Starting phenix.real_space_refine on Mon Feb 19 14:08:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amy_11827/02_2024/7amy_11827.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amy_11827/02_2024/7amy_11827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amy_11827/02_2024/7amy_11827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amy_11827/02_2024/7amy_11827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amy_11827/02_2024/7amy_11827.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amy_11827/02_2024/7amy_11827.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 72 5.16 5 C 15750 2.51 5 N 4320 2.21 5 O 4707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 351": "OD1" <-> "OD2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A ASP 480": "OD1" <-> "OD2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 351": "OD1" <-> "OD2" Residue "B ASP 352": "OD1" <-> "OD2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B ASP 480": "OD1" <-> "OD2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B GLU 558": "OE1" <-> "OE2" Residue "B ARG 641": "NH1" <-> "NH2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 351": "OD1" <-> "OD2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C ARG 402": "NH1" <-> "NH2" Residue "C ARG 404": "NH1" <-> "NH2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 463": "OE1" <-> "OE2" Residue "C ASP 480": "OD1" <-> "OD2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "C GLU 558": "OE1" <-> "OE2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 668": "NH1" <-> "NH2" Residue "C PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 351": "OD1" <-> "OD2" Residue "D ASP 352": "OD1" <-> "OD2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D ARG 402": "NH1" <-> "NH2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "D TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D ASP 480": "OD1" <-> "OD2" Residue "D GLU 506": "OE1" <-> "OE2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "D GLU 558": "OE1" <-> "OE2" Residue "D ARG 641": "NH1" <-> "NH2" Residue "D ARG 668": "NH1" <-> "NH2" Residue "D PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 351": "OD1" <-> "OD2" Residue "E ASP 352": "OD1" <-> "OD2" Residue "E ARG 387": "NH1" <-> "NH2" Residue "E ARG 402": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "E TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 463": "OE1" <-> "OE2" Residue "E ASP 480": "OD1" <-> "OD2" Residue "E GLU 506": "OE1" <-> "OE2" Residue "E ARG 550": "NH1" <-> "NH2" Residue "E GLU 558": "OE1" <-> "OE2" Residue "E ARG 641": "NH1" <-> "NH2" Residue "E ARG 668": "NH1" <-> "NH2" Residue "E PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 351": "OD1" <-> "OD2" Residue "F ASP 352": "OD1" <-> "OD2" Residue "F ARG 387": "NH1" <-> "NH2" Residue "F ARG 402": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "F TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 463": "OE1" <-> "OE2" Residue "F ASP 480": "OD1" <-> "OD2" Residue "F GLU 506": "OE1" <-> "OE2" Residue "F ARG 550": "NH1" <-> "NH2" Residue "F GLU 558": "OE1" <-> "OE2" Residue "F ARG 641": "NH1" <-> "NH2" Residue "F ARG 668": "NH1" <-> "NH2" Residue "F PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 351": "OD1" <-> "OD2" Residue "G ASP 352": "OD1" <-> "OD2" Residue "G ARG 387": "NH1" <-> "NH2" Residue "G ARG 402": "NH1" <-> "NH2" Residue "G ARG 404": "NH1" <-> "NH2" Residue "G TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 463": "OE1" <-> "OE2" Residue "G ASP 480": "OD1" <-> "OD2" Residue "G GLU 506": "OE1" <-> "OE2" Residue "G ARG 550": "NH1" <-> "NH2" Residue "G GLU 558": "OE1" <-> "OE2" Residue "G ARG 641": "NH1" <-> "NH2" Residue "G ARG 668": "NH1" <-> "NH2" Residue "G PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 351": "OD1" <-> "OD2" Residue "H ASP 352": "OD1" <-> "OD2" Residue "H ARG 387": "NH1" <-> "NH2" Residue "H ARG 402": "NH1" <-> "NH2" Residue "H ARG 404": "NH1" <-> "NH2" Residue "H TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 463": "OE1" <-> "OE2" Residue "H ASP 480": "OD1" <-> "OD2" Residue "H GLU 506": "OE1" <-> "OE2" Residue "H ARG 550": "NH1" <-> "NH2" Residue "H GLU 558": "OE1" <-> "OE2" Residue "H ARG 641": "NH1" <-> "NH2" Residue "H ARG 668": "NH1" <-> "NH2" Residue "H PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 351": "OD1" <-> "OD2" Residue "I ASP 352": "OD1" <-> "OD2" Residue "I ARG 387": "NH1" <-> "NH2" Residue "I ARG 402": "NH1" <-> "NH2" Residue "I ARG 404": "NH1" <-> "NH2" Residue "I TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 463": "OE1" <-> "OE2" Residue "I ASP 480": "OD1" <-> "OD2" Residue "I GLU 506": "OE1" <-> "OE2" Residue "I ARG 550": "NH1" <-> "NH2" Residue "I GLU 558": "OE1" <-> "OE2" Residue "I ARG 641": "NH1" <-> "NH2" Residue "I ARG 668": "NH1" <-> "NH2" Residue "I PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24849 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2761 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain: "B" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2761 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain: "C" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2761 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain: "D" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2761 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain: "E" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2761 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain: "F" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2761 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain: "G" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2761 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain: "H" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2761 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain: "I" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2761 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Time building chain proxies: 12.66, per 1000 atoms: 0.51 Number of scatterers: 24849 At special positions: 0 Unit cell: (187.416, 185.772, 76.446, 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 72 16.00 O 4707 8.00 N 4320 7.00 C 15750 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: 9.47 Conformation dependent library (CDL) restraints added in 4.5 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6012 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 36 sheets defined 49.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER A 380 " --> pdb=" O ALA A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 479 through 495 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 503 through 514 removed outlier: 3.541A pdb=" N ALA A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.898A pdb=" N ALA A 520 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP A 542 " --> pdb=" O GLN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 4.148A pdb=" N THR A 555 " --> pdb=" O THR A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 Processing helix chain 'A' and resid 598 through 613 removed outlier: 3.677A pdb=" N SER A 608 " --> pdb=" O MET A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 644 Proline residue: A 638 - end of helix removed outlier: 3.695A pdb=" N LEU A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 659 through 670 removed outlier: 3.993A pdb=" N ARG A 665 " --> pdb=" O PRO A 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 368 Processing helix chain 'B' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER B 380 " --> pdb=" O ALA B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 380' Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 479 through 495 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 503 through 514 removed outlier: 3.542A pdb=" N ALA B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 509 " --> pdb=" O VAL B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 3.898A pdb=" N ALA B 520 