJ1, first strand: chain 'I' and resid 418 through 421 removed outlier: 3.700A pdb=" N SER I 420 " --> pdb=" O LEU I 412 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE I 476 " --> pdb=" O THR I 365 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER I 330 " --> pdb=" O SER I 364 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE I 460 " --> pdb=" O ILE I 389 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 352 through 353 removed outlier: 3.596A pdb=" N PHE I 580 " --> pdb=" O ASN I 352 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N ILE I 611 " --> pdb=" O SER I 514 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER I 516 " --> pdb=" O ILE I 611 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE I 613 " --> pdb=" O SER I 516 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE I 518 " --> pdb=" O ILE I 613 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'I' and resid 489 through 490 removed outlier: 3.967A pdb=" N THR I 489 " --> pdb=" O VAL I 497 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL I 497 " --> pdb=" O THR I 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'I' and resid 618 through 620 removed outlier: 6.549A pdb=" N ARG I 668 " --> pdb=" O LEU I 741 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'I' and resid 653 through 659 Processing sheet with id=AJ6, first strand: chain 'I' and resid 768 through 771 removed outlier: 3.646A pdb=" N MET I 786 " --> pdb=" O VAL I 840 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE I 788 " --> pdb=" O ASN I 838 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN I 838 " --> pdb=" O PHE I 788 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'I' and resid 816 through 822 removed outlier: 3.695A pdb=" N ALA I 808 " --> pdb=" O LYS I 816 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL I 806 " --> pdb=" O ILE I 818 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR I 820 " --> pdb=" O TYR I 804 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR I 804 " --> pdb=" O THR I 820 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS I 856 " --> pdb=" O LEU I 871 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU I 871 " --> pdb=" O LYS I 856 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU I 858 " --> pdb=" O GLU I 869 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP I 867 " --> pdb=" O ILE I 860 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'J' and resid 235 through 238 Processing sheet with id=AJ9, first strand: chain 'J' and resid 298 through 299 Processing sheet with id=AK1, first strand: chain 'J' and resid 303 through 311 removed outlier: 5.658A pdb=" N MET J 304 " --> pdb=" O ARG J 394 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG J 394 " --> pdb=" O MET J 304 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'J' and resid 303 through 311 removed outlier: 5.658A pdb=" N MET J 304 " --> pdb=" O ARG J 394 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG J 394 " --> pdb=" O MET J 304 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA J 387 " --> pdb=" O ILE J 462 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'J' and resid 420 through 423 removed outlier: 3.820A pdb=" N SER J 420 " --> pdb=" O LEU J 412 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LYS J 405 " --> pdb=" O ASN J 486 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN J 486 " --> pdb=" O LYS J 405 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN J 482 " --> pdb=" O THR J 409 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN J 411 " --> pdb=" O THR J 480 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR J 480 " --> pdb=" O ASN J 411 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL J 413 " --> pdb=" O LEU J 478 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU J 478 " --> pdb=" O VAL J 413 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'J' and resid 489 through 490 removed outlier: 3.502A pdb=" N THR J 489 " --> pdb=" O VAL J 497 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'J' and resid 525 through 530 Processing sheet with id=AK6, first strand: chain 'J' and resid 558 through 560 removed outlier: 3.658A pdb=" N THR J 558 " --> pdb=" O TYR J 565 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR J 565 " --> pdb=" O THR J 558 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU J 564 " --> pdb=" O ILE J 571 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'J' and resid 618 through 619 removed outlier: 3.837A pdb=" N TYR J 618 " --> pdb=" O ILE J 738 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE J 711 " --> pdb=" O TYR J 669 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'J' and resid 652 through 659 Processing sheet with id=AK9, first strand: chain 'J' and resid 770 through 774 removed outlier: 5.774A pdb=" N ASN J 773 " --> pdb=" O ILE J 783 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE J 783 " --> pdb=" O ASN J 773 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET J 786 " --> pdb=" O VAL J 840 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 840 " --> pdb=" O MET J 786 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG J 826 " --> pdb=" O THR J 837 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'J' and resid 816 through 822 removed outlier: 5.541A pdb=" N ASP J 817 " --> pdb=" O ALA J 808 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA J 808 " --> pdb=" O ASP J 817 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLY J 819 " --> pdb=" O VAL J 806 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL J 806 " --> pdb=" O GLY J 819 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS J 821 " --> pdb=" O TYR J 804 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS J 803 " --> pdb=" O TYR J 861 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TYR J 855 " --> pdb=" O THR J 809 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE J 860 " --> pdb=" O ARG J 868 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ARG J 868 " --> pdb=" O ILE J 860 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'K' and resid 235 through 238 Processing sheet with id=AL3, first strand: chain 'K' and resid 418 through 422 removed outlier: 3.849A pdb=" N SER K 420 " --> pdb=" O LEU K 412 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER K 364 " --> pdb=" O SER K 330 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER K 330 " --> pdb=" O SER K 364 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA K 366 " --> pdb=" O THR K 328 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU K 305 " --> pdb=" O THR K 327 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ASN K 329 " --> pdb=" O GLY K 303 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N GLY K 303 " --> pdb=" O ASN K 329 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY K 301 " --> pdb=" O TYR K 396 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASN K 392 " --> pdb=" O GLU K 305 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU K 307 " --> pdb=" O ASN K 390 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASN K 390 " --> pdb=" O LEU K 307 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE K 309 " --> pdb=" O TYR K 388 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR K 388 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE K 460 " --> pdb=" O ILE K 389 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'K' and resid 352 through 353 removed outlier: 3.669A pdb=" N ASP K 520 " --> pdb=" O ILE K 613 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'K' and resid 564 through 565 removed outlier: 3.626A pdb=" N LEU K 564 " --> pdb=" O ILE K 571 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'K' and resid 618 through 621 removed outlier: 5.441A pdb=" N ASN K 735 " --> pdb=" O TYR K 674 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR K 674 " --> pdb=" O ASN K 735 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG K 668 " --> pdb=" O LEU K 741 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'K' and resid 653 through 658 Processing sheet with id=AL8, first strand: chain 'K' and resid 768 through 771 removed outlier: 3.636A pdb=" N MET K 786 " --> pdb=" O VAL K 840 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL K 840 " --> pdb=" O MET K 786 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE K 788 " --> pdb=" O ASN K 838 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN K 838 " --> pdb=" O PHE K 788 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'K' and resid 816 through 822 removed outlier: 5.221A pdb=" N ASP K 817 " --> pdb=" O ALA K 808 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA K 808 " --> pdb=" O ASP K 817 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLY K 819 " --> pdb=" O VAL K 806 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL K 806 " --> pdb=" O GLY K 819 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU K 870 " --> pdb=" O LEU K 858 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE K 860 " --> pdb=" O ARG K 868 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG K 868 " --> pdb=" O ILE K 860 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'L' and resid 235 through 238 Processing sheet with id=AM2, first strand: chain 'L' and resid 298 through 311 removed outlier: 3.757A pdb=" N GLY L 301 " --> pdb=" O TYR L 396 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY L 303 " --> pdb=" O ARG L 394 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG L 394 " --> pdb=" O GLY L 303 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN L 392 " --> pdb=" O GLU L 305 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU L 307 " --> pdb=" O ASN L 390 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN L 390 " --> pdb=" O LEU L 307 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE L 309 " --> pdb=" O TYR L 388 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR L 388 " --> pdb=" O ILE L 309 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'L' and resid 298 through 311 removed outlier: 3.757A pdb=" N GLY L 301 " --> pdb=" O TYR L 396 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY L 303 " --> pdb=" O ARG L 394 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG L 394 " --> pdb=" O GLY L 303 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN L 392 " --> pdb=" O GLU L 305 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU L 307 " --> pdb=" O ASN L 390 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN L 390 " --> pdb=" O LEU L 307 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE L 309 " --> pdb=" O TYR L 388 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR L 388 " --> pdb=" O ILE L 309 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA L 387 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'L' and resid 403 through 406 removed outlier: 7.120A pdb=" N ASN L 431 " --> pdb=" O LYS L 405 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'L' and resid 420 through 423 removed outlier: 3.763A pdb=" N SER L 420 " --> pdb=" O LEU L 412 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR L 409 " --> pdb=" O THR L 481 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR L 481 " --> pdb=" O THR L 409 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'L' and resid 525 through 531 Processing sheet with id=AM7, first strand: chain 'L' and resid 558 through 560 removed outlier: 3.794A pdb=" N THR L 558 " --> pdb=" O TYR L 565 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'L' and resid 618 through 619 removed outlier: 3.817A pdb=" N TYR L 618 " --> pdb=" O ILE L 738 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE L 738 " --> pdb=" O TYR L 618 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'L' and resid 652 through 659 Processing sheet with id=AN1, first strand: chain 'L' and resid 770 through 775 removed outlier: 7.131A pdb=" N ASP L 771 " --> pdb=" O ASN L 784 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN L 780 " --> pdb=" O ASN L 775 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN L 838 " --> pdb=" O PHE L 788 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU L 824 " --> pdb=" O TYR L 839 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'L' and resid 816 through 822 removed outlier: 3.652A pdb=" N ALA L 808 " --> pdb=" O LYS L 816 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL L 806 " --> pdb=" O ILE L 818 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR L 820 " --> pdb=" O TYR L 804 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR L 804 " --> pdb=" O THR L 820 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS L 803 " --> pdb=" O TYR L 861 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE L 860 " --> pdb=" O ARG L 868 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG L 868 " --> pdb=" O ILE L 860 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'M' and resid 235 through 238 Processing sheet with id=AN4, first strand: chain 'M' and resid 322 through 326 removed outlier: 6.543A pdb=" N ASN M 392 " --> pdb=" O GLU M 305 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LEU M 307 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN M 390 " --> pdb=" O LEU M 307 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE M 309 " --> pdb=" O TYR M 388 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR M 388 " --> pdb=" O ILE M 309 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'M' and resid 322 through 326 removed outlier: 6.543A pdb=" N ASN M 392 " --> pdb=" O GLU M 305 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LEU M 307 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN M 390 " --> pdb=" O LEU M 307 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE M 309 " --> pdb=" O TYR M 388 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR M 388 " --> pdb=" O ILE M 309 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE M 460 " --> pdb=" O ILE M 389 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'M' and resid 328 through 330 removed outlier: 3.591A pdb=" N SER M 330 " --> pdb=" O SER M 364 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER M 364 " --> pdb=" O SER M 330 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER M 420 " --> pdb=" O LEU M 412 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'M' and resid 352 through 353 removed outlier: 6.007A pdb=" N ASN M 352 " --> pdb=" O PHE M 580 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER M 516 " --> pdb=" O ILE M 611 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE M 613 " --> pdb=" O SER M 516 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE M 518 " --> pdb=" O ILE M 613 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'M' and resid 558 through 559 removed outlier: 4.004A pdb=" N LEU M 564 " --> pdb=" O ILE M 571 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'M' and resid 618 through 620 Processing sheet with id=AO1, first strand: chain 'M' and resid 654 through 659 removed outlier: 4.061A pdb=" N SER M 683 " --> pdb=" O THR M 695 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR M 695 " --> pdb=" O SER M 683 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'M' and resid 768 through 771 removed outlier: 3.664A pdb=" N MET M 786 " --> pdb=" O VAL M 840 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL M 840 " --> pdb=" O MET M 786 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE M 788 " --> pdb=" O ASN M 838 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN M 838 " --> pdb=" O PHE M 788 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'M' and resid 816 through 822 removed outlier: 3.725A pdb=" N ALA M 808 " --> pdb=" O LYS M 816 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL M 806 " --> pdb=" O ILE M 818 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N THR M 820 " --> pdb=" O TYR M 804 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR M 804 " --> pdb=" O THR M 820 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS M 856 " --> pdb=" O LEU M 871 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU M 871 " --> pdb=" O LYS M 856 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU M 858 " --> pdb=" O GLU M 869 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'Z' and resid 235 through 238 Processing sheet with id=AO5, first strand: chain 'Z' and resid 323 through 326 removed outlier: 7.016A pdb=" N ASN Z 392 " --> pdb=" O GLU Z 305 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU Z 307 " --> pdb=" O ASN Z 390 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN Z 390 " --> pdb=" O LEU Z 307 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE Z 309 " --> pdb=" O TYR Z 388 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR Z 388 " --> pdb=" O ILE Z 309 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE Z 460 " --> pdb=" O ILE Z 389 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'Z' and resid 352 through 353 removed outlier: 6.765A pdb=" N SER Z 516 " --> pdb=" O ILE Z 611 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE Z 613 " --> pdb=" O SER Z 516 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE Z 518 " --> pdb=" O ILE Z 613 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'Z' and resid 362 through 365 removed outlier: 3.974A pdb=" N ILE Z 476 " --> pdb=" O THR Z 365 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER Z 420 " --> pdb=" O LEU Z 412 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'Z' and resid 489 through 490 