Starting phenix.real_space_refine on Tue Apr 16 03:28:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sih_10210/04_2024/6sih_10210.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sih_10210/04_2024/6sih_10210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sih_10210/04_2024/6sih_10210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sih_10210/04_2024/6sih_10210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sih_10210/04_2024/6sih_10210.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sih_10210/04_2024/6sih_10210.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 110 5.16 5 C 23150 2.51 5 N 6140 2.21 5 O 7910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 397": "OD1" <-> "OD2" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 604": "OD1" <-> "OD2" Residue "H TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 604": "OD1" <-> "OD2" Residue "B TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 397": "OD1" <-> "OD2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 604": "OD1" <-> "OD2" Residue "F TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 397": "OD1" <-> "OD2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 604": "OD1" <-> "OD2" Residue "C TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 397": "OD1" <-> "OD2" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 604": "OD1" <-> "OD2" Residue "G TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 397": "OD1" <-> "OD2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 604": "OD1" <-> "OD2" Residue "D TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 397": "OD1" <-> "OD2" Residue "I PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 604": "OD1" <-> "OD2" Residue "I TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 397": "OD1" <-> "OD2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 604": "OD1" <-> "OD2" Residue "E TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 397": "OD1" <-> "OD2" Residue "J PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 604": "OD1" <-> "OD2" Residue "J TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 37310 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3731 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 7, 'TRANS': 480} Chain breaks: 2 Chain: "H" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3731 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 7, 'TRANS': 480} Chain breaks: 2 Chain: "B" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3731 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 7, 'TRANS': 480} Chain breaks: 2 Chain: "F" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3731 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 7, 'TRANS': 480} Chain breaks: 2 Chain: "C" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3731 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 7, 'TRANS': 480} Chain breaks: 2 Chain: "G" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3731 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 7, 'TRANS': 480} Chain breaks: 2 Chain: "D" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3731 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 7, 'TRANS': 480} Chain breaks: 2 Chain: "I" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3731 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 7, 'TRANS': 480} Chain breaks: 2 Chain: "E" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3731 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 7, 'TRANS': 480} Chain breaks: 2 Chain: "J" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3731 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 7, 'TRANS': 480} Chain breaks: 2 Time building chain proxies: 19.32, per 1000 atoms: 0.52 Number of scatterers: 37310 At special positions: 0 Unit cell: (138, 144.9, 296.7, 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 110 16.00 O 7910 8.00 N 6140 7.00 C 23150 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: 16.27 Conformation dependent library (CDL) restraints added in 7.3 seconds 9640 Ramachandran restraints generated. 4820 Oldfield, 0 Emsley, 4820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9080 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 51 sheets defined 46.9% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 17 through 67 Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 154 through 166 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 302 through 326 removed outlier: 4.149A pdb=" N LYS A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 357 removed outlier: 4.363A pdb=" N ASN A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 397 through 408 Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.754A pdb=" N THR A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 638 removed outlier: 3.546A pdb=" N ILE A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 590 " --> pdb=" O THR A 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 606 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 67 Proline residue: H 35 - end of helix Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 154 through 166 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 218 through 225 Processing helix chain 'H' and resid 302 through 326 removed