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU B 521 " --> pdb=" O PRO B 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 542 removed outlier: 3.735A pdb=" N LYS B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP B 542 " --> pdb=" O GLN B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 4.150A pdb=" N THR B 555 " --> pdb=" O THR B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 Processing helix chain 'B' and resid 598 through 613 removed outlier: 3.677A pdb=" N SER B 608 " --> pdb=" O MET B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 644 Proline residue: B 638 - end of helix removed outlier: 3.695A pdb=" N LEU B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 659 through 670 removed outlier: 3.993A pdb=" N ARG B 665 " --> pdb=" O PRO B 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 368 Processing helix chain 'C' and resid 377 through 380 removed outlier: 3.763A pdb=" N SER C 380 " --> pdb=" O ALA C 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 380' Processing helix chain 'C' and resid 381 through 390 Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 479 through 495 Processing helix chain 'C' and resid 496 through 500 Processing helix chain 'C' and resid 503 through 514 removed outlier: 3.542A pdb=" N ALA C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 509 " --> pdb=" O VAL C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 524 removed outlier: 3.897A pdb=" N ALA C 520 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU C 521 " --> pdb=" O PRO C 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 535 " --> pdb=" O GLN C 531 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP C 542 " --> pdb=" O GLN C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 removed outlier: 4.149A pdb=" N THR C 555 " --> pdb=" O THR C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 577 removed outlier: 3.566A pdb=" N ASP C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 Processing helix chain 'C' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER C 608 " --> pdb=" O MET C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 644 Proline residue: C 638 - end of helix removed outlier: 3.695A pdb=" N LEU C 644 " --> pdb=" O ILE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 647 No H-bonds generated for 'chain 'C' and resid 645 through 647' Processing helix chain 'C' and resid 659 through 670 removed outlier: 3.994A pdb=" N ARG C 665 " --> pdb=" O PRO C 661 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 365 through 368 Processing helix chain 'D' and resid 377 through 380 removed outlier: 3.763A pdb=" N SER D 380 " --> pdb=" O ALA D 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 381 through 390 Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 466 through 474 Processing helix chain 'D' and resid 479 through 495 Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.543A pdb=" N ALA D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 509 " --> pdb=" O VAL D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 524 removed outlier: 3.898A pdb=" N ALA D 520 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU D 521 " --> pdb=" O PRO D 517 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 522 " --> pdb=" O LYS D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 535 " --> pdb=" O GLN D 531 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP D 542 " --> pdb=" O GLN D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 removed outlier: 4.148A pdb=" N THR D 555 " --> pdb=" O THR D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 577 removed outlier: 3.566A pdb=" N ASP D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 Processing helix chain 'D' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER D 608 " --> pdb=" O MET D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 644 Proline residue: D 638 - end of helix removed outlier: 3.696A pdb=" N LEU D 644 " --> pdb=" O ILE D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 647 No H-bonds generated for 'chain 'D' and resid 645 through 647' Processing helix chain 'D' and resid 659 through 670 removed outlier: 3.993A pdb=" N ARG D 665 " --> pdb=" O PRO D 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR D 666 " --> pdb=" O LEU D 662 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 368 Processing helix chain 'E' and resid 377 through 380 removed outlier: 3.763A pdb=" N SER E 380 " --> pdb=" O ALA E 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 466 through 474 Processing helix chain 'E' and resid 479 through 495 Processing helix chain 'E' and resid 496 through 500 Processing helix chain 'E' and resid 503 through 514 removed outlier: 3.542A pdb=" N ALA E 507 " --> pdb=" O ASP E 503 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR E 509 " --> pdb=" O VAL E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 524 removed outlier: 3.898A pdb=" N ALA E 520 " --> pdb=" O ALA E 516 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU E 521 " --> pdb=" O PRO E 517 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 522 " --> pdb=" O LYS E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 535 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP E 542 " --> pdb=" O GLN E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 560 removed outlier: 4.149A pdb=" N THR E 555 " --> pdb=" O THR E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 586 Processing helix chain 'E' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER E 608 " --> pdb=" O MET E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 644 Proline residue: E 638 - end of helix removed outlier: 3.695A pdb=" N LEU E 644 " --> pdb=" O ILE E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 647 No H-bonds generated for 'chain 'E' and resid 645 through 647' Processing helix chain 'E' and resid 659 through 670 removed outlier: 3.993A pdb=" N ARG E 665 " --> pdb=" O PRO E 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR E 666 " --> pdb=" O LEU E 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 365 through 368 Processing helix chain 'F' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER F 380 " --> pdb=" O ALA F 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 381 through 390 Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 466 through 474 Processing helix chain 'F' and resid 479 through 495 Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 503 through 514 removed outlier: 3.543A pdb=" N ALA F 507 " --> pdb=" O ASP F 503 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR F 509 " --> pdb=" O VAL F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 524 removed outlier: 3.898A pdb=" N ALA F 520 " --> pdb=" O ALA F 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU F 521 " --> pdb=" O PRO F 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 522 " --> pdb=" O LYS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 542 removed outlier: 3.735A pdb=" N LYS F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 535 " --> pdb=" O GLN F 531 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP F 542 " --> pdb=" O GLN F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 560 removed outlier: 4.149A pdb=" N THR F 555 " --> pdb=" O THR F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 586 Processing helix chain 'F' and resid 598 through 613 removed outlier: 3.677A pdb=" N SER F 608 " --> pdb=" O MET F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 644 Proline residue: F 638 - end of helix removed outlier: 3.696A pdb=" N LEU F 644 " --> pdb=" O ILE F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 647 No H-bonds generated for 'chain 'F' and resid 645 through 647' Processing helix chain 'F' and resid 659 through 670 removed outlier: 3.993A pdb=" N ARG F 665 " --> pdb=" O PRO F 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR F 666 " --> pdb=" O LEU F 662 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 353 Processing helix chain 