removed outlier: 4.146A pdb=" N THR Z 489 " --> pdb=" O VAL Z 497 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL Z 497 " --> pdb=" O THR Z 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO8 Processing sheet with id=AO9, first strand: chain 'Z' and resid 618 through 621 removed outlier: 6.183A pdb=" N ASN Z 735 " --> pdb=" O TYR Z 674 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR Z 674 " --> pdb=" O ASN Z 735 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG Z 668 " --> pdb=" O LEU Z 741 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'Z' and resid 654 through 659 Processing sheet with id=AP2, first strand: chain 'Z' and resid 768 through 772 removed outlier: 6.266A pdb=" N PHE Z 769 " --> pdb=" O MET Z 786 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET Z 786 " --> pdb=" O PHE Z 769 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP Z 771 " --> pdb=" O ASN Z 784 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET Z 786 " --> pdb=" O VAL Z 840 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL Z 840 " --> pdb=" O MET Z 786 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE Z 788 " --> pdb=" O ASN Z 838 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN Z 838 " --> pdb=" O PHE Z 788 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'Z' and resid 816 through 822 removed outlier: 3.661A pdb=" N ALA Z 808 " --> pdb=" O LYS Z 816 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL Z 806 " --> pdb=" O ILE Z 818 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR Z 820 " --> pdb=" O TYR Z 804 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR Z 804 " --> pdb=" O THR Z 820 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS Z 856 " --> pdb=" O LEU Z 871 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU Z 871 " --> pdb=" O LYS Z 856 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU Z 858 " --> pdb=" O GLU Z 869 " (cutoff:3.500A) 1912 hydrogen bonds defined for protein. 4971 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: 27.49 Time building geometry restraints manager: 21.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23372 1.34 - 1.46: 14285 1.46 - 1.58: 36072 1.58 - 1.70: 0 1.70 - 1.81: 266 Bond restraints: 73995 Sorted by residual: bond pdb=" C ARG J 868 " pdb=" N GLU J 869 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.29e-02 6.01e+03 7.01e+00 bond pdb=" C LEU J 293 " pdb=" N VAL J 294 " ideal model delta sigma weight residual 1.332 1.298 0.034 1.36e-02 5.41e+03 6.32e+00 bond pdb=" CA ASP I 749 " pdb=" CB ASP I 749 " ideal model delta sigma weight residual 1.526 1.569 -0.043 1.76e-02 3.23e+03 5.99e+00 bond pdb=" C SER L 229 " pdb=" N TYR L 230 " ideal model delta sigma weight residual 1.331 1.300 0.031 1.38e-02 5.25e+03 5.05e+00 bond pdb=" C THR L 864 " pdb=" N PRO L 865 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.99e+00 ... (remaining 73990 not shown) Histogram of bond angle deviations from ideal: 97.04 - 105.09: 1293 105.09 - 113.15: 40058 113.15 - 121.21: 37154 121.21 - 129.27: 21712 129.27 - 137.33: 228 Bond angle restraints: 100445 Sorted by residual: angle pdb=" N VAL L 686 " pdb=" CA VAL L 686 " pdb=" C VAL L 686 " ideal model delta sigma weight residual 112.83 106.25 6.58 9.90e-01 1.02e+00 4.42e+01 angle pdb=" C LEU C 444 " pdb=" N SER C 445 " pdb=" CA SER C 445 " ideal model delta sigma weight residual 120.97 137.33 -16.36 2.84e+00 1.24e-01 3.32e+01 angle pdb=" N THR C 864 " pdb=" CA THR C 864 " pdb=" C THR C 864 " ideal model delta sigma weight residual 109.81 121.51 -11.70 2.21e+00 2.05e-01 2.80e+01 angle pdb=" C ARG L 868 " pdb=" N GLU L 869 " pdb=" CA GLU L 869 " ideal model delta sigma weight residual 122.17 114.09 8.08 1.54e+00 4.22e-01 2.75e+01 angle pdb=" N THR M 864 " pdb=" CA THR M 864 " pdb=" C THR M 864 " ideal model delta sigma weight residual 109.81 120.89 -11.08 2.21e+00 2.05e-01 2.52e+01 ... (remaining 100440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 39652 17.98 - 35.97: 4498 35.97 - 53.95: 625 53.95 - 71.94: 76 71.94 - 89.92: 34 Dihedral angle restraints: 44885 sinusoidal: 17819 harmonic: 27066 Sorted by residual: dihedral pdb=" CA ILE E 863 " pdb=" C ILE E 863 " pdb=" N THR E 864 " pdb=" CA THR E 864 " ideal model delta harmonic sigma weight residual 180.00 -132.29 -47.71 0 5.00e+00 4.00e-02 9.10e+01 dihedral pdb=" CA ILE G 863 " pdb=" C ILE G 863 " pdb=" N THR G 864 " pdb=" CA THR G 864 " ideal model delta harmonic sigma weight residual 180.00 -133.75 -46.25 0 5.00e+00 4.00e-02 8.56e+01 dihedral pdb=" CA ILE K 863 " pdb=" C ILE K 863 " pdb=" N THR K 864 " pdb=" CA THR K 864 " ideal model delta harmonic sigma weight residual -180.00 -136.73 -43.27 0 5.00e+00 4.00e-02 7.49e+01 ... (remaining 44882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 9718 0.082 - 0.164: 1406 0.164 - 0.246: 112 0.246 - 0.328: 20 0.328 - 0.410: 6 Chirality restraints: 11262 Sorted by residual: chirality pdb=" CB ILE D 761 " pdb=" CA ILE D 761 " pdb=" CG1 ILE D 761 " pdb=" CG2 ILE D 761 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA THR G 864 " pdb=" N THR G 864 " pdb=" C THR G 864 " pdb=" CB THR G 864 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB ILE A 863 " pdb=" CA ILE A 863 " pdb=" CG1 ILE A 863 " pdb=" CG2 ILE A 863 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 11259 not shown) Planarity restraints: 13130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 269 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO A 270 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 291 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.92e+00 pdb=" N PRO I 292 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO I 292 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 292 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 407 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO I 408 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO I 408 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 408 " -0.035 5.00e-02 4.00e+02 ... (remaining 13127 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 6992 2.73 - 3.27: 68341 3.27 - 3.82: 115718 3.82 - 4.36: 127945 4.36 - 4.90: 221623 Nonbonded interactions: 540619 Sorted by model distance: nonbonded pdb=" OE2 GLU I 722 " pdb=" OG1 THR I 724 " model vdw 2.191 2.440 nonbonded pdb=" O GLY D 642 " pdb=" OH TYR D 732 " model vdw 2.203 2.440 nonbonded pdb=" OG SER H 340 " pdb=" OG1 THR H 354 " model vdw 2.212 2.440 nonbonded pdb=" OG SER K 374 " pdb=" O LEU K 748 " model vdw 2.234 2.440 nonbonded pdb=" O SER Z 374 " pdb=" OG1 THR Z 377 " model vdw 2.246 2.440 ... (remaining 540614 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' and resid 216 through 872) selection = (chain 'B' and resid 216 through 872) selection = (chain 'C' and resid 216 through 872) selection = (chain 'D' and resid 216 through 872) selection = (chain 'E' and resid 216 through 872) selection = (chain 'F' and resid 216 through 872) selection = (chain 'G' and resid 216 through 872) selection = (chain 'H' and resid 216 through 872) selection = (chain 'I' and resid 216 through 872) selection = (chain 'J' and resid 216 through 872) selection = (chain 'K' and resid 216 through 872) selection = (chain 'L' and resid 216 through 872) selection = (chain 'M' and resid 216 through 872) selection = chain 'Z' } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 6.510 Check model and map are aligned: 0.800 Set scattering table: 0.480 Process input model: 139.730 Find NCS groups from input model: 4.360 Set up NCS constraints: 0.210 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.006 0.082 73995 Z= 0.378 Angle : 1.000 16.366 100445 Z= 0.562 Chirality : 0.058 0.410 11262 Planarity : 0.006 0.070 13130 Dihedral : 14.752 89.922 27597 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 0.42 % Allowed : 12.33 % Favored : 87.25 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.31 (0.07), residues: 9190 helix: -4.02 (0.09), residues: 817 sheet: -1.61 (0.10), residues: 2323 loop : -3.44 (0.06), residues: 6050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 375 HIS 0.011 0.002 HIS H 765 PHE 0.035 0.003 PHE J 281 TYR 0.025 0.002 TYR J 230 ARG 0.010 0.001 ARG A 805 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 539 time to evaluate : 6.