outlier: 4.149A pdb=" N LYS H 306 " --> pdb=" O GLU H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 357 removed outlier: 4.364A pdb=" N ASN H 345 " --> pdb=" O ILE H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 384 Processing helix chain 'H' and resid 397 through 408 Processing helix chain 'H' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR H 412 " --> pdb=" O ASP H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS H 563 " --> pdb=" O GLY H 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU H 564 " --> pdb=" O ILE H 560 " (cutoff:3.500A) Processing helix chain 'H' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE H 589 " --> pdb=" O LEU H 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS H 590 " --> pdb=" O THR H 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG H 606 " --> pdb=" O MET H 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR H 607 " --> pdb=" O ILE H 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR H 609 " --> pdb=" O THR H 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 67 Proline residue: B 35 - end of helix Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 154 through 166 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 302 through 326 removed outlier: 4.149A pdb=" N LYS B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 357 removed outlier: 4.363A pdb=" N ASN B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 564 " --> pdb=" O ILE B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 638 removed outlier: 3.546A pdb=" N ILE B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 590 " --> pdb=" O THR B 586 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 606 " --> pdb=" O MET B 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 67 Proline residue: F 35 - end of helix Processing helix chain 'F' and resid 69 through 73 Processing helix chain 'F' and resid 154 through 166 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 218 through 225 Processing helix chain 'F' and resid 302 through 326 removed outlier: 4.148A pdb=" N LYS F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 357 removed outlier: 4.362A pdb=" N ASN F 345 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 384 Processing helix chain 'F' and resid 397 through 408 Processing helix chain 'F' and resid 408 through 418 removed outlier: 3.754A pdb=" N THR F 412 " --> pdb=" O ASP F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS F 563 " --> pdb=" O GLY F 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F 564 " --> pdb=" O ILE F 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE F 589 " --> pdb=" O LEU F 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 590 " --> pdb=" O THR F 586 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG F 606 " --> pdb=" O MET F 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR F 607 " --> pdb=" O ILE F 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR F 609 " --> pdb=" O THR F 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 67 Proline residue: C 35 - end of helix Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 154 through 166 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 302 through 326 removed outlier: 4.149A pdb=" N LYS C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 357 removed outlier: 4.364A pdb=" N ASN C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 397 through 408 Processing helix chain 'C' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS C 563 " --> pdb=" O GLY C 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 564 " --> pdb=" O ILE C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 590 " --> pdb=" O THR C 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 606 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 607 " --> pdb=" O ILE C 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 609 " --> pdb=" O THR C 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 67 Proline residue: G 35 - end of helix Processing helix chain 'G' and resid 69 through 73 Processing helix chain 'G' and resid 154 through 166 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 218 through 225 Processing helix chain 'G' and resid 302 through 326 removed outlier: 4.150A pdb=" N LYS G 306 " --> pdb=" O GLU G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 357 removed outlier: 4.364A pdb=" N ASN G 345 " --> pdb=" O ILE G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 384 Processing helix chain 'G' and resid 397 through 408 Processing helix chain 'G' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR G 412 " --> pdb=" O ASP G 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 573 removed outlier: 3.830A pdb=" N LYS G 563 " --> pdb=" O GLY G 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G 564 " --> pdb=" O ILE G 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 576 through 638 removed outlier: 3.546A pdb=" N ILE G 589 " --> pdb=" O LEU G 585 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS G 590 " --> pdb=" O THR G 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG G 606 " --> pdb=" O MET G 602 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR G 607 " --> pdb=" O ILE G 603 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR G 609 " --> pdb=" O