'G' and resid 365 through 368 Processing helix chain 'G' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER G 380 " --> pdb=" O ALA G 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 377 through 380' Processing helix chain 'G' and resid 381 through 390 Processing helix chain 'G' and resid 390 through 395 Processing helix chain 'G' and resid 466 through 474 Processing helix chain 'G' and resid 479 through 495 Processing helix chain 'G' and resid 496 through 500 Processing helix chain 'G' and resid 503 through 514 removed outlier: 3.542A pdb=" N ALA G 507 " --> pdb=" O ASP G 503 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR G 509 " --> pdb=" O VAL G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 524 removed outlier: 3.899A pdb=" N ALA G 520 " --> pdb=" O ALA G 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU G 521 " --> pdb=" O PRO G 517 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA G 522 " --> pdb=" O LYS G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS G 534 " --> pdb=" O ALA G 530 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL G 535 " --> pdb=" O GLN G 531 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP G 542 " --> pdb=" O GLN G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 560 removed outlier: 4.147A pdb=" N THR G 555 " --> pdb=" O THR G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 567 through 577 removed outlier: 3.566A pdb=" N ASP G 572 " --> pdb=" O LEU G 568 " (cutoff:3.500A) Processing helix chain 'G' and resid 577 through 586 Processing helix chain 'G' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER G 608 " --> pdb=" O MET G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 629 through 644 Proline residue: G 638 - end of helix removed outlier: 3.696A pdb=" N LEU G 644 " --> pdb=" O ILE G 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 645 through 647 No H-bonds generated for 'chain 'G' and resid 645 through 647' Processing helix chain 'G' and resid 659 through 670 removed outlier: 3.994A pdb=" N ARG G 665 " --> pdb=" O PRO G 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR G 666 " --> pdb=" O LEU G 662 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 353 Processing helix chain 'H' and resid 365 through 368 Processing helix chain 'H' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER H 380 " --> pdb=" O ALA H 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 377 through 380' Processing helix chain 'H' and resid 381 through 390 Processing helix chain 'H' and resid 390 through 395 Processing helix chain 'H' and resid 466 through 474 Processing helix chain 'H' and resid 479 through 495 Processing helix chain 'H' and resid 496 through 500 Processing helix chain 'H' and resid 503 through 514 removed outlier: 3.542A pdb=" N ALA H 507 " --> pdb=" O ASP H 503 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 509 " --> pdb=" O VAL H 505 " (cutoff:3.500A) Processing helix chain 'H' and resid 516 through 524 removed outlier: 3.897A pdb=" N ALA H 520 " --> pdb=" O ALA H 516 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU H 521 " --> pdb=" O PRO H 517 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 522 " --> pdb=" O LYS H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS H 534 " --> pdb=" O ALA H 530 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL H 535 " --> pdb=" O GLN H 531 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP H 542 " --> pdb=" O GLN H 538 " (cutoff:3.500A) Processing helix chain 'H' and resid 549 through 560 removed outlier: 4.148A pdb=" N THR H 555 " --> pdb=" O THR H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP H 572 " --> pdb=" O LEU H 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 577 through 586 Processing helix chain 'H' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER H 608 " --> pdb=" O MET H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 629 through 644 Proline residue: H 638 - end of helix removed outlier: 3.696A pdb=" N LEU H 644 " --> pdb=" O ILE H 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 645 through 647 No H-bonds generated for 'chain 'H' and resid 645 through 647' Processing helix chain 'H' and resid 659 through 670 removed outlier: 3.995A pdb=" N ARG H 665 " --> pdb=" O PRO H 661 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR H 666 " --> pdb=" O LEU H 662 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 353 Processing helix chain 'I' and resid 365 through 368 Processing helix chain 'I' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER I 380 " --> pdb=" O ALA I 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 377 through 380' Processing helix chain 'I' and resid 381 through 390 Processing helix chain 'I' and resid 390 through 395 Processing helix chain 'I' and resid 466 through 474 Processing helix chain 'I' and resid 479 through 495 Processing helix chain 'I' and resid 496 through 500 Processing helix chain 'I' and resid 503 through 514 removed outlier: 3.541A pdb=" N ALA I 507 " --> pdb=" O ASP I 503 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR I 509 " --> pdb=" O VAL I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 516 through 524 removed outlier: 3.897A pdb=" N ALA I 520 " --> pdb=" O ALA I 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU I 521 " --> pdb=" O PRO I 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA I 522 " --> pdb=" O LYS I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS I 534 " --> pdb=" O ALA I 530 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL I 535 " --> pdb=" O GLN I 531 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP I 542 " --> pdb=" O GLN I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 549 through 560 removed outlier: 4.149A pdb=" N THR I 555 " --> pdb=" O THR I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP I 572 " --> pdb=" O LEU I 568 " (cutoff:3.500A) Processing helix chain 'I' and resid 577 through 586 Processing helix chain 'I' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER I 608 " --> pdb=" O MET I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 629 through 644 Proline residue: I 638 - end of helix removed outlier: 3.695A pdb=" N LEU I 644 " --> pdb=" O ILE I 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 645 through 647 No H-bonds generated for 'chain 'I' and resid 645 through 647' Processing helix chain 'I' and resid 659 through 670 removed outlier: 3.994A pdb=" N ARG I 665 " --> pdb=" O PRO I 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR I 666 " --> pdb=" O LEU I 662 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 402 through 404 removed outlier: 6.660A pdb=" N LEU A 359 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG A 404 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU A 361 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR A 414 " --> pdb=" O GLN A 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN A 425 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 416 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA A 459 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 434 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 592 through 594 Processing sheet with id=AA4, first strand: chain 'A' and resid 653 through 654 removed outlier: 5.814A pdb=" N LEU A 653 " --> pdb=" O LEU A 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 402 through 404 removed outlier: 6.661A pdb=" N LEU B 359 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ARG B 404 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU B 361 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR B 414 " --> pdb=" O GLN B 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN B 425 " --> pdb=" O TYR B 414 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 416 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 448 through 451 removed outlier: 3.811A pdb=" N ALA B 459 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 434 