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8016 (ttp) cc_final: 0.7474 (ttp) REVERT: A 552 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6743 (tm-30) REVERT: A 740 GLU cc_start: 0.7713 (pm20) cc_final: 0.6971 (pm20) REVERT: A 825 MET cc_start: 0.8547 (mmp) cc_final: 0.8296 (mmm) REVERT: B 507 ILE cc_start: 0.9180 (mm) cc_final: 0.8973 (mm) REVERT: B 536 GLN cc_start: 0.8327 (mm110) cc_final: 0.7897 (tt0) REVERT: B 762 MET cc_start: 0.7929 (ppp) cc_final: 0.7082 (ppp) REVERT: C 688 ILE cc_start: 0.8064 (mp) cc_final: 0.7527 (tp) REVERT: D 649 LYS cc_start: 0.6794 (mttt) cc_final: 0.6569 (mmmt) REVERT: D 660 MET cc_start: 0.5928 (mmp) cc_final: 0.5590 (mmp) REVERT: D 825 MET cc_start: 0.8005 (mmt) cc_final: 0.7782 (tpp) REVERT: D 860 ILE cc_start: 0.8586 (mm) cc_final: 0.8373 (mm) REVERT: E 643 LEU cc_start: 0.7261 (tp) cc_final: 0.6943 (tt) REVERT: E 786 MET cc_start: 0.8444 (tpp) cc_final: 0.8240 (mmm) REVERT: F 233 ASN cc_start: 0.7592 (m-40) cc_final: 0.7204 (t0) REVERT: F 255 LYS cc_start: 0.9130 (mptt) cc_final: 0.8634 (mtmm) REVERT: F 660 MET cc_start: 0.7524 (mmp) cc_final: 0.7143 (mmp) REVERT: F 787 TYR cc_start: 0.8984 (m-10) cc_final: 0.8723 (m-10) REVERT: F 860 ILE cc_start: 0.9074 (mm) cc_final: 0.8857 (mm) REVERT: G 697 TYR cc_start: 0.7255 (t80) cc_final: 0.6757 (t80) REVERT: H 319 GLN cc_start: 0.7678 (tt0) cc_final: 0.7270 (tm-30) REVERT: H 403 MET cc_start: 0.8783 (ttp) cc_final: 0.8568 (mtp) REVERT: H 520 ASP cc_start: 0.8391 (m-30) cc_final: 0.8118 (m-30) REVERT: H 657 LYS cc_start: 0.7719 (tmtt) cc_final: 0.7379 (tmtt) REVERT: H 754 LYS cc_start: 0.7541 (ttmm) cc_final: 0.6300 (tmtt) REVERT: I 660 MET cc_start: 0.7774 (mmm) cc_final: 0.7385 (tpp) REVERT: I 700 PRO cc_start: 0.7797 (Cg_endo) cc_final: 0.7579 (Cg_exo) REVERT: I 825 MET cc_start: 0.8225 (ttm) cc_final: 0.7882 (tpp) REVERT: J 632 TRP cc_start: 0.7603 (t-100) cc_final: 0.7259 (m100) REVERT: J 660 MET cc_start: 0.5811 (mmp) cc_final: 0.5329 (mmm) REVERT: K 428 GLN cc_start: 0.7053 (tt0) cc_final: 0.6463 (tp40) REVERT: K 691 LYS cc_start: 0.7777 (tttp) cc_final: 0.7208 (mppt) REVERT: L 396 TYR cc_start: 0.6304 (p90) cc_final: 0.6098 (p90) REVERT: M 403 MET cc_start: 0.8378 (mtp) cc_final: 0.8024 (mtp) REVERT: Z 283 LYS cc_start: 0.9205 (mmtp) cc_final: 0.8893 (mmmt) outliers start: 34 outliers final: 15 residues processed: 571 average time/residue: 0.6817 time to fit residues: 660.2046 Evaluate side-chains 321 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 306 time to evaluate : 6.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 768 optimal weight: 0.8980 chunk 689 optimal weight: 8.9990 chunk 382 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 465 optimal weight: 5.9990 chunk 368 optimal weight: 30.0000 chunk 713 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 433 optimal weight: 9.9990 chunk 530 optimal weight: 30.0000 chunk 826 optimal weight: 7.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 735 ASN A 759 GLN A 775 ASN B 265 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN B 775 ASN B 841 ASN ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 486 ASN C 491 ASN C 501 ASN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN ** C 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN D 501 ASN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 ASN E 319 GLN ** E 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN E 450 ASN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN E 834 GLN ** E 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 841 ASN F 359 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 ASN F 509 GLN F 648 ASN F 651 ASN F 742 ASN ** F 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 ASN G 509 GLN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 682 ASN G 742 ASN H 359 HIS H 431 ASN H 466 GLN ** H 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 682 ASN H 720 ASN I 450 ASN I 651 ASN I 735 ASN I 775 ASN ** I 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 260 ASN J 427 ASN J 602 ASN ** J 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 811 GLN K 223 ASN K 335 ASN K 432 ASN K 450 ASN K 486 ASN K 509 GLN K 627 ASN K 644 GLN K 735 ASN K 802 GLN ** K 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 346 GLN ** L 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 454 GLN L 491 ASN L 621 ASN ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 759 GLN L 775 ASN M 371 ASN M 390 ASN ** M 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 682 ASN M 775 ASN ** M 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 841 ASN M 851 ASN Z 347 ASN ** Z 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 450 ASN Z 735 ASN Z 775 ASN Z 794 ASN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 73995 Z= 0.262 Angle : 0.675 12.334 100445 Z= 0.356 Chirality : 0.046 0.218 11262 Planarity : 0.005 0.110 13130 Dihedral : 6.349 39.563 9974 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.17 % Allowed : 6.89 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.74 (0.08), residues: 9190 helix: -3.01 (0.13), residues: 881 sheet: -1.20 (0.10), residues: 2334 loop : -3.15 (0.07), residues: 5975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 375 HIS 0.006 0.001 HIS H 765 PHE 0.018 0.002 PHE E 815 TYR 0.024 0.002 TYR J 230 ARG 0.012 0.001 ARG C 868 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 420 time to evaluate : 6.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 VAL cc_start: 0.4252 (OUTLIER) cc_final: 0.4022 (m) REVERT: A 740 GLU cc_start: 0.7747 (pm20) cc_final: 0.6885 (pm20) REVERT: A 825 MET cc_start: 0.8669 (mmp) cc_final: 0.8309 (mmm) REVERT: B 536 GLN cc_start: 0.8334 (mm110) cc_final: 0.7633 (tt0) REVERT: B 762 MET cc_start: 0.7675 (ppp) cc_final: 0.7439 (ppp) REVERT: C 362 ASP cc_start: 0.8142 (m-30) cc_final: 0.7404 (p0) REVERT: C 688 ILE cc_start: 0.8090 (mp) cc_final: 0.7529 (tp) REVERT: D 649 LYS cc_start: 0.6788 (mttt) cc_final: 0.6544 (mmmt) REVERT: D 660 MET cc_start: 0.6049 (mmp) cc_final: 0.5663 (mmp) REVERT: D 841 ASN cc_start: 0.8516 (t0) cc_final: 0.7913 (t0) REVERT: E 643 LEU cc_start: 0.7335 (tp) cc_final: 0.6963 (tt) REVERT: E 786 MET cc_start: 0.8788 (tpp) cc_final: 0.8538 (tpp) REVERT: F 660 MET cc_start: 0.7171 (mmp) cc_final: 0.6154 (mmp) REVERT: F 860 ILE cc_start: 0.8337 (mm) cc_final: 0.8100 (mm) REVERT: G 660 MET cc_start: 0.9081 (tpt) cc_final: 0.8858 (tpt) REVERT: G 697 TYR cc_start: 0.7305 (t80) cc_final: 0.6940 (t80) REVERT: H 546 THR cc_start: 0.8814 (m) cc_final: 0.8570 (p) REVERT: H 754 LYS cc_start: 0.7447 (ttmm) cc_final: 0.6154 (tmtt) REVERT: I 660 MET cc_start: 0.7505 (mmm) cc_final: 0.7271 (tpp) REVERT: I 700 PRO cc_start: 0.7744 (Cg_endo) cc_final: 0.7489 (Cg_exo) REVERT: J 660 MET cc_start: 0.6190 (mmp) cc_final: 0.5857 (mmm) REVERT: K 428 GLN cc_start: 0.7253 (tt0) cc_final: 0.6584 (tp40) REVERT: K 455 PHE cc_start: 0.8535 (m-80) cc_final: 0.8028 (m-80) REVERT: L 787 TYR cc_start: 0.6881 (m-80) cc_final: 0.6013 (m-80) REVERT: M 403 MET cc_start: 0.8379 (mtp) cc_final: 0.7984 (mtp) REVERT: Z 283 LYS cc_start: 0.9295 (mmtp) cc_final: 0.8921 (mmmt) REVERT: Z 304 MET cc_start: 0.8431 (tmm) cc_final: 0.7715 (tmm) REVERT: Z 786 MET cc_start: 0.7863 (tpp) cc_final: 0.7375 (tpp) outliers start: 14 outliers final: 4 residues processed: 433 average time/residue: 0.6571 time to fit residues: 494.3311 Evaluate side-chains 279 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 274 time to evaluate : 6.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 459 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 687 optimal weight: 7.9990 chunk 562 optimal weight: 0.9990 chunk 227 optimal weight: 20.0000 chunk 827 optimal weight: 10.0000 chunk 894 optimal weight: 10.0000 chunk 737 optimal weight: 1.9990 chunk 820 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 664 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 ASN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 ASN D 841 ASN E 342 ASN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 802 GLN ** E 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 ASN F 775 ASN G 225 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 427 ASN ** H 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 720 ASN ** I 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 432 ASN I 636 ASN I 775 ASN ** I 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 811 GLN K 640 GLN ** K 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 GLN ** L 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 390 ASN ** M 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 486 ASN ** Z 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 775 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 73995 Z= 0.223 Angle : 0.627 12.415 100445 Z= 0.329 Chirality : 0.045 0.228 11262 Planarity : 0.004 0.063 13130 Dihedral : 5.946 39.966 9974 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.41 (0.08), residues: 9190 helix: -2.46 (0.14), residues: 881 sheet: -0.96 (0.10), residues: 2334 loop : -2.98 (0.07), residues: 5975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 632 HIS 0.005 0.001 HIS A 765 PHE 0.018 0.001 PHE F 622 TYR 0.019 0.001 TYR