THR G 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 67 Proline residue: D 35 - end of helix Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 154 through 166 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 302 through 326 removed outlier: 4.150A pdb=" N LYS D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 357 removed outlier: 4.363A pdb=" N ASN D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 397 through 408 Processing helix chain 'D' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 573 removed outlier: 3.830A pdb=" N LYS D 563 " --> pdb=" O GLY D 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 564 " --> pdb=" O ILE D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 638 removed outlier: 3.548A pdb=" N ILE D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 590 " --> pdb=" O THR D 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 606 " --> pdb=" O MET D 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR D 607 " --> pdb=" O ILE D 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR D 609 " --> pdb=" O THR D 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 67 Proline residue: I 35 - end of helix Processing helix chain 'I' and resid 69 through 73 Processing helix chain 'I' and resid 154 through 166 Processing helix chain 'I' and resid 194 through 197 Processing helix chain 'I' and resid 218 through 225 Processing helix chain 'I' and resid 302 through 326 removed outlier: 4.150A pdb=" N LYS I 306 " --> pdb=" O GLU I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 357 removed outlier: 4.362A pdb=" N ASN I 345 " --> pdb=" O ILE I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 384 Processing helix chain 'I' and resid 397 through 408 Processing helix chain 'I' and resid 408 through 418 removed outlier: 3.754A pdb=" N THR I 412 " --> pdb=" O ASP I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 573 removed outlier: 3.830A pdb=" N LYS I 563 " --> pdb=" O GLY I 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU I 564 " --> pdb=" O ILE I 560 " (cutoff:3.500A) Processing helix chain 'I' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE I 589 " --> pdb=" O LEU I 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS I 590 " --> pdb=" O THR I 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG I 606 " --> pdb=" O MET I 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR I 607 " --> pdb=" O ILE I 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR I 609 " --> pdb=" O THR I 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 67 Proline residue: E 35 - end of helix Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 154 through 166 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 302 through 326 removed outlier: 4.148A pdb=" N LYS E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 357 removed outlier: 4.363A pdb=" N ASN E 345 " --> pdb=" O ILE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 384 Processing helix chain 'E' and resid 397 through 408 Processing helix chain 'E' and resid 408 through 418 removed outlier: 3.753A pdb=" N THR E 412 " --> pdb=" O ASP E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 573 removed outlier: 3.830A pdb=" N LYS E 563 " --> pdb=" O GLY E 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 564 " --> pdb=" O ILE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE E 589 " --> pdb=" O LEU E 585 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS E 590 " --> pdb=" O THR E 586 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG E 606 " --> pdb=" O MET E 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR E 607 " --> pdb=" O ILE E 603 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR E 609 " --> pdb=" O THR E 605 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 67 Proline residue: J 35 - end of helix Processing helix chain 'J' and resid 69 through 73 Processing helix chain 'J' and resid 154 through 166 Processing helix chain 'J' and resid 194 through 197 Processing helix chain 'J' and resid 218 through 225 Processing helix chain 'J' and resid 302 through 326 removed outlier: 4.150A pdb=" N LYS J 306 " --> pdb=" O GLU J 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 341 through 357 removed outlier: 4.362A pdb=" N ASN J 345 " --> pdb=" O ILE J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 384 Processing helix chain 'J' and resid 397 through 408 Processing helix chain 'J' and resid 408 through 418 removed outlier: 3.754A pdb=" N THR J 412 " --> pdb=" O ASP J 408 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 573 removed outlier: 3.829A pdb=" N LYS J 563 " --> pdb=" O GLY J 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU J 564 " --> pdb=" O ILE J 560 " (cutoff:3.500A) Processing helix chain 'J' and resid 576 through 638 removed outlier: 3.547A pdb=" N ILE J 589 " --> pdb=" O LEU J 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS J 590 " --> pdb=" O THR J 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG J 606 " --> pdb=" O MET J 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR J 607 " --> pdb=" O ILE J 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR J 609 " --> pdb=" O THR J 605 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN A 99 