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 592 through 594 Processing sheet with id=AA8, first strand: chain 'B' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU B 653 " --> pdb=" O LEU B 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 402 through 404 removed outlier: 6.659A pdb=" N LEU C 359 " --> pdb=" O ARG C 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG C 404 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU C 361 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR C 414 " --> pdb=" O GLN C 425 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN C 425 " --> pdb=" O TYR C 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 416 " --> pdb=" O ILE C 423 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA C 459 " --> pdb=" O GLY C 450 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C 434 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 592 through 594 Processing sheet with id=AB3, first strand: chain 'C' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU C 653 " --> pdb=" O LEU C 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 402 through 404 removed outlier: 6.660A pdb=" N LEU D 359 " --> pdb=" O ARG D 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG D 404 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU D 361 " --> pdb=" O ARG D 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR D 414 " --> pdb=" O GLN D 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN D 425 " --> pdb=" O TYR D 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE D 416 " --> pdb=" O ILE D 423 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 448 through 451 removed outlier: 3.811A pdb=" N ALA D 459 " --> pdb=" O GLY D 450 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET D 434 " --> pdb=" O VAL D 478 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 592 through 594 Processing sheet with id=AB7, first strand: chain 'D' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU D 653 " --> pdb=" O LEU D 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 402 through 404 removed outlier: 6.659A pdb=" N LEU E 359 " --> pdb=" O ARG E 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG E 404 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU E 361 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR E 414 " --> pdb=" O GLN E 425 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN E 425 " --> pdb=" O TYR E 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE E 416 " --> pdb=" O ILE E 423 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA E 459 " --> pdb=" O GLY E 450 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET E 434 " --> pdb=" O VAL E 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 592 through 594 Processing sheet with id=AC2, first strand: chain 'E' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU E 653 " --> pdb=" O LEU E 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 402 through 404 removed outlier: 6.659A pdb=" N LEU F 359 " --> pdb=" O ARG F 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG F 404 " --> pdb=" O LEU F 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU F 361 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR F 414 " --> pdb=" O GLN F 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN F 425 " --> pdb=" O TYR F 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE F 416 " --> pdb=" O ILE F 423 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA F 459 " --> pdb=" O GLY F 450 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET F 434 " --> pdb=" O VAL F 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 592 through 594 Processing sheet with id=AC6, first strand: chain 'F' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU F 653 " --> pdb=" O LEU F 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 402 through 404 removed outlier: 6.659A pdb=" N LEU G 359 " --> pdb=" O ARG G 402 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG G 404 " --> pdb=" O LEU G 359 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU G 361 " --> pdb=" O ARG G 404 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR G 414 " --> pdb=" O GLN G 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN G 425 " --> pdb=" O TYR G 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE G 416 " --> pdb=" O ILE G 423 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA G 459 " --> pdb=" O GLY G 450 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET G 434 " --> pdb=" O VAL G 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 592 through 594 Processing sheet with id=AD1, first strand: chain 'G' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU G 653 " --> pdb=" O LEU G 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 402 through 404 removed outlier: 6.660A pdb=" N LEU H 359 " --> pdb=" O ARG H 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG H 404 " --> pdb=" O LEU H 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU H 361 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR H 414 " --> pdb=" O GLN H 425 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN H 425 " --> pdb=" O TYR H 414 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE H 416 " --> pdb=" O ILE H 423 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 448 through 451 removed outlier: 3.811A pdb=" N ALA H 459 " --> pdb=" O GLY H 450 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET H 434 " --> pdb=" O VAL H 478 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 592 through 594 Processing sheet with id=AD5, first strand: chain 'H' and resid 653 through 654 removed outlier: 5.814A pdb=" N LEU H 653 " --> pdb=" O LEU H 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'I' and resid 402 through 404 removed outlier: 6.661A pdb=" N LEU I 359 " --> pdb=" O ARG I 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG I 404 " --> pdb=" O LEU I 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU I 361 " --> pdb=" O ARG I 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR I 414 " --> pdb=" O GLN I 425 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN I 425 " --> pdb=" O TYR I 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE I 416 " --> pdb=" O ILE I 423 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA I 459 " --> pdb=" O GLY I 450 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET I 434 " --> pdb=" O VAL I 478 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 592 through 594 Processing sheet with id=AD9, first strand: chain 'I' and resid 653 through 654 removed outlier: 5.814A pdb=" N LEU I 653 " --> pdb=" O LEU I 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 972 hydrogen bonds defined for protein. 2700 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: 8.23 Time building geometry restraints manager: 10.28 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: 8485 1.34 - 1.45: 3269 1.45 - 1.57: 13365 1.57 - 1.69: 0 1.69 - 1.80: 135 Bond restraints: 25254 Sorted by residual: bond pdb=" CA ASN D 389 " pdb=" C ASN D 389 " ideal model delta sigma weight residual 1.522 1.456 0.066 1.72e-02 3.38e+03 1.45e+01 bond pdb=" CA ASN E 389 " pdb=" C ASN E 389 " ideal model delta sigma weight residual 1.522 1.456 0.065 1.72e-02 3.38e+03 1.45e+01 bond pdb=" CA ASN H 389 " pdb=" C ASN H 389 " ideal model delta sigma weight residual 1.522 1.456 0.065 1.72e-02 3.38e+03 1.44e+01 bond pdb=" CA ASN B 389 " pdb=" C ASN B 389 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.72e-02 3.38e+03 1.43e+01 bond pdb=" CA ASN G 389 " pdb=" C ASN G 389 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.72e-02 3.38e+03 1.43e+01 ... (remaining 25249 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.72: 875 106.72 - 113.52: 14865 113.52 - 120.33: 9208 120.33 - 127.13: 9142 127.13 - 133.93: 281 Bond angle restraints: 34371 Sorted by residual: angle pdb=" N ASP F 345 " pdb=" CA ASP F 345 " pdb=" C ASP F 345 " ideal model delta sigma weight residual 112.97 106.14 6.83 1.06e+00 8.90e-01 4.15e+01 angle pdb=" N ASP G 345 " pdb=" CA ASP G 345 " pdb=" C ASP G 345 " ideal model delta sigma weight residual 112.97 106.14 6.83 1.06e+00 8.90e-01 4.15e+01 angle pdb=" N ASP I 345 " pdb=" CA ASP I 345 " pdb=" C ASP I 345 " ideal model delta sigma weight residual 112.97 106.17 6.80 1.06e+00 8.90e-01 4.12e+01 angle pdb=" N ASP B 345 " pdb=" CA ASP B 345 " pdb=" C ASP B 345 " ideal model delta sigma weight residual 112.97 106.17 6.80 1.06e+00 8.90e-01 4.12e+01 angle pdb=" N ASP E 345 " pdb=" CA ASP E 345 " pdb=" C ASP E 345 " ideal model delta sigma weight residual 112.97 106.19 6.78 1.06e+00 8.90e-01 4.10e+01 ... (remaining 34366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.75: 13276 14.75 - 29.49: 1673 29.49 - 44.24: 558 44.24 - 58.99: 99 58.99 - 73.73: 45 Dihedral angle restraints: 15651 sinusoidal: 6390 harmonic: 9261 Sorted by residual: dihedral pdb=" CA GLY G 420 " pdb=" C GLY G 420 " pdb=" N GLU G 421 " pdb=" CA GLU G 421 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLY H 420 " pdb=" C GLY H 420 " pdb=" N GLU H 421 " pdb=" CA GLU H 421 " ideal model delta harmonic sigma weight residual -180.00 -153.47 -26.53 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLY I 420 " pdb=" C GLY I 420 " pdb=" N GLU I 421 " pdb=" CA GLU I 421 " ideal model delta harmonic sigma weight residual -180.00 -153.48 -26.52 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 15648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2082 0.035 - 0.070: 1315 0.070 - 0.106: 527 0.106 - 0.141: 126 0.141 - 0.176: 36 Chirality restraints: 4086 Sorted by residual: chirality pdb=" CA ASN E 389 " pdb=" N ASN E 389 " pdb=" C ASN E 389 " pdb=" CB ASN E 389 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA ASN G 389 " pdb=" N ASN G 389 " pdb=" C ASN G 389 " pdb=" CB ASN G 389 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA ASN B 389 " pdb=" N ASN B 389 " pdb=" C ASN B 389 " pdb=" CB ASN B 389 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.57e-01 ... (remaining 4083 not shown) Planarity restraints: 4509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 391 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C SER E 391 " -0.036 2.00e-02 2.50e+03 pdb=" O SER E 391 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU E 392 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 391 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C SER H 391 " 0.035 2.00e-02 2.50e+03 pdb=" O SER H 391 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU H 392 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 391 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C SER D 391 " -0.035 2.00e-02 2.50e+03 pdb=" O SER D 391 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU D 392 " 0.012 2.00e-02 2.50e+03 ... (remaining 4506 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2627 2.72 - 3.27: 27081 3.27 - 3.81: 39793 3.81 - 4.36: 49396 4.36 - 4.90: 79948 Nonbonded interactions: 198845 Sorted by model distance: nonbonded pdb=" O HIS H 502 " pdb=" ND1 HIS H 502 " model vdw 2.177 2.520 nonbonded pdb=" O HIS I 502 " pdb=" ND1 HIS I 502 " model vdw 2.177 2.520 nonbonded pdb=" O HIS E 502 " pdb=" ND1 HIS E 502 " model vdw 2.178 2.520 nonbonded pdb=" O HIS A 502 " pdb=" ND1 HIS A 502 " model vdw 2.178 2.520 nonbonded pdb=" O HIS C 502 " pdb=" ND1 HIS C 502 " model vdw 2.178 2.520 ... (remaining 198840 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' } 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: 5.340 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: 17.350 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 63.930 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.180 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 : 0.010 0.066 25254 Z= 0.626 Angle : 0.890 7.978 34371 Z= 0.472 Chirality : 0.051 0.176 4086 Planarity : 0.005 0.040 4509 Dihedral : 14.934 73.735 9639 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.77 % Favored : 85.94 % Rotamer: Outliers : 0.66 % Allowed : 12.17 % Favored : 87.18 % 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: -5.40 (0.11), residues: 3159 helix: -3.63 (0.09), residues: 1467 sheet: -2.85 (0.17), residues: 558 loop : -3.55 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 350 HIS 0.004 0.001 HIS B 502 PHE 0.006 0.001 PHE E 633 TYR 0.015 0.002 TYR G 595 ARG 0.005 0.001 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 297 time to evaluate : 2.734 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: A 473 MET cc_start: 0.6684 (mtp) cc_final: 0.6358 (tpt) REVERT: A 567 ILE cc_start: 0.9387 (mp) cc_final: 0.9127 (mt) REVERT: B 473 MET cc_start: 0.6864 (mtp) cc_final: 0.6591 (tpt) REVERT: C 473 MET cc_start: 0.6878 (mtp) cc_final: 0.6437 (tpt) REVERT: D 473 MET cc_start: 0.6843 (mtp) cc_final: 0.6393 (tpt) REVERT: D 567 ILE cc_start: 0.9382 (mp) cc_final: 0.9149 (mt) REVERT: E 473 MET cc_start: 0.6936 (mtp) cc_final: 0.6515 (tpt) REVERT: F 473 MET cc_start: 0.6741 (mtp) cc_final: 0.6254 (tpt) REVERT: G 473 MET cc_start: 0.6745 (mtp) cc_final: 0.6437 (tpt) REVERT: G 567 ILE cc_start: 0.9431 (mp) cc_final: 0.9197 (mt) REVERT: H 473 MET cc_start: 0.6789 (mtp) cc_final: 0.6481 (tpt) REVERT: I 473 MET cc_start: 0.6824 (mtp) cc_final: 0.6407 (tpt) REVERT: I 567 ILE cc_start: 0.9411 (mp) cc_final: 0.9178 (mt) outliers start: 18 outliers final: 7 residues processed: 315 average time/residue: 0.3681 time to fit residues: 181.5245 Evaluate side-chains 214 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 207 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain I residue 488 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 25254 Z= 0.263 Angle : 0.709 8.535 34371 Z= 0.350 Chirality : 0.047 0.256 4086 Planarity : 0.004 0.041 4509 Dihedral : 5.759 31.115 3416 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.90 % Favored : 90.82 % Rotamer: Outliers : 3.32 % Allowed : 16.10 % Favored : 80.58 % 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: -3.49 (0.14), residues: 3159 helix: -2.07 (0.12), residues: 1548 sheet: -2.10 (0.21), residues: 558 loop : -2.45 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 461 HIS 0.002 0.001 HIS I 464 PHE 0.006 0.001 PHE B 396 TYR 0.005 0.001 TYR D 414 ARG 0.004 0.001 ARG F 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 259 time to evaluate : 3.102 Fit side-chains revert: symmetry clash REVERT: A 473 MET cc_start: 0.6626 (mtp) cc_final: 0.6035 (tpt) REVERT: A 665 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7805 (ttp-110) REVERT: D 367 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7404 (pp) REVERT: D 665 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7841 (ttp-110) REVERT: E 473 MET cc_start: 0.6782 (mtp) cc_final: 0.6195 (tpt) REVERT: E 665 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7607 (ttp80) REVERT: F 455 TYR cc_start: 0.7379 (m-10) cc_final: 0.7163 (m-10) REVERT: G 455 TYR cc_start: 0.7336 (m-10) cc_final: 0.7077 (m-10) REVERT: G 519 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9135 (tt) REVERT: G 665 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7865 (ttp-110) REVERT: I 455 TYR cc_start: 0.7414 (m-10) cc_final: 0.7209 (m-10) REVERT: I 665 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7881 (ttp-110) outliers start: 91 outliers final: 35 residues processed: 332 average time/residue: 0.3522 time to fit residues: 184.4974 Evaluate side-chains 239 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 202 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 475 TYR Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain E residue 372 ASN Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 372 ASN Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 372 ASN Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 519 LEU Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 372 ASN Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 372 ASN Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 491 