D 697 ARG 0.004 0.000 ARG J 868 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 410 time to evaluate : 6.616 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: A 740 GLU cc_start: 0.7716 (pm20) cc_final: 0.6836 (pm20) REVERT: A 825 MET cc_start: 0.8670 (mmp) cc_final: 0.8404 (tpp) REVERT: A 870 LEU cc_start: 0.8993 (tp) cc_final: 0.8754 (tp) REVERT: B 536 GLN cc_start: 0.8366 (mm110) cc_final: 0.7612 (tt0) REVERT: B 762 MET cc_start: 0.7895 (ppp) cc_final: 0.7564 (ppp) REVERT: B 853 MET cc_start: 0.5268 (tmm) cc_final: 0.4759 (tmm) REVERT: D 649 LYS cc_start: 0.6801 (mttt) cc_final: 0.6515 (mmmt) REVERT: D 660 MET cc_start: 0.5896 (mmp) cc_final: 0.5513 (mmp) REVERT: E 643 LEU cc_start: 0.7257 (tp) cc_final: 0.6949 (tt) REVERT: E 786 MET cc_start: 0.8789 (tpp) cc_final: 0.8528 (tpp) REVERT: E 825 MET cc_start: 0.7358 (tpp) cc_final: 0.7091 (mmt) REVERT: F 660 MET cc_start: 0.7208 (mmp) cc_final: 0.6188 (mmp) REVERT: F 762 MET cc_start: 0.7717 (ppp) cc_final: 0.7499 (ppp) REVERT: G 691 LYS cc_start: 0.8925 (tttp) cc_final: 0.8374 (tmtt) REVERT: G 825 MET cc_start: 0.7892 (mtp) cc_final: 0.7665 (mtp) REVERT: H 352 ASN cc_start: 0.8347 (m-40) cc_final: 0.7998 (t0) REVERT: H 520 ASP cc_start: 0.8553 (m-30) cc_final: 0.8304 (m-30) REVERT: H 754 LYS cc_start: 0.7481 (mttm) cc_final: 0.6214 (tmtt) REVERT: I 660 MET cc_start: 0.7447 (mmm) cc_final: 0.7224 (tpp) REVERT: J 660 MET cc_start: 0.6307 (mmp) cc_final: 0.5765 (mmm) REVERT: J 853 MET cc_start: 0.7704 (tmm) cc_final: 0.7338 (tmm) REVERT: K 428 GLN cc_start: 0.7678 (tt0) cc_final: 0.6968 (tp40) REVERT: K 455 PHE cc_start: 0.8143 (m-80) cc_final: 0.7723 (m-80) REVERT: L 787 TYR cc_start: 0.7102 (m-80) cc_final: 0.6255 (m-80) REVERT: L 825 MET cc_start: 0.8765 (mmm) cc_final: 0.8154 (mmt) REVERT: M 403 MET cc_start: 0.8758 (mtp) cc_final: 0.8433 (mtp) REVERT: M 660 MET cc_start: 0.6181 (tpt) cc_final: 0.5858 (tpt) REVERT: Z 283 LYS cc_start: 0.9232 (mmtp) cc_final: 0.8877 (mmmt) REVERT: Z 304 MET cc_start: 0.8488 (tmm) cc_final: 0.8257 (tmm) REVERT: Z 733 LEU cc_start: 0.7336 (mt) cc_final: 0.7053 (mt) REVERT: Z 759 GLN cc_start: 0.6604 (pt0) cc_final: 0.5948 (pt0) REVERT: Z 786 MET cc_start: 0.7677 (tpp) cc_final: 0.7220 (tpp) outliers start: 4 outliers final: 1 residues processed: 413 average time/residue: 0.6529 time to fit residues: 470.9172 Evaluate side-chains 275 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 6.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 817 optimal weight: 0.5980 chunk 622 optimal weight: 3.9990 chunk 429 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 395 optimal weight: 20.0000 chunk 555 optimal weight: 8.9990 chunk 830 optimal weight: 1.9990 chunk 879 optimal weight: 20.0000 chunk 434 optimal weight: 0.0980 chunk 787 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 ASN ** B 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN C 432 ASN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 GLN C 841 ASN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 838 ASN F 427 ASN G 486 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 640 GLN G 735 ASN ** H 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 GLN ** J 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 627 ASN K 811 GLN ** L 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 735 ASN M 390 ASN M 702 GLN M 720 ASN ** M 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 775 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 73995 Z= 0.148 Angle : 0.574 12.329 100445 Z= 0.298 Chirality : 0.044 0.230 11262 Planarity : 0.004 0.063 13130 Dihedral : 5.389 38.083 9974 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.12 (0.08), residues: 9190 helix: -2.11 (0.15), residues: 914 sheet: -0.76 (0.10), residues: 2377 loop : -2.81 (0.07), residues: 5899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 632 HIS 0.003 0.001 HIS Z 765 PHE 0.011 0.001 PHE I 671 TYR 0.020 0.001 TYR D 697 ARG 0.008 0.000 ARG B 868 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 432 time to evaluate : 6.420 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 740 GLU cc_start: 0.7639 (pm20) cc_final: 0.7033 (pm20) REVERT: A 825 MET cc_start: 0.8709 (mmt) cc_final: 0.8368 (mmm) REVERT: B 403 MET cc_start: 0.9155 (tpp) cc_final: 0.8942 (tpp) REVERT: B 452 MET cc_start: 0.8226 (tmm) cc_final: 0.7806 (tmm) REVERT: B 536 GLN cc_start: 0.8332 (mm110) cc_final: 0.7582 (tt0) REVERT: B 762 MET cc_start: 0.7889 (ppp) cc_final: 0.7386 (ppp) REVERT: B 853 MET cc_start: 0.5401 (tmm) cc_final: 0.4884 (tmm) REVERT: B 861 TYR cc_start: 0.6968 (m-80) cc_final: 0.6485 (m-80) REVERT: C 362 ASP cc_start: 0.8228 (m-30) cc_final: 0.7824 (t70) REVERT: D 452 MET cc_start: 0.8330 (pmm) cc_final: 0.8016 (pmm) REVERT: D 507 ILE cc_start: 0.8721 (mm) cc_final: 0.8467 (mm) REVERT: D 649 LYS cc_start: 0.6815 (mttt) cc_final: 0.6551 (mmmt) REVERT: D 841 ASN cc_start: 0.8232 (t0) cc_final: 0.7618 (t0) REVERT: E 643 LEU cc_start: 0.7340 (tp) cc_final: 0.7031 (tt) REVERT: E 786 MET cc_start: 0.8804 (tpp) cc_final: 0.8561 (tpp) REVERT: E 825 MET cc_start: 0.7736 (tpp) cc_final: 0.7482 (mmt) REVERT: F 660 MET cc_start: 0.7045 (mmp) cc_final: 0.6622 (mmp) REVERT: F 706 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7940 (mmtm) REVERT: F 762 MET cc_start: 0.7509 (ppp) cc_final: 0.7277 (ppp) REVERT: G 304 MET cc_start: 0.8080 (tmm) cc_final: 0.7560 (tmm) REVERT: G 609 MET cc_start: 0.7600 (mmp) cc_final: 0.7340 (mmp) REVERT: H 352 ASN cc_start: 0.8307 (m-40) cc_final: 0.7920 (t0) REVERT: H 520 ASP cc_start: 0.8467 (m-30) cc_final: 0.8232 (m-30) REVERT: H 754 LYS cc_start: 0.7350 (mttm) cc_final: 0.5953 (tmtt) REVERT: H 762 MET cc_start: 0.7517 (pmm) cc_final: 0.7235 (mpp) REVERT: I 537 ASP cc_start: 0.8214 (p0) cc_final: 0.7981 (p0) REVERT: J 304 MET cc_start: 0.8236 (ttp) cc_final: 0.7982 (tmm) REVERT: J 613 ILE cc_start: 0.9038 (pt) cc_final: 0.8742 (mt) REVERT: J 660 MET cc_start: 0.6201 (mmp) cc_final: 0.5641 (mmm) REVERT: K 403 MET cc_start: 0.8374 (tpp) cc_final: 0.7991 (tpp) REVERT: K 428 GLN cc_start: 0.7645 (tt0) cc_final: 0.6946 (tp40) REVERT: K 455 PHE cc_start: 0.8114 (m-80) cc_final: 0.7630 (m-80) REVERT: K 811 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6912 (tp40) REVERT: L 403 MET cc_start: 0.8419 (ttp) cc_final: 0.8007 (ttt) REVERT: L 787 TYR cc_start: 0.7419 (m-80) cc_final: 0.6605 (m-80) REVERT: L 825 MET cc_start: 0.8827 (mmm) cc_final: 0.7533 (mmm) REVERT: M 403 MET cc_start: 0.8756 (mtp) cc_final: 0.8368 (mtp) REVERT: M 660 MET cc_start: 0.6134 (tpt) cc_final: 0.5900 (tpt) REVERT: Z 283 LYS cc_start: 0.9164 (mmtp) cc_final: 0.8853 (mmmt) REVERT: Z 304 MET cc_start: 0.8453 (tmm) cc_final: 0.7707 (tmm) REVERT: Z 698 LEU cc_start: 0.8285 (pt) cc_final: 0.7839 (tp) REVERT: Z 786 MET cc_start: 0.7596 (tpp) cc_final: 0.7116 (tpp) outliers start: 2 outliers final: 0 residues processed: 434 average time/residue: 0.6552 time to fit residues: 496.4893 Evaluate side-chains 288 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 287 time to evaluate : 6.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 732 optimal weight: 5.9990 chunk 499 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 654 optimal weight: 2.9990 chunk 362 optimal weight: 20.0000 chunk 750 optimal weight: 1.9990 chunk 608 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 449 optimal weight: 20.0000 chunk 789 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS ** B 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 639 ASN ** E 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 720 ASN I 682 ASN ** I 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 775 ASN K 627 ASN L 359 HIS L 368 GLN ** L 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 634 ASN ** M 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 73995 Z= 0.151 Angle : 0.566 12.030 100445 Z= 0.292 Chirality : 0.044 0.244 11262 Planarity : 0.003 0.053 13130 Dihedral : 5.179 37.466 9974 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.04 % Allowed : 2.47 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.96 (0.08), residues: 9190 helix: -1.85 (0.16), residues: 913 sheet: -0.75 (0.10), residues: 2376 loop : -2.68 (0.07), residues: 5901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 632 HIS 0.005 0.001 HIS L 359 PHE 0.013 0.001 PHE B 622 TYR 0.026 0.001 TYR J 697 ARG 0.006 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 404 time to evaluate : 6.529 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 740 GLU cc_start: 0.7646 (pm20) cc_final: 0.7051 (pm20) REVERT: A 825 MET cc_start: 0.8736 (mmt) cc_final: 0.8401 (mmm) REVERT: B 403 MET cc_start: 0.9198 (tpp) cc_final: 0.8935 (tpp) REVERT: B 452 MET cc_start: 0.8271 (tmm) cc_final: 0.7807 (tmm) REVERT: B 496 ILE cc_start: 0.8566 (mt) cc_final: 0.8358 (mt) REVERT: B 536 GLN cc_start: 0.8380 (mm110) cc_final: 0.7395 (tt0) REVERT: B 660 MET cc_start: 0.6670 (mmm) cc_final: 0.6417 (tpp) REVERT: B 762 MET cc_start: 0.7869 (ppp) cc_final: 0.7275 (ppp) REVERT: B 853 MET cc_start: 0.5491 (tmm) cc_final: 0.5075 (tmm) REVERT: D 437 ASP cc_start: 0.8038 (t0) cc_final: 0.7790 (t0) REVERT: D 452 MET cc_start: 0.8494 (pmm) cc_final: 0.8047 (pmm) REVERT: D 507 ILE cc_start: 0.8717 (mm) cc_final: 0.8476 (mm) REVERT: D 649 LYS cc_start: 0.6842 (mttt) cc_final: 0.6556 (mmmt) REVERT: D 841 ASN cc_start: 0.8249 (t0) cc_final: 0.7668 (t0) REVERT: E 639 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7816 (t0) REVERT: E 643 LEU cc_start: 0.7319 (tp) cc_final: 0.7030 (tt) REVERT: E 786 MET cc_start: 0.8820 (tpp) cc_final: 0.8569 (tpp) REVERT: E 825 MET cc_start: 0.7734 (tpp) cc_final: 0.7474 (mmt) REVERT: F 232 ARG cc_start: 0.7392 (ptm160) cc_final: 0.6931 (ptm-80) REVERT: F 660 MET cc_start: 0.7022 (mmp) cc_final: 0.6485 (mmp) REVERT: F 762 MET cc_start: 0.7545 (ppp) cc_final: 0.7019 (ppp) REVERT: G 452 MET cc_start: 0.5825 (mmp) cc_final: 0.5618 (mmm) REVERT: G 762 MET cc_start: 0.7245 (tpp) cc_final: 0.6403 (tpp) REVERT: G 825 MET cc_start: 0.7502 (mtp) cc_final: 0.7224 (mtp) REVERT: H 304 MET cc_start: 0.8389 (tmm) cc_final: 0.7853 (tmm) REVERT: H 352 ASN cc_start: 0.8409 (m-40) cc_final: 0.7921 (t0) REVERT: H 520 ASP cc_start: 0.8463 (m-30) cc_final: 0.8257 (m-30) REVERT: H 754 LYS cc_start: 0.7437 (mttm) cc_final: 0.6041 (tmtt) REVERT: H 762 MET cc_start: 0.7542 (pmm) cc_final: 0.7228 (mpp) REVERT: H 786 MET cc_start: 0.9463 (tpp) cc_final: 0.8914 (tpt) REVERT: H 825 MET cc_start: 0.8789 (tpp) cc_final: 0.8563 (tpp) REVERT: I 432 ASN cc_start: 0.8788 (m110) cc_final: 0.8280 (t0) REVERT: J 304 MET cc_start: 0.8221 (ttp) cc_final: 0.7984 (tmm) REVERT: J 613 ILE cc_start: 0.9093 (pt) cc_final: 0.8876 (mt) REVERT: J 660 MET cc_start: 0.6270 (mmp) cc_final: 0.5347 (mmm) REVERT: K 403 MET cc_start: 0.8347 (tpp) cc_final: 0.7965 (tpp) REVERT: K 428 GLN cc_start: 0.7547 (tt0) cc_final: 0.6928 (tp-100) REVERT: K 455 PHE cc_start: 0.8099 (m-80) cc_final: 0.7621 (m-80) REVERT: K 625 TYR cc_start: 0.6202 (t80) cc_final: 0.5976 (t80) REVERT: L 368 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: L 787 TYR cc_start: 0.7454 (m-80) cc_final: 0.6761 (m-80) REVERT: L 825 MET cc_start: 0.8824 (mmm) cc_final: 0.7514 (mmm) REVERT: M 403 MET cc_start: 0.8753 (mtp) cc_final: 0.8342 (mtp) REVERT: M 625 TYR cc_start: 0.7807 (t80) cc_final: 0.7605 (p90) REVERT: M 660 MET cc_start: 0.6133 (tpt) cc_final: 0.5838 (tpt) REVERT: Z 283 LYS cc_start: 0.9160 (mmtp) cc_final: 0.8856 (mmmt) REVERT: Z 304 MET cc_start: 0.8523 (tmm) cc_final: 0.8226 (tmm) REVERT: Z 698 LEU cc_start: 0.8289 (pt) cc_final: 0.7873 (tp) REVERT: Z 723 ILE cc_start: 0.8932 (mm) cc_final: 0.8412 (tt) REVERT: Z 733 LEU cc_start: 0.6972 (mt) cc_final: 0.6376 (pt) REVERT: Z 786 MET cc_start: 0.7448 (tpp) cc_final: 0.6983 (tpp) outliers start: 3 outliers final: 0 residues processed: 406 average time/residue: 0.6368 time to fit residues: 454.8946 Evaluate side-chains 291 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 289 time to evaluate : 6.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 295 optimal weight: 0.1980 chunk 792 optimal weight: 30.0000 chunk 173 optimal weight: 6.9990 chunk 516 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 chunk 880 optimal weight: 20.0000 chunk 730 optimal weight: 20.0000 chunk 407 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 462 optimal weight: 20.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 ASN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN D 792 GLN ** E 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 720 ASN ** I 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 627 ASN ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 431 ASN ** M 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 73995 Z= 0.175 Angle : 0.575 11.710 100445 Z= 0.297 Chirality : 0.044 0.265 11262 Planarity : 0.004 0.069 13130 Dihedral : 5.148 37.979 9974 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.04 % Allowed : 2.53 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.08), residues: 9190 helix: -1.67 (0.16), residues: 915 sheet: -0.62 (0.10), residues: 2390 loop : -2.61 (0.08), residues: 5885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 632 HIS 0.004 0.001 HIS E 765 PHE 0.012 0.001 PHE J 671 TYR 0.020 0.001 TYR B 230 ARG 0.005 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 385 time to evaluate : 6.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 GLU cc_start: 0.7635 (pm20) cc_final: 0.6984 (pm20) REVERT: A 825 MET cc_start: 0.8731 (mmt) cc_final: 0.8461 (tpp) REVERT: B 452 MET cc_start: 0.8249 (tmm) cc_final: 0.7830 (tmm) REVERT: B 536 GLN cc_start: 0.8338 (mm110) cc_final: 0.7686 (tt0) REVERT: B 697 TYR cc_start: 0.6044 (t80) cc_final: 0.5786 (t80) REVERT: B 762 MET cc_start: 0.7926 (ppp) cc_final: 0.7284 (ppp) REVERT: B 853 MET cc_start: 0.5539 (tmm) cc_final: 0.5101 (tmm) REVERT: C 362 ASP cc_start: 0.8406 (m-30) cc_final: 0.8137 (t0) REVERT: D 437 ASP cc_start: 0.8046 (t0) cc_final: 0.7802 (t0) REVERT: D 452 MET cc_start: 0.8505 (pmm) cc_final: 0.8114 (pmm) REVERT: D 507 ILE cc_start: 0.8751 (mm) cc_final: 0.8513 (mm) REVERT: D 649 LYS cc_start: 0.6899 (mttt) cc_final: 0.6576 (mmmt) REVERT: D 841 ASN cc_start: 0.8311 (t0) cc_final: 0.7768 (t0) REVERT: E 786 MET cc_start: 0.8801 (tpp) cc_final: 0.8557 (tpp) REVERT: E 825 MET cc_start: 0.7650 (tpp) cc_final: 0.7445 (tpp) REVERT: F 232 ARG cc_start: 0.7484 (ptm160) cc_final: 0.7179 (ptm160) REVERT: F 660 MET cc_start: 0.6854 (mmp) cc_final: 0.6317 (mmp) REVERT: F 762 MET cc_start: 0.7519 (ppp) cc_final: 0.7122 (ppp) REVERT: F 825 MET cc_start: 0.8057 (mtm) cc_final: 0.7772 (mtp) REVERT: G 304 MET cc_start: 0.8000 (tmm) cc_final: 0.7558 (tmm) REVERT: G 691 LYS cc_start: 0.8857 (tttp) cc_final: 0.8329 (tmtt) REVERT: G 825 MET cc_start: 0.7597 (mtp) cc_final: 0.7306 (mtp) REVERT: H 304 MET cc_start: 0.8360 (tmm) cc_final: 0.7884 (tmm) REVERT: H 352 ASN cc_start: 0.8415 (m-40) cc_final: 0.7961 (t0) REVERT: H 520 ASP cc_start: 0.8496 (m-30) cc_final: 0.8249 (m-30) REVERT: H 754 LYS cc_start: 0.7474 (mttm) cc_final: 0.6038 (tmtt) REVERT: H 762 MET cc_start: 0.7489 (pmm) cc_final: 0.7192 (mpp) REVERT: I 432 ASN cc_start: 0.8740 (m110) cc_final: 0.8293 (t0) REVERT: I 537 ASP cc_start: 0.8292 (p0) cc_final: 0.8061 (p0) REVERT: J 304 MET cc_start: 0.8247 (ttp) cc_final: 0.8005 (tmm) REVERT: J 660 MET cc_start: 0.6339 (mmp) cc_final: 0.5388 (mmm) REVERT: K 403 MET cc_start: 0.8348 (tpp) cc_final: 0.7795 (tpp) REVERT: K 428 GLN cc_start: 0.7586 (tt0) cc_final: 0.6923 (tp40) REVERT: L 787 TYR cc_start: 0.7456 (m-80) cc_final: 0.6772 (m-80) REVERT: L 825 MET cc_start: 0.8819 (mmm) cc_final: 0.7512 (mmm) REVERT: M 403 MET cc_start: 0.8751 (mtp) cc_final: 0.8379 (mtp) REVERT: M 660 MET cc_start: 0.6162 (tpt) cc_final: 0.5863 (tpt) REVERT: Z 283 LYS cc_start: 0.9162 (mmtp) cc_final: 0.8869 (mmmt) REVERT: Z 304 MET cc_start: 0.8518 (tmm) cc_final: 0.7879 (tmm) REVERT: Z 733 LEU cc_start: 0.6963 (mt) cc_final: 0.6405 (pt) REVERT: Z 786 MET cc_start: 0.7492 (tpp) cc_final: 0.6788 (mmm) outliers start: 3 outliers final: 0 residues processed: 387 average time/residue: 0.6351 time to fit residues: 433.1272 Evaluate side-chains 273 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 6.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 848 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 501 optimal weight: 20.0000 chunk 642 optimal weight: 9.9990 chunk 498 optimal weight: 6.9990 chunk 741 optimal weight: 10.0000 chunk 491 optimal weight: 20.0000 chunk 877 optimal weight: 30.0000 chunk 548 optimal weight: 0.0980 chunk 534 optimal weight: 10.0000 chunk 404 optimal weight: 8.9990 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 ASN ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 509 GLN H 610 ASN ** H 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 720 ASN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 627 ASN ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 314 HIS ** M 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 735 ASN ** M 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 73995 Z= 0.220 Angle : 0.611 11.496 100445 Z= 0.317 Chirality : 0.044 0.274 11262 Planarity : 0.004 0.058 13130 Dihedral : 5.345 40.035 9974 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.01 % Allowed : 2.18 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.08), residues: 9190 helix: -1.42 (0.17), residues: 881 sheet: -0.74 (0.10), residues: 2440 loop : -2.53 (0.08), residues: 5869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 632 HIS 0.005 0.001 HIS E 765 PHE 0.017 0.001 PHE H 619 TYR 0.021 0.001 TYR F 230 ARG 0.006 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 6.979 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: A 740 GLU cc_start: 0.7927 (pm20) cc_final: 0.7535 (pm20) REVERT: B 452 MET cc_start: 0.8346 (tmm) cc_final: 0.7927 (tmm) REVERT: B 536 GLN cc_start: 0.8302 (mm110) cc_final: 0.7664 (tt0) REVERT: B 609 MET cc_start: 0.6767 (mtt) cc_final: 0.6348 (mtt) REVERT: B 660 MET cc_start: 0.6690 (mmm) cc_final: 0.6461 (tpp) REVERT: B 762 MET cc_start: 0.8033 (ppp) cc_final: 0.7297 (ppp) REVERT: B 853 MET cc_start: 0.5607 (tmm) cc_final: 0.5244 (tmm) REVERT: C 362 ASP cc_start: 0.8549 (m-30) cc_final: 0.8269 (t0) REVERT: D 437 ASP cc_start: 0.8073 (t0) cc_final: 0.7828 (t0) REVERT: D 452 MET cc_start: 0.8479 (pmm) cc_final: 0.8060 (pmm) REVERT: D 507 ILE cc_start: 0.8805 (mm) cc_final: 0.8550 (mm) REVERT: D 649 LYS cc_start: 0.6745 (mttt) cc_final: 0.6394 (mmmt) REVERT: D 841 ASN cc_start: 0.8304 (t0) cc_final: 0.7755 (t0) REVERT: E 452 MET cc_start: 0.8747 (mtm) cc_final: 0.8405 (mpp) REVERT: E 786 MET cc_start: 0.8827 (tpp) cc_final: 0.8598 (tpp) REVERT: E 825 MET cc_start: 0.7729 (tpp) cc_final: 0.7495 (tpp) REVERT: F 232 ARG cc_start: 0.7573 (ptm160) cc_final: 0.6986 (ptm-80) REVERT: F 660 MET cc_start: 0.6971 (mmp) cc_final: 0.6473 (mmp) REVERT: F 762 MET cc_start: 0.7617 (ppp) cc_final: 0.7113 (ppp) REVERT: F 825 MET cc_start: 0.8079 (mtm) cc_final: 0.7836 (mtp) REVERT: G 609 MET cc_start: 0.6865 (mmm) cc_final: 0.6608 (mmm) REVERT: G 691 LYS cc_start: 0.8924 (tttp) cc_final: 0.8472 (tmtt) REVERT: G 762 MET cc_start: 0.7498 (tpp) cc_final: 0.6826 (tpp) REVERT: H 304 MET cc_start: 0.8335 (tmm) cc_final: 0.8102 (tmm) REVERT: H 352 ASN cc_start: 0.8398 (m-40) cc_final: 0.7973 (t0) REVERT: H 520 ASP cc_start: 0.8593 (m-30) cc_final: 0.8313 (m-30) REVERT: H 754 LYS cc_start: 0.7527 (mttm) cc_final: 0.6060 (tmtt) REVERT: H 762 MET cc_start: 0.7347 (pmm) cc_final: 0.7137 (mpp) REVERT: H 853 MET cc_start: 0.6250 (ppp) cc_final: 0.5990 (ppp) REVERT: I 432 ASN cc_start: 0.8583 (m110) cc_final: 0.8314 (t0) REVERT: J 304 MET cc_start: 0.8223 (ttp) cc_final: 0.8008 (tmm) REVERT: J 660 MET cc_start: 0.6139 (mmp) cc_final: 0.5321 (mmm) REVERT: J 853 MET cc_start: 0.7717 (tmm) cc_final: 0.7340 (tmm) REVERT: K 304 MET cc_start: 0.7838 (ttm) cc_final: 0.7509 (tmm) REVERT: K 403 MET cc_start: 0.8343 (tpp) cc_final: 0.8001 (tpp) REVERT: K 428 GLN cc_start: 0.7614 (tt0) cc_final: 0.6914 (tp40) REVERT: L 787 TYR cc_start: 0.7507 (m-80) cc_final: 0.6795 (m-80) REVERT: L 825 MET cc_start: 0.8829 (mmm) cc_final: 0.7521 (mmm) REVERT: M 403 MET cc_start: 0.8773 (mtp) cc_final: 0.8397 (mtp) REVERT: M 660 MET cc_start: 0.6133 (tpt) cc_final: 0.5898 (tpt) REVERT: Z 283 LYS cc_start: 0.9283 (mmtp) cc_final: 0.8928 (mmmt) REVERT: Z 733 LEU cc_start: 0.6970 (mt) cc_final: 0.6399 (pt) REVERT: Z 786 MET cc_start: 0.7559 (tpp) cc_final: 0.6866 (mmm) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.6341 time to fit residues: 405.2627 Evaluate side-chains 268 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 6.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 542 optimal weight: 9.9990 chunk 350 optimal weight: 6.9990 chunk 523 optimal weight: 6.9990 chunk 264 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 557 optimal weight: 9.9990 chunk 597 optimal weight: 10.0000 chunk 433 optimal weight: 50.0000 chunk 81 optimal weight: 3.9990 chunk 689 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 GLN ** B 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 ASN ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 534 ASN H 610 ASN H 720 ASN ** I 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 431 ASN M 509 GLN ** M 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 312 ASN Z 356 ASN ** Z 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 610 ASN ** Z 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 73995 Z= 0.238 Angle : 0.627 11.644 100445 Z= 0.325 Chirality : 0.045 0.233 11262 Planarity : 0.004 0.058 13130 Dihedral : 5.460 38.972 9974 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 0.05 % Allowed : 1.41 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.08), residues: 9190 helix: -1.52 (0.16), residues: 923 sheet: -0.77 (0.10), residues: 2433 loop : -2.56 (0.08), residues: 5834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 632 HIS 0.005 0.001 HIS H 765 PHE 0.014 0.001 PHE J 281 TYR 0.022 0.001 TYR G 697 ARG 0.005 0.000 ARG E 805 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 353 time to evaluate : 6.455 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: B 452 MET cc_start: 0.8421 (tmm) cc_final: 0.8018 (tmm) REVERT: B 536 GLN cc_start: 0.8301 (mm110) cc_final: 0.7616 (tt0) REVERT: B 609 MET cc_start: 0.7002 (mtt) cc_final: 0.6510 (mtt) REVERT: B 660 MET cc_start: 0.6906 (mmm) cc_final: 0.6594 (tpp) REVERT: B 762 MET cc_start: 0.7948 (ppp) cc_final: 0.7329 (ppp) REVERT: B 853 MET cc_start: 0.5421 (tmm) cc_final: 0.5075 (tmm) REVERT: D 437 ASP cc_start: 0.8108 (t0) cc_final: 0.7851 (t0) REVERT: D 452 MET cc_start: 0.8497 (pmm) cc_final: 0.7997 (pmm) REVERT: D 507 ILE cc_start: 0.8839 (mm) cc_final: 0.8576 (mm) REVERT: D 609 MET cc_start: 0.7197 (mtt) cc_final: 0.6912 (mtt) REVERT: D 649 LYS cc_start: 0.6878 (mttt) cc_final: 0.6454 (mmmt) REVERT: D 841 ASN cc_start: 0.8244 (t0) cc_final: 0.7862 (t0) REVERT: E 452 MET cc_start: 0.8748 (mtm) cc_final: 0.8484 (mtm) REVERT: E 786 MET cc_start: 0.8845 (tpp) cc_final: 0.8617 (tpp) REVERT: E 825 MET cc_start: 0.7760 (tpp) cc_final: 0.7515 (tpp) REVERT: F 232 ARG cc_start: 0.7556 (ptm160) cc_final: 0.7154 (ptm-80) REVERT: F 660 MET cc_start: 0.7003 (mmp) cc_final: 0.6308 (mmp) REVERT: F 762 MET cc_start: 0.7593 (ppp) cc_final: 0.7228 (ppp) REVERT: F 786 MET cc_start: 0.7722 (mmm) cc_final: 0.7501 (mmm) REVERT: F 825 MET cc_start: 0.8115 (mtm) cc_final: 0.7880 (mtp) REVERT: G 304 MET cc_start: 0.8017 (tmm) cc_final: 0.7600 (tmm) REVERT: G 691 LYS cc_start: 0.8995 (tttp) cc_final: 0.8549 (tmtt) REVERT: G 762 MET cc_start: 0.7381 (tpp) cc_final: 0.6897 (tpp) REVERT: G 825 MET cc_start: 0.7499 (mtp) cc_final: 0.7197 (mmm) REVERT: H 352 ASN cc_start: 0.8400 (m-40) cc_final: 0.7986 (t0) REVERT: H 520 ASP cc_start: 0.8581 (m-30) cc_final: 0.8280 (m-30) REVERT: H 754 LYS cc_start: 0.7576 (mttm) cc_final: 0.6067 (tmtt) REVERT: H 786 MET cc_start: 0.9287 (tpp) cc_final: 0.8666 (tpt) REVERT: I 432 ASN cc_start: 0.8568 (m110) cc_final: 0.8333 (t0) REVERT: I 537 ASP cc_start: 0.8094 (p0) cc_final: 0.7806 (p0) REVERT: J 304 MET cc_start: 0.8201 (ttp) cc_final: 0.7886 (ttp) REVERT: J 660 MET cc_start: 0.6135 (mmp) cc_final: 0.5322 (mmm) REVERT: K 403 MET cc_start: 0.8380 (tpp) cc_final: 0.8030 (tpp) REVERT: K 428 GLN cc_start: 0.7650 (tt0) cc_final: 0.6908 (tp40) REVERT: L 787 TYR cc_start: 0.7549 (m-80) cc_final: 0.6859 (m-80) REVERT: L 825 MET cc_start: 0.8825 (mmm) cc_final: 0.7559 (mmm) REVERT: M 403 MET cc_start: 0.8769 (mtp) cc_final: 0.8468 (mtp) REVERT: M 660 MET cc_start: 0.6244 (tpt) cc_final: 0.5610 (tpt) REVERT: Z 283 LYS cc_start: 0.9264 (mmtp) cc_final: 0.8922 (mmmt) REVERT: Z 304 MET cc_start: 0.8379 (tmm) cc_final: 0.7926 (tmm) REVERT: Z 733 LEU cc_start: 0.6969 (mt) cc_final: 0.6399 (pt) REVERT: Z 786 MET cc_start: 0.7852 (tpp) cc_final: 0.7531 (tpp) outliers start: 4 outliers final: 1 residues processed: 356 average time/residue: 0.6653 time to fit residues: 418.5496 Evaluate side-chains 255 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 6.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 797 optimal weight: 7.9990 chunk 840 optimal weight: 9.9990 chunk 766 optimal weight: 40.0000 chunk 817 optimal weight: 7.9990 chunk 491 optimal weight: 8.9990 chunk 356 optimal weight: 5.9990 chunk 641 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 chunk 738 optimal weight: 8.9990 chunk 773 optimal weight: 8.9990 chunk 814 optimal weight: 20.0000 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 509 GLN H 610 ASN H 720 ASN ** I 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 775 ASN ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 73995 Z= 0.211 Angle : 0.615 12.972 100445 Z= 0.317 Chirality : 0.045 0.307 11262 Planarity : 0.004 0.059 13130 Dihedral : 5.389 40.153 9974 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.02 % Allowed : 0.87 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.76 (0.08), residues: 9190 helix: -1.46 (0.16), residues: 923 sheet: -0.76 (0.10), residues: 2444 loop : -2.53 (0.08), residues: 5823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 632 HIS 0.005 0.001 HIS A 765 PHE 0.013 0.001 PHE J 281 TYR 0.026 0.001 TYR Z 861 ARG 0.006 0.000 ARG A 805 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 342 time to evaluate : 6.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 GLN cc_start: 0.8297 (mm110) cc_final: 0.7596 (tt0) REVERT: B 609 MET cc_start: 0.6871 (mtt) cc_final: 0.6391 (mtt) REVERT: B 660 MET cc_start: 0.6968 (mmm) cc_final: 0.6642 (tpp) REVERT: B 762 MET cc_start: 0.7927 (ppp) cc_final: 0.7319 (ppp) REVERT: C 786 MET cc_start: 0.7873 (tpp) cc_final: 0.7151 (tpp) REVERT: D 437 ASP cc_start: 0.8088 (t0) cc_final: 0.7830 (t0) REVERT: D 452 MET cc_start: 0.8672 (pmm) cc_final: 0.8125 (pmm) REVERT: D 649 LYS cc_start: 0.7039 (mttt) cc_final: 0.6561 (mmmt) REVERT: D 841 ASN cc_start: 0.8348 (t0) cc_final: 0.7838 (t0) REVERT: E 300 VAL cc_start: 0.9056 (m) cc_final: 0.8693 (p) REVERT: E 452 MET cc_start: 0.8714 (mtm) cc_final: 0.8437 (mtm) REVERT: E 786 MET cc_start: 0.8853 (tpp) cc_final: 0.8617 (tpp) REVERT: E 825 MET cc_start: 0.7717 (tpp) cc_final: 0.7488 (tpp) REVERT: F 232 ARG cc_start: 0.7550 (ptm160) cc_final: 0.7167 (ptm-80) REVERT: F 660 MET cc_start: 0.7030 (mmp) cc_final: 0.6336 (mmp) REVERT: F 691 LYS cc_start: 0.7566 (ptpp) cc_final: 0.7169 (pttt) REVERT: F 762 MET cc_start: 0.7647 (ppp) cc_final: 0.7268 (ppp) REVERT: F 825 MET cc_start: 0.8142 (mtm) cc_final: 0.7909 (mtp) REVERT: G 304 MET cc_start: 0.7987 (tmm) cc_final: 0.7614 (tmm) REVERT: G 691 LYS cc_start: 0.8990 (tttp) cc_final: 0.8545 (tmtt) REVERT: G 697 TYR cc_start: 0.7955 (t80) cc_final: 0.7605 (t80) REVERT: G 762 MET cc_start: 0.7532 (tpp) cc_final: 0.7174 (tpp) REVERT: G 825 MET cc_start: 0.7537 (mtp) cc_final: 0.7269 (mmm) REVERT: H 352 ASN cc_start: 0.8410 (m-40) cc_final: 0.7994 (t0) REVERT: H 520 ASP cc_start: 0.8679 (m-30) cc_final: 0.8376 (m-30) REVERT: H 754 LYS cc_start: 0.7505 (mttm) cc_final: 0.6076 (tmtt) REVERT: H 786 MET cc_start: 0.9417 (tpp) cc_final: 0.8724 (tpt) REVERT: I 537 ASP cc_start: 0.8155 (p0) cc_final: 0.7932 (p0) REVERT: J 304 MET cc_start: 0.8207 (ttp) cc_final: 0.7913 (ttp) REVERT: J 660 MET cc_start: 0.6140 (mmp) cc_final: 0.5318 (mmm) REVERT: J 853 MET cc_start: 0.7997 (tmm) cc_final: 0.7223 (tmm) REVERT: K 403 MET cc_start: 0.8443 (tpp) cc_final: 0.8065 (tpp) REVERT: K 428 GLN cc_start: 0.7660 (tt0) cc_final: 0.6907 (tp40) REVERT: L 787 TYR cc_start: 0.7702 (m-80) cc_final: 0.7102 (m-80) REVERT: L 825 MET cc_start: 0.8826 (mmm) cc_final: 0.7553 (mmm) REVERT: M 403 MET cc_start: 0.8728 (mtp) cc_final: 0.8441 (mtp) REVERT: M 660 MET cc_start: 0.5789 (tpt) cc_final: 0.5568 (tpt) REVERT: Z 283 LYS cc_start: 0.9246 (mmtp) cc_final: 0.8918 (mmmt) REVERT: Z 304 MET cc_start: 0.8247 (tmm) cc_final: 0.7739 (tmm) REVERT: Z 733 LEU cc_start: 0.7084 (mt) cc_final: 0.6525 (pt) REVERT: Z 786 MET cc_start: 0.7624 (tpp) cc_final: 0.7378 (tpp) outliers start: 2 outliers final: 0 residues processed: 343 average time/residue: 0.6642 time to fit residues: 400.1643 Evaluate side-chains 255 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 6.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 536 optimal weight: 20.0000 chunk 864 optimal weight: 6.9990 chunk 527 optimal weight: 7.9990 chunk 410 optimal weight: 7.9990 chunk 600 optimal weight: 9.9990 chunk 906 optimal weight: 20.0000 chunk 834 optimal weight: 6.9990 chunk 721 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 557 optimal weight: 6.9990 chunk 442 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS B 735 ASN C 223 ASN C 428 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN ** D 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 ASN ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 627 ASN ** H 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 GLN ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 682 ASN ** M 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 73995 Z= 0.302 Angle : 0.686 11.925 100445 Z= 0.358 Chirality : 0.046 0.314 11262 Planarity : 0.004 0.062 13130 Dihedral : 5.821 40.953 9974 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.89 (0.08), residues: 9190 helix: -1.56 (0.16), residues: 875 sheet: -0.88 (0.10), residues: 2481 loop : -2.60 (0.08), residues: 5834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 632 HIS 0.007 0.001 HIS A 765 PHE 0.023 0.002 PHE J 788 TYR 0.027 0.002 TYR Z 861 ARG 0.007 0.001 ARG A 805 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 331 time to evaluate : 6.439 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: B 452 MET cc_start: 0.8444 (tmm) cc_final: 0.8083 (tmm) REVERT: B 536 GLN cc_start: 0.8327 (mm110) cc_final: 0.7605 (tt0) REVERT: B 762 MET cc_start: 0.8072 (ppp) cc_final: 0.7456 (ppp) REVERT: C 362 ASP cc_start: 0.8402 (t70) cc_final: 0.8164 (t0) REVERT: C 786 MET cc_start: 0.7825 (tpp) cc_final: 0.7043 (tpp) REVERT: D 437 ASP cc_start: 0.8135 (t0) cc_final: 0.7873 (t0) REVERT: D 452 MET cc_start: 0.8736 (pmm) cc_final: 0.8194 (pmm) REVERT: D 507 ILE cc_start: 0.8874 (mm) cc_final: 0.8607 (mm) REVERT: D 609 MET cc_start: 0.7195 (mtt) cc_final: 0.6885 (mtt) REVERT: D 649 LYS cc_start: 0.6458 (mttt) cc_final: 0.5749 (tttp) REVERT: D 841 ASN cc_start: 0.8361 (t0) cc_final: 0.7880 (t0) REVERT: E 300 VAL cc_start: 0.9034 (m) cc_final: 0.8687 (p) REVERT: E 786 MET cc_start: 0.8858 (tpp) cc_final: 0.8655 (tpp) REVERT: F 660 MET cc_start: 0.7178 (mmp) cc_final: 0.6633 (mmp) REVERT: F 691 LYS cc_start: 0.8337 (ptpp) cc_final: 0.7643 (pttt) REVERT: F 762 MET cc_start: 0.7624 (ppp) cc_final: 0.7402 (ppp) REVERT: F 786 MET cc_start: 0.7788 (mmm) cc_final: 0.7436 (mmm) REVERT: F 825 MET cc_start: 0.8220 (mtm) cc_final: 0.7865 (mtp) REVERT: G 304 MET cc_start: 0.8074 (tmm) cc_final: 0.7687 (tmm) REVERT: G 691 LYS cc_start: 0.9076 (tttp) cc_final: 0.8616 (tmtt) REVERT: G 697 TYR cc_start: 0.7955 (t80) cc_final: 0.7490 (t80) REVERT: G 825 MET cc_start: 0.7576 (mtp) cc_final: 0.7295 (mmm) REVERT: H 352 ASN cc_start: 0.8344 (m-40) cc_final: 0.7979 (t0) REVERT: H 520 ASP cc_start: 0.8713 (m-30) cc_final: 0.8396 (m-30) REVERT: H 754 LYS cc_start: 0.7645 (mttm) cc_final: 0.6334 (tmtt) REVERT: H 786 MET cc_start: 0.9410 (tpp) cc_final: 0.8809 (tpt) REVERT: I 537 ASP cc_start: 0.8040 (p0) cc_final: 0.7829 (p0) REVERT: J 304 MET cc_start: 0.8121 (ttp) cc_final: 0.7831 (ttp) REVERT: J 660 MET cc_start: 0.6180 (mmp) cc_final: 0.5390 (mmm) REVERT: J 853 MET cc_start: 0.7801 (tmm) cc_final: 0.7054 (tmm) REVERT: K 403 MET cc_start: 0.8496 (tpp) cc_final: 0.8049 (tpp) REVERT: K 428 GLN cc_start: 0.7764 (tt0) cc_final: 0.7031 (tp40) REVERT: L 787 TYR cc_start: 0.7825 (m-80) cc_final: 0.7169 (m-80) REVERT: L 825 MET cc_start: 0.8862 (mmm) cc_final: 0.7612 (mmm) REVERT: M 403 MET cc_start: 0.8695 (mtp) cc_final: 0.8407 (mtp) REVERT: Z 283 LYS cc_start: 0.9219 (mmtp) cc_final: 0.8945 (mmmt) REVERT: Z 304 MET cc_start: 0.8777 (tmm) cc_final: 0.8226 (tmm) REVERT: Z 733 LEU cc_start: 0.6953 (mt) cc_final: 0.6363 (pt) REVERT: Z 786 MET cc_start: 0.7762 (tpp) cc_final: 0.7334 (mmm) outliers start: 3 outliers final: 0 residues processed: 334 average time/residue: 0.6711 time to fit residues: 394.3133 Evaluate side-chains 252 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 6.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 573 optimal weight: 20.0000 chunk 769 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 665 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 723 optimal weight: 4.9990 chunk 302 optimal weight: 30.0000 chunk 742 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 GLN ** F 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 627 ASN H 720 ASN ** I 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 GLN ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.060266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050600 restraints weight = 423294.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051796 restraints weight = 251687.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052609 restraints weight = 169349.865| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 73995 Z= 0.240 Angle : 0.643 12.017 100445 Z= 0.333 Chirality : 0.045 0.284 11262 Planarity : 0.004 0.058 13130 Dihedral : 5.655 40.472 9974 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 0.04 % Allowed : 0.51 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.85 (0.08), residues: 9190 helix: -1.57 (0.16), residues: 887 sheet: -0.89 (0.10), residues: 2520 loop : -2.55 (0.08), residues: 5783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 632 HIS 0.006 0.001 HIS A 765 PHE 0.022 0.001 PHE J 788 TYR 0.023 0.002 TYR Z 861 ARG 0.007 0.000 ARG A 805 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9610.80 seconds wall clock time: 176 minutes 36.04 seconds (10596.04 seconds total)