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL A 105 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 263 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 107 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 92 removed outlier: 7.700A pdb=" N MET A 283 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP A 278 " --> pdb=" O MET A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG A 185 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 149 Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AA6, first strand: chain 'H' and resid 76 through 80 removed outlier: 3.591A pdb=" N GLN H 99 " --> pdb=" O VAL H 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL H 105 " --> pdb=" O THR H 263 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR H 263 " --> pdb=" O VAL H 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN H 107 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 88 through 92 removed outlier: 7.700A pdb=" N MET H 283 " --> pdb=" O ASP H 278 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP H 278 " --> pdb=" O MET H 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG H 185 " --> pdb=" O VAL H 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 143 through 149 Processing sheet with id=AB1, first strand: chain 'H' and resid 386 through 387 Processing sheet with id=AB2, first strand: chain 'B' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN B 99 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL B 105 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR B 263 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 107 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET B 283 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP B 278 " --> pdb=" O MET B 283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG B 185 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 143 through 149 Processing sheet with id=AB6, first strand: chain 'B' and resid 386 through 387 Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 80 removed outlier: 3.591A pdb=" N GLN F 99 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL F 105 " --> pdb=" O THR F 263 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR F 263 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN F 107 " --> pdb=" O GLU F 261 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET F 283 " --> pdb=" O ASP F 278 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP F 278 " --> pdb=" O MET F 283 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG F 185 " --> pdb=" O VAL F 175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 143 through 149 Processing sheet with id=AC2, first strand: chain 'F' and resid 386 through 387 Processing sheet with id=AC3, first strand: chain 'C' and resid 8 through 9 removed outlier: 3.715A pdb=" N LEU C 9 " --> pdb=" O LEU G 9 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU G 9 " --> pdb=" O LEU C 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN C 99 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL C 105 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 263 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN C 107 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET C 283 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP C 278 " --> pdb=" O MET C 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG C 185 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 143 through 149 Processing sheet with id=AC8, first strand: chain 'C' and resid 386 through 387 Processing sheet with id=AC9, first strand: chain 'G' and resid 76 through 80 removed outlier: 3.591A pdb=" N GLN G 99 " --> pdb=" O VAL G 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL G 105 " --> pdb=" O THR G 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR G 263 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN G 107 " --> pdb=" O GLU G 261 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET G 283 " --> pdb=" O ASP G 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP G 278 " --> pdb=" O MET G 283 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG G 185 " --> pdb=" O VAL G 175 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 143 through 149 Processing sheet with id=AD4, first strand: chain 'G' and resid 386 through 387 Processing sheet with id=AD5, first strand: chain 'D' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN D 99 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL D 105 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR D 263 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN D 107 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 88 through 92 removed outlier: 7.700A pdb=" N MET D 283 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP D 278 " --> pdb=" O MET D 283 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG D 185 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 143 through 149 Processing sheet with id=AD9, first strand: chain 'D' and resid 386 through 387 Processing sheet with id=AE1, first strand: chain 'I' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN I 99 " --> pdb=" O VAL I 297 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL I 105 " --> pdb=" O THR I 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR I 263 " --> pdb=" O VAL I 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN I 107 " --> pdb=" O GLU I 261 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET I 283 " --> pdb=" O ASP I 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP I 278 " --> pdb=" O MET I 283 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG I 185 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 143 through 149 Processing sheet with id=AE5, first strand: chain 'I' and resid 386 through 387 Processing sheet with id=AE6, first strand: chain 'E' and resid 76 through 80 removed outlier: 3.592A pdb=" N GLN E 99 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL E 105 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR E 263 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN E 107 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 88 through 92 removed outlier: 7.700A pdb=" N MET E 283 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP E 278 " --> pdb=" O MET E 283 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG E 185 " --> pdb=" O VAL E 175 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 143 through 149 Processing sheet with id=AF1, first strand: chain 'E' and resid 386 through 387 Processing sheet with id=AF2, first strand: chain 'J' and resid 76 through 80 removed outlier: 3.591A pdb=" N GLN J 99 " --> pdb=" O VAL J 297 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL J 105 " --> pdb=" O THR J 263 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR J 263 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN J 107 " --> pdb=" O GLU J 261 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 88 through 92 removed outlier: 7.701A pdb=" N MET J 283 " --> pdb=" O ASP J 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP J 278 " --> pdb=" O MET J 283 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 113 through 115 removed outlier: 3.650A pdb=" N ARG J 185 " --> pdb=" O VAL J 175 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 143 through 149 Processing sheet with id=AF6, first strand: chain 'J' and resid 386 through 387 2160 hydrogen bonds defined for protein. 6150 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: 15.52 Time building geometry restraints manager: 17.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12480 1.34 - 1.46: 6947 1.46 - 1.57: 18083 1.57 - 1.69: 0 1.69 - 1.80: 220 Bond restraints: 37730 Sorted by residual: bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.42e+00 bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.41e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.41e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.38e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.38e+00 ... (remaining 37725 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.12: 450 107.12 - 113.82: 22247 113.82 - 120.52: 13726 120.52 - 127.22: 14398 127.22 - 133.92: 119 Bond angle restraints: 50940 Sorted by residual: angle pdb=" N ASP H 249 " pdb=" CA ASP H 249 " pdb=" C ASP H 249 " ideal model delta sigma weight residual 110.80 116.31 -5.51 2.13e+00 2.20e-01 6.68e+00 angle pdb=" N ASP A 249 " pdb=" CA ASP A 249 " pdb=" C ASP A 249 " ideal model delta sigma weight residual 110.80 116.29 -5.49 2.13e+00 2.20e-01 6.63e+00 angle pdb=" N ASP E 249 " pdb=" CA ASP E 249 " pdb=" C ASP E 249 " ideal model delta sigma weight residual 110.80 116.26 -5.46 2.13e+00 2.20e-01 6.57e+00 angle pdb=" N ASP D 249 " pdb=" CA ASP D 249 " pdb=" C ASP D 249 " ideal model delta sigma weight residual 110.80 116.26 -5.46 2.13e+00 2.20e-01 6.57e+00 angle pdb=" N ASP G 249 " pdb=" CA ASP G 249 " pdb=" C ASP G 249 " ideal model delta sigma weight residual 110.80 116.26 -5.46 2.13e+00 2.20e-01 6.57e+00 ... (remaining 50935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 21214 16.81 - 33.62: 1396 33.62 - 50.43: 220 50.43 - 67.23: 80 67.23 - 84.04: 50 Dihedral angle restraints: 22960 sinusoidal: 8900 harmonic: 14060 Sorted by residual: dihedral pdb=" CA LYS B 248 " pdb=" C LYS B 248 " pdb=" N ASP B 249 " pdb=" CA ASP B 249 " ideal model delta harmonic sigma weight residual 180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA LYS F 248 " pdb=" C LYS F 248 " pdb=" N ASP F 249 " pdb=" CA ASP F 249 " ideal model delta harmonic sigma weight residual 180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LYS A 248 " pdb=" C LYS A 248 " pdb=" N ASP A 249 " pdb=" CA ASP A 249 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 22957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 3726 0.024 - 0.049: 1502 0.049 - 0.073: 393 0.073 - 0.098: 267 0.098 - 0.122: 122 Chirality restraints: 6010 Sorted by residual: chirality pdb=" CA ILE E 236 " pdb=" N ILE E 236 " pdb=" C ILE E 236 " pdb=" CB ILE E 236 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA ILE B 236 " pdb=" N ILE B 236 " pdb=" C ILE B 236 " pdb=" CB ILE B 236 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA ILE C 236 " pdb=" N ILE C 236 " pdb=" C ILE C 236 " pdb=" CB ILE C 236 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 6007 not shown) Planarity restraints: 6610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 248 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C LYS F 248 " -0.023 2.00e-02 2.50e+03 pdb=" O