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 286 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 chunk 255 optimal weight: 8.9990 chunk 284 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 ASN ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25254 Z= 0.399 Angle : 0.733 7.509 34371 Z= 0.357 Chirality : 0.048 0.163 4086 Planarity : 0.004 0.046 4509 Dihedral : 5.784 32.938 3416 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.80 % Favored : 90.91 % Rotamer: Outliers : 5.61 % Allowed : 18.98 % Favored : 75.41 % 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: -3.00 (0.15), residues: 3159 helix: -1.70 (0.12), residues: 1548 sheet: -1.80 (0.22), residues: 558 loop : -2.21 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 461 HIS 0.004 0.001 HIS A 502 PHE 0.005 0.001 PHE D 500 TYR 0.015 0.001 TYR D 455 ARG 0.004 0.000 ARG H 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 227 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 665 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7831 (ttp-110) REVERT: C 475 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.6494 (m-10) REVERT: D 367 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7472 (pp) REVERT: E 473 MET cc_start: 0.6928 (mtp) cc_final: 0.6245 (tpt) REVERT: G 533 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9080 (tt) REVERT: G 665 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7982 (ttp80) REVERT: I 665 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7883 (ttp80) outliers start: 154 outliers final: 108 residues processed: 347 average time/residue: 0.3436 time to fit residues: 189.3239 Evaluate side-chains 310 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 199 time to evaluate : 3.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ASN Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 475 TYR Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 ASN Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 372 ASN Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 480 ASP Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 372 ASN Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 480 ASP Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 365 TYR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 372 ASN Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 480 ASP Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 372 ASN Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 491 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 0.0050 chunk 215 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 287 optimal weight: 0.9990 chunk 304 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 272 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 543 GLN ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25254 Z= 0.202 Angle : 0.642 10.340 34371 Z= 0.315 Chirality : 0.044 0.241 4086 Planarity : 0.004 0.065 4509 Dihedral : 5.410 29.935 3416 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.20 % Favored : 91.52 % Rotamer: Outliers : 4.23 % Allowed : 23.10 % Favored : 72.68 % 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: -2.48 (0.15), residues: 3159 helix: -1.31 (0.13), residues: 1548 sheet: -1.63 (0.23), residues: 558 loop : -1.84 (0.21), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 461 HIS 0.002 0.001 HIS G 464 PHE 0.006 0.001 PHE D 396 TYR 0.015 0.001 TYR I 455 ARG 0.008 0.001 ARG H 665 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 248 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 619 VAL cc_start: 0.2680 (OUTLIER) cc_final: 0.2383 (t) REVERT: D 367 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7518 (pp) REVERT: D 619 VAL cc_start: 0.2800 (OUTLIER) cc_final: 0.2514 (t) REVERT: G 619 VAL cc_start: 0.2588 (OUTLIER) cc_final: 0.2288 (t) REVERT: G 665 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7881 (ttp80) REVERT: H 619 VAL cc_start: 0.2985 (OUTLIER) cc_final: 0.2771 (t) REVERT: I 619 VAL cc_start: 0.2836 (OUTLIER) cc_final: 0.2572 (t) outliers start: 116 outliers final: 80 residues processed: 333 average time/residue: 0.3333 time to fit residues: 178.3178 Evaluate side-chains 289 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 203 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ASN Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 575 CYS Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 480 ASP Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 575 CYS Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 480 ASP Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 619 VAL Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 528 ASN Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 CYS Chi-restraints excluded: chain I residue 595 TYR Chi-restraints excluded: chain I residue 619 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 226 optimal weight: 0.0980 chunk 125 optimal weight: 0.8980 chunk 259 optimal weight: 0.8980 chunk 210 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 273 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 554 ASN ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25254 Z= 0.248 Angle : 0.631 7.439 34371 Z= 0.306 Chirality : 0.044 0.193 4086 Planarity : 0.004 0.047 4509 Dihedral : 5.316 28.973 3416 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.63 % Favored : 92.09 % Rotamer: Outliers : 4.81 % Allowed : 23.17 % Favored : 72.02 % 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: -2.27 (0.15), residues: 3159 helix: -1.16 (0.13), residues: 1548 sheet: -1.49 (0.23), residues: 558 loop : -1.73 (0.21), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 461 HIS 0.002 0.001 HIS E 357 PHE 0.005 0.001 PHE I 427 TYR 0.021 0.001 TYR B 414 ARG 0.009 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 206 time to evaluate : 2.975 Fit side-chains revert: symmetry clash REVERT: C 665 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7680 (ttp80) REVERT: D 367 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7563 (pp) REVERT: F 619 VAL cc_start: 0.3043 (OUTLIER) cc_final: 0.2722 (t) REVERT: I 512 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9001 (tt) REVERT: I 518 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8431 (tppt) outliers start: 132 outliers final: 95 residues processed: 307 average time/residue: 0.3166 time to fit residues: 159.5609 Evaluate side-chains 280 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 182 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ASN Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 475 TYR Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 ASN Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 528 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 372 ASN Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 575 CYS Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 372 ASN Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 480 ASP Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 372 ASN Chi-restraints excluded: chain H residue 422 VAL Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 480 ASP Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 372 ASN Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 CYS Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 100 optimal weight: 0.0980 chunk 160 optimal weight: 3.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25254 Z= 0.334 Angle : 0.682 11.687 34371 Z= 0.326 Chirality : 0.047 0.300 4086 Planarity : 0.004 0.050 4509 Dihedral : 5.417 31.071 3416 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.14 % Favored : 91.58 % Rotamer: Outliers : 5.83 % Allowed : 22.44 % Favored : 71.73 % 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: -2.15 (0.15), residues: 3159 helix: -1.05 (0.13), residues: 1548 sheet: -1.40 (0.23), residues: 558 loop : -1.71 (0.21), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 461 HIS 0.002 0.001 HIS A 502 PHE 0.022 0.001 PHE F 670 TYR 0.019 0.001 TYR C 455 ARG 0.006 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 186 time to evaluate : 3.172 Fit side-chains revert: symmetry clash REVERT: C 475 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.6489 (m-10) REVERT: D 367 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7584 (pp) REVERT: E 512 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9080 (tp) REVERT: F 619 VAL cc_start: 0.2799 (OUTLIER) cc_final: 0.2514 (t) REVERT: G 619 VAL cc_start: 0.2509 (OUTLIER) cc_final: 0.2186 (t) REVERT: G 630 LEU cc_start: 0.7959 (mm) cc_final: 0.7706 (tp) REVERT: H 619 VAL cc_start: 0.2893 (OUTLIER) cc_final: 0.2639 (t) REVERT: I 512 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9130 (tt) outliers start: 160 outliers final: 120 residues processed: 310 average time/residue: 0.3043 time to fit residues: 159.7338 Evaluate side-chains 304 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 177 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 562 ASN Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ASN Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 475 TYR Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 ASN Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 528 ASN Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain E residue 608 SER Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 372 ASN Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 575 CYS Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 372 ASN Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 480 ASP Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 562 ASN Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 372 ASN Chi-restraints excluded: chain H residue 422 VAL Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 480 ASP Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 608 SER Chi-restraints excluded: chain H residue 619 VAL Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 365 TYR Chi-restraints excluded: chain I residue 372 ASN Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 562 ASN Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 TYR Chi-restraints excluded: chain I residue 608 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 173 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 303 optimal weight: 0.7980 chunk 190 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 GLN ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25254 Z= 0.269 Angle : 0.644 10.922 34371 Z= 0.309 Chirality : 0.045 0.260 4086 Planarity : 0.004 0.034 4509 Dihedral : 5.299 30.364 3416 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.66 % Favored : 92.05 % Rotamer: Outliers : 5.57 % Allowed : 22.91 % Favored : 71.51 % 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: -1.97 (0.16), residues: 3159 helix: -0.90 (0.13), residues: 1548 sheet: -1.35 (0.23), residues: 558 loop : -1.62 (0.21), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 461 HIS 0.002 0.001 HIS B 357 PHE 0.022 0.001 PHE F 670 TYR 0.017 0.001 TYR B 414 ARG 0.005 0.001 ARG H 665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 209 time to evaluate : 3.220 Fit side-chains REVERT: C 475 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.6329 (m-10) REVERT: C 665 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7650 (ttp80) REVERT: D 367 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7521 (pp) REVERT: D 619 VAL cc_start: 0.2447 (OUTLIER) cc_final: 0.2239 (t) REVERT: E 512 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9000 (tp) REVERT: F 619 VAL cc_start: 0.2852 (OUTLIER) cc_final: 0.2603 (t) REVERT: G 512 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8883 (tp) REVERT: G 619 VAL cc_start: 0.2482 (OUTLIER) cc_final: 0.2107 (t) REVERT: I 512 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9088 (tt) REVERT: I 619 VAL cc_start: 0.2583 (OUTLIER) cc_final: 0.2300 (t) outliers start: 153 outliers final: 107 residues processed: 330 average time/residue: 0.3102 time to fit residues: 171.4220 Evaluate side-chains 303 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 187 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ASN Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 475 TYR Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 ASN Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 528 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 372 ASN Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 562 ASN Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 575 CYS Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain F residue 680 ASN Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 372 ASN Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 480 ASP Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain G residue 680 ASN Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 372 ASN Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 480 ASP Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 680 ASN Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 365 TYR Chi-restraints excluded: chain I residue 372 ASN Chi-restraints excluded: chain I residue 433 LEU Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 TYR Chi-restraints excluded: chain I residue 619 VAL Chi-restraints excluded: chain I residue 680 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 193 optimal weight: 0.3980 chunk 206 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 238 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** D 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 472 ASN ** H 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25254 Z= 0.166 Angle : 0.623 10.415 34371 Z= 0.299 Chirality : 0.043 0.174 4086 Planarity : 0.004 0.039 4509 Dihedral : 5.027 26.709 3416 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.69 % Favored : 92.02 % Rotamer: Outliers : 4.26 % Allowed : 24.88 % Favored : 70.86 % 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: -1.68 (0.16), residues: 3159 helix: -0.65 (0.13), residues: 1548 sheet: -1.27 (0.23), residues: 558 loop : -1.44 (0.21), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 461 HIS 0.003 0.001 HIS G 502 PHE 0.020 0.001 PHE D 670 TYR 0.017 0.001 TYR H 414 ARG 0.007 0.000 ARG I 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 213 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 472 ASN cc_start: 0.8016 (m110) cc_final: 0.7799 (m-40) REVERT: C 475 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.6316 (m-10) REVERT: D 512 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8714 (tp) REVERT: D 619 VAL cc_start: 0.2122 (OUTLIER) cc_final: 0.1872 (t) REVERT: E 512 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8822 (tp) REVERT: F 619 VAL cc_start: 0.2453 (OUTLIER) cc_final: 0.2192 (t) REVERT: G 512 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8708 (tp) REVERT: G 533 LEU cc_start: 0.8841 (tt) cc_final: 0.8512 (tp) REVERT: G 619 VAL cc_start: 0.2240 (OUTLIER) cc_final: 0.1854 (t) REVERT: I 619 VAL cc_start: 0.2066 (OUTLIER) cc_final: 0.1834 (t) outliers start: 117 outliers final: 79 residues processed: 302 average time/residue: 0.3227 time to fit residues: 159.4968 Evaluate side-chains 276 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 189 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain D residue 372 ASN Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 475 TYR Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 475 TYR Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 528 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 562 ASN Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 575 CYS Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 528 ASN Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 575 CYS Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 422 VAL Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 365 TYR Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 528 ASN Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 CYS Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 TYR Chi-restraints excluded: chain I residue 619 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 chunk 282 optimal weight: 0.8980 chunk 170 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 255 optimal weight: 5.9990 chunk 267 optimal weight: 0.6980 chunk 281 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 ASN ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25254 Z= 0.269 Angle : 0.660 13.088 34371 Z= 0.315 Chirality : 0.045 0.322 4086 Planarity : 0.004 0.038 4509 Dihedral : 4.963 27.868 3404 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.31 % Favored : 92.40 % Rotamer: Outliers : 4.19 % Allowed : 25.36 % Favored : 70.46 % 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 (0.16), residues: 3159 helix: -0.58 (0.14), residues: 1548 sheet: -1.22 (0.23), residues: 558 loop : -1.46 (0.21), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 461 HIS 0.002 0.001 HIS D 502 PHE 0.027 0.001 PHE C 670 TYR 0.016 0.001 TYR B 414 ARG 0.010 0.000 ARG H 665 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 201 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 472 ASN cc_start: 0.8023 (m110) cc_final: 0.7799 (m-40) REVERT: C 475 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.6242 (m-10) REVERT: D 512 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8856 (tp) REVERT: D 619 VAL cc_start: 0.2149 (OUTLIER) cc_final: 0.1903 (t) REVERT: E 512 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8997 (tt) REVERT: F 619 VAL cc_start: 0.2555 (OUTLIER) cc_final: 0.2285 (t) REVERT: G 512 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8874 (tp) REVERT: G 533 LEU cc_start: 0.8920 (tt) cc_final: 0.8655 (tp) REVERT: G 619 VAL cc_start: 0.2262 (OUTLIER) cc_final: 0.1845 (t) REVERT: H 434 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7413 (ppp) REVERT: I 472 ASN cc_start: 0.7943 (m110) cc_final: 0.7668 (m-40) REVERT: I 619 VAL cc_start: 0.2327 (OUTLIER) cc_final: 0.2082 (t) outliers start: 115 outliers final: 96 residues processed: 288 average time/residue: 0.3022 time to fit residues: 145.9348 Evaluate side-chains 293 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 188 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 562 ASN Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 372 ASN Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 475 TYR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 ASN Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 475 TYR Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 528 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 562 ASN Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 575 CYS Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 372 ASN Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 528 ASN Chi-restraints excluded: chain G residue 562 ASN Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 372 ASN Chi-restraints excluded: chain H residue 434 MET Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 680 ASN Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 365 TYR Chi-restraints excluded: chain I residue 372 ASN Chi-restraints excluded: chain I residue 528 ASN Chi-restraints excluded: chain I residue 562 ASN Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 TYR Chi-restraints excluded: chain I residue 619 VAL Chi-restraints excluded: chain I residue 680 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 313 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 193 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 ASN F 628 ASN ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25254 Z= 0.222 Angle : 0.653 12.870 34371 Z= 0.314 Chirality : 0.044 0.255 4086 Planarity : 0.004 0.038 4509 Dihedral : 4.918 26.918 3404 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.57 % Favored : 92.15 % Rotamer: Outliers : 4.12 % Allowed : 25.43 % Favored : 70.46 % 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: -1.52 (0.16), residues: 3159 helix: -0.49 (0.14), residues: 1548 sheet: -1.19 (0.23), residues: 558 loop : -1.42 (0.21), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 461 HIS 0.002 0.000 HIS C 487 PHE 0.025 0.001 PHE C 670 TYR 0.016 0.001 TYR B 414 ARG 0.010 0.000 ARG H 665 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 201 time to evaluate : 3.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 472 ASN cc_start: 0.8039 (m110) cc_final: 0.7801 (m-40) REVERT: C 475 TYR cc_start: 0.6515 (OUTLIER) cc_final: 0.6214 (m-10) REVERT: D 512 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8804 (tp) REVERT: D 619 VAL cc_start: 0.2008 (OUTLIER) cc_final: 0.1798 (t) REVERT: F 619 VAL cc_start: 0.2477 (OUTLIER) cc_final: 0.2220 (t) REVERT: G 512 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8847 (tp) REVERT: G 533 LEU cc_start: 0.8876 (tt) cc_final: 0.8572 (tp) REVERT: G 619 VAL cc_start: 0.2066 (OUTLIER) cc_final: 0.1679 (t) REVERT: H 434 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7515 (ppp) REVERT: I 472 ASN cc_start: 0.7881 (m110) cc_final: 0.7633 (m-40) REVERT: I 512 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9008 (tt) REVERT: I 619 VAL cc_start: 0.2208 (OUTLIER) cc_final: 0.1967 (t) outliers start: 113 outliers final: 96 residues processed: 288 average time/residue: 0.3135 time to fit residues: 151.7069 Evaluate side-chains 296 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 191 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 372 ASN Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 475 TYR Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 ASN Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 475 TYR Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 528 ASN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 562 ASN Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 575 CYS Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain F residue 680 ASN Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 372 ASN Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 528 ASN Chi-restraints excluded: chain G residue 562 ASN Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 372 ASN Chi-restraints excluded: chain H residue 434 MET Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 365 TYR Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 372 ASN Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 528 ASN Chi-restraints excluded: chain I residue 562 ASN Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 TYR Chi-restraints excluded: chain I residue 619 VAL Chi-restraints excluded: chain I residue 680 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 0.9980 chunk 266 optimal weight: 0.4980 chunk 76 optimal weight: 8.9990 chunk 230 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 257 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 ASN ** F 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 554 ASN ** G 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.110359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081860 restraints weight = 55806.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.084197 restraints weight = 31577.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.085678 restraints weight = 22378.594| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25254 Z= 0.174 Angle : 0.639 13.069 34371 Z= 0.308 Chirality : 0.043 0.208 4086 Planarity : 0.004 0.040 4509 Dihedral : 4.765 23.847 3404 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.06 % Favored : 92.66 % Rotamer: Outliers : 3.68 % Allowed : 26.08 % Favored : 70.24 % 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: -1.34 (0.16), residues: 3159 helix: -0.34 (0.14), residues: 1539 sheet: -1.20 (0.22), residues: 567 loop : -1.28 (0.21), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 461 HIS 0.002 0.000 HIS G 502 PHE 0.024 0.001 PHE C 670 TYR 0.017 0.001 TYR B 414 ARG 0.010 0.000 ARG H 665 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4384.58 seconds wall clock time: 81 minutes 32.06 seconds (4892.06 seconds total)