LYS F 248 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP F 249 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 248 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C LYS J 248 " -0.023 2.00e-02 2.50e+03 pdb=" O LYS J 248 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP J 249 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 248 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C LYS I 248 " 0.023 2.00e-02 2.50e+03 pdb=" O LYS I 248 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP I 249 " -0.008 2.00e-02 2.50e+03 ... (remaining 6607 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 601 2.52 - 3.12: 32758 3.12 - 3.71: 60122 3.71 - 4.31: 84182 4.31 - 4.90: 135944 Nonbonded interactions: 313607 Sorted by model distance: nonbonded pdb=" O GLY A 14 " pdb=" OG SER B 7 " model vdw 1.931 2.440 nonbonded pdb=" O GLY B 14 " pdb=" OG SER C 7 " model vdw 1.960 2.440 nonbonded pdb=" O GLY H 14 " pdb=" OG SER I 7 " model vdw 1.978 2.440 nonbonded pdb=" OG SER F 7 " pdb=" O GLY G 14 " model vdw 1.982 2.440 nonbonded pdb=" OG SER H 7 " pdb=" O GLY F 14 " model vdw 1.987 2.440 ... (remaining 313602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set refine NCS operators NCS operators will be refined. 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: 1.160 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: 0.020 Extract box with map and model: 6.810 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 101.940 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 37730 Z= 0.292 Angle : 0.544 5.506 50940 Z= 0.327 Chirality : 0.035 0.122 6010 Planarity : 0.002 0.013 6610 Dihedral : 12.608 84.043 13880 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.11), residues: 4820 helix: -0.40 (0.10), residues: 2090 sheet: -0.96 (0.16), residues: 770 loop : -1.77 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 614 HIS 0.002 0.001 HIS H 253 PHE 0.012 0.001 PHE E 139 TYR 0.005 0.001 TYR E 607 ARG 0.002 0.000 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9640 Ramachandran restraints generated. 4820 Oldfield, 0 Emsley, 4820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9640 Ramachandran restraints generated. 4820 Oldfield, 0 Emsley, 4820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 201 PHE cc_start: 0.6738 (m-80) cc_final: 0.5743 (m-80) REVERT: A 212 TYR cc_start: 0.7966 (m-10) cc_final: 0.7321 (t80) REVERT: A 610 MET cc_start: 0.8621 (mmm) cc_final: 0.8301 (mmm) REVERT: A 624 LEU cc_start: 0.8830 (tt) cc_final: 0.8583 (mm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2332 time to fit residues: 9.3650 Evaluate side-chains 21 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 20.0000 chunk 363 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 124 optimal weight: 0.0060 chunk 245 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 376 optimal weight: 0.3980 chunk 145 optimal weight: 9.9990 chunk 228 optimal weight: 0.0270 chunk 280 optimal weight: 0.0030 chunk 435 optimal weight: 0.8980 overall best weight: 0.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN H 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 37730 Z= 0.145 Angle : 0.599 10.708 50940 Z= 0.308 Chirality : 0.040 0.155 6010 Planarity : 0.004 0.077 6610 Dihedral : 5.212 29.455 5050 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.12), residues: 4820 helix: 1.34 (0.11), residues: 2100 sheet: -0.42 (0.17), residues: 810 loop : -1.50 (0.15), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 227 HIS 0.002 0.001 HIS G 253 PHE 0.011 0.002 PHE B 384 TYR 0.023 0.002 TYR F 617 ARG 0.014 0.001 ARG H 606 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: H 283 MET cc_start: 0.8123 (ptp) cc_final: 0.7851 (ptp) REVERT: H 603 ILE cc_start: 0.8703 (mt) cc_final: 0.8467 (mt) REVERT: H 617 TYR cc_start: 0.6676 (p90) cc_final: 0.6137 (m-10) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1981 time to fit residues: 7.7204 Evaluate side-chains 17 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 0.9990 chunk 135 optimal weight: 0.0370 chunk 362 optimal weight: 7.9990 chunk 296 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 436 optimal weight: 0.4980 chunk 471 optimal weight: 10.0000 chunk 388 optimal weight: 1.9990 chunk 433 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 350 optimal weight: 10.0000 overall best weight: 0.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 298 GLN H 626 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 37730 Z= 0.141 Angle : 0.563 8.054 50940 Z= 0.292 Chirality : 0.040 0.185 6010 Planarity : 0.003 0.062 6610 Dihedral : 5.161 29.514 5050 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.13), residues: 4820 helix: 1.62 (0.11), residues: 2090 sheet: -0.20 (0.17), residues: 810 loop : -1.28 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP J 614 HIS 0.001 0.001 HIS G 253 PHE 0.010 0.001 PHE J 139 TYR 0.011 0.001 TYR F 202 ARG 0.005 0.001 ARG I 606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 269 MET cc_start: 0.7262 (mmp) cc_final: 0.7054 (mmm) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2155 time to fit residues: 6.7105 Evaluate side-chains 17 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 0.3980 chunk 328 optimal weight: 5.9990 chunk 226 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 208 optimal weight: 0.0570 chunk 293 optimal weight: 6.9990 chunk 438 optimal weight: 0.0040 chunk 463 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 415 optimal weight: 3.9990 chunk 125 optimal weight: 0.0770 overall best weight: 0.3068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37730 Z= 0.160 Angle : 0.592 9.483 50940 Z= 0.303 Chirality : 0.041 0.220 6010 Planarity : 0.006 0.133 6610 Dihedral : 5.103 31.262 5050 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 4820 helix: 2.05 (0.11), residues: 2040 sheet: -0.18 (0.17), residues: 810 loop : -1.28 (0.15), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 614 HIS 0.001 0.001 HIS G 253 PHE 0.018 0.001 PHE G 3 TYR 0.042 0.002 TYR D 617 ARG 0.017 0.001 ARG E 606 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1704 time to fit residues: 5.7483 Evaluate side-chains 19 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 0.9990 chunk 263 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 345 optimal weight: 9.9990 chunk 191 optimal weight: 0.7980 chunk 395 optimal weight: 4.9990 chunk 320 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 416 optimal weight: 0.4980 chunk 117 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 37730 Z= 0.148 Angle : 0.537 7.755 50940 Z= 0.275 Chirality : 0.038 0.137 6010 Planarity : 0.003 0.068 6610 Dihedral : 4.861 25.163 5050 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.24 % Allowed : 1.43 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.12), residues: 4820 helix: 2.24 (0.11), residues: 2040 sheet: -0.18 (0.17), residues: 810 loop : -1.46 (0.15), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 614 HIS 0.000 0.000 HIS C 253 PHE 0.011 0.001 PHE A 3 TYR 0.014 0.001 TYR H 607 ARG 0.008 0.001 ARG F 606 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: G 212 TYR cc_start: 0.8025 (m-10) cc_final: 0.7289 (t80) REVERT: G 269 MET cc_start: 0.7742 (mmp) cc_final: 0.7471 (mmm) REVERT: G 308 MET cc_start: 0.8809 (mmp) cc_final: 0.8213 (mmm) REVERT: G 615 LEU cc_start: 0.9218 (tp) cc_final: 0.8612 (pp) REVERT: G 634 MET cc_start: 0.6252 (tmm) cc_final: 0.5459 (ppp) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.1533 time to fit residues: 4.9021 Evaluate side-chains 17 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 0.0270 chunk 417 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 272 optimal weight: 8.9990 chunk 114 optimal weight: 0.0030 chunk 464 optimal weight: 8.9990 chunk 385 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 153 optimal weight: 9.9990 chunk 243 optimal weight: 1.9990 overall best weight: 0.7452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 37730 Z= 0.140 Angle : 0.506 7.767 50940 Z= 0.259 Chirality : 0.038 0.136 6010 Planarity : 0.003 0.058 6610 Dihedral : 4.641 22.957 5050 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.12), residues: 4820 helix: 2.48 (0.11), residues: 2040 sheet: 0.00 (0.17), residues: 790 loop : -1.51 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 227 HIS 0.000 0.000 HIS G 253 PHE 0.011 0.001 PHE I 262 TYR 0.015 0.001 TYR I 607 ARG 0.005 0.001 ARG I 606 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: H 212 TYR cc_start: 0.7605 (m-10) cc_final: 0.7013 (t80) REVERT: H 269 MET cc_start: 0.7397 (mmp) cc_final: 0.7126 (mmm) REVERT: H 634 MET cc_start: 0.6261 (tmm) cc_final: 0.5334 (ppp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1789 time to fit residues: 4.9698 Evaluate side-chains 16 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 264 optimal weight: 7.9990 chunk 339 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 chunk 390 optimal weight: 4.9990 chunk 259 optimal weight: 0.9980 chunk 462 optimal weight: 2.9990 chunk 289 optimal weight: 8.9990 chunk 282 optimal weight: 0.0270 chunk 213 optimal weight: 0.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 37730 Z= 0.122 Angle : 0.488 7.617 50940 Z= 0.249 Chirality : 0.038 0.128 6010 Planarity : 0.003 0.044 6610 Dihedral : 4.491 21.247 5050 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.12), residues: 4820 helix: 2.37 (0.11), residues: 2100 sheet: -0.01 (0.17), residues: 790 loop : -1.47 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 227 HIS 0.000 0.000 HIS H 253 PHE 0.010 0.001 PHE H 295 TYR 0.016 0.001 TYR C 607 ARG 0.004 0.000 ARG B 606 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7712 Ramachandran restraints generated. 3856 Oldfield, 0 Emsley, 3856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: H 634 MET cc_start: 0.6109 (tmm) cc_final: 0.5275 (ppp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1590 time to fit residues: 4.2284 Evaluate side-chains 16 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 1.9990 chunk 184 optimal weight: 0.0370 chunk 276 optimal weight: 0.0270 chunk 139 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 294 optimal weight: 3.9990 chunk 315 optimal weight: 0.9980 chunk 228 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 363 optimal weight: 4.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN H 629 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4162 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: