Starting phenix.real_space_refine on Sun Nov 19 01:24:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amy_11827/11_2023/7amy_11827.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amy_11827/11_2023/7amy_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_11827/11_2023/7amy_11827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amy_11827/11_2023/7amy_11827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amy_11827/11_2023/7amy_11827.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7amy_11827/11_2023/7amy_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 12.75, 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: 9.70 Conformation dependent library (CDL) restraints added in 4.4 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: 3.15 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: 8.10 Time building geometry restraints manager: 10.40 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: 13.480 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: 0.000 Extract box with map and model: 17.280 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 64.420 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.150 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.210 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.986 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 outliers start: 18 outliers final: 7 residues processed: 315 average time/residue: 0.3623 time to fit residues: 178.6468 Evaluate side-chains 210 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 203 time to evaluate : 2.905 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2067 time to fit residues: 6.6918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 81 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 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: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 25254 Z= 0.263 Angle : 0.720 9.448 34371 Z= 0.355 Chirality : 0.048 0.315 4086 Planarity : 0.004 0.041 4509 Dihedral : 5.609 26.619 3402 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.05 % Favored : 90.66 % Rotamer: Outliers : 3.02 % Allowed : 16.47 % Favored : 80.51 % 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: -3.53 (0.14), residues: 3159 helix: -2.08 (0.12), residues: 1548 sheet: -2.12 (0.21), residues: 558 loop : -2.51 (0.19), residues: 1053 *********************** 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 344 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 261 time to evaluate : 2.645 Fit side-chains revert: symmetry clash outliers start: 83 outliers final: 28 residues processed: 328 average time/residue: 0.3653 time to fit residues: 188.6751 Evaluate side-chains 233 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 2.867 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2144 time to fit residues: 14.9921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 238 optimal weight: 5.9990 chunk 194 optimal weight: 0.2980 chunk 78 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 309 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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: 0.8371 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 25254 Z= 0.351 Angle : 0.704 7.397 34371 Z= 0.344 Chirality : 0.046 0.162 4086 Planarity : 0.004 0.045 4509 Dihedral : 5.555 25.164 3402 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.20 % Favored : 91.52 % Rotamer: Outliers : 4.15 % Allowed : 19.85 % Favored : 75.99 % 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: -2.95 (0.15), residues: 3159 helix: -1.67 (0.12), residues: 1548 sheet: -1.77 (0.22), residues: 558 loop : -2.16 (0.20), residues: 1053 *********************** 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 333 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 219 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 66 residues processed: 310 average time/residue: 0.3697 time to fit residues: 186.3999 Evaluate side-chains 261 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 195 time to evaluate : 2.985 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.2552 time to fit residues: 35.1350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 0.0170 chunk 215 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 192 optimal weight: 0.9980 chunk 287 optimal weight: 6.9990 chunk 304 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 overall best weight: 3.2024 ------------------------------------------------------------------------------- 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** F 693 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 25254 Z= 0.384 Angle : 0.723 10.610 34371 Z= 0.351 Chirality : 0.048 0.308 4086 Planarity : 0.004 0.044 4509 Dihedral : 5.538 24.276 3402 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.34 % Favored : 90.38 % Rotamer: Outliers : 2.73 % Allowed : 23.46 % Favored : 73.81 % 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: -2.70 (0.15), residues: 3159 helix: -1.45 (0.13), residues: 1557 sheet: -1.62 (0.23), residues: 558 loop : -2.10 (0.21), residues: 1044 *********************** 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 299 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 224 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 43 residues processed: 281 average time/residue: 0.3386 time to fit residues: 153.8307 Evaluate side-chains 235 residues out of total 2745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 192 time to evaluate : 3.033 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2188 time to fit residues: 21.7824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.2965 > 50: distance: 100 - 104: 22.747 distance: 104 - 105: 19.524 distance: 105 - 106: 19.554 distance: 105 - 108: 33.270 distance: 106 - 107: 39.773 distance: 106 - 112: 15.706 distance: 108 - 109: 34.742 distance: 109 - 110: 12.562 distance: 109 - 111: 24.854 distance: 112 - 113: 31.268 distance: 113 - 114: 13.161 distance: 113 - 116: 19.664 distance: 114 - 115: 22.948 distance: 114 - 121: 24.112 distance: 116 - 117: 20.237 distance: 117 - 118: 26.369 distance: 118 - 119: 23.006 distance: 118 - 120: 22.719 distance: 121 - 122: 19.296 distance: 122 - 123: 15.620 distance: 122 - 125: 26.047 distance: 123 - 124: 16.158 distance: 123 - 128: 22.749 distance: 125 - 126: 28.126 distance: 125 - 127: 11.571 distance: 128 - 129: 15.364 distance: 128 - 134: 19.978 distance: 129 - 130: 30.644 distance: 129 - 132: 15.004 distance: 130 - 131: 12.242 distance: 130 - 135: 25.160 distance: 132 - 133: 16.531 distance: 133 - 134: 22.112 distance: 135 - 136: 30.940 distance: 136 - 137: 12.867 distance: 136 - 139: 13.048 distance: 137 - 138: 22.369 distance: 137 - 143: 10.885 distance: 139 - 140: 22.510 distance: 140 - 141: 28.206 distance: 140 - 142: 15.623 distance: 143 - 144: 18.965 distance: 144 - 145: 12.483 distance: 144 - 147: 16.935 distance: 145 - 146: 3.383 distance: 145 - 152: 19.655 distance: 147 - 148: 6.173 distance: 148 - 149: 15.904 distance: 150 - 151: 24.344 distance: 152 - 153: 13.222 distance: 153 - 154: 23.175 distance: 153 - 156: 18.130 distance: 154 - 155: 7.612 distance: 154 - 160: 7.337 distance: 156 - 157: 19.899 distance: 157 - 158: 24.294 distance: 157 - 159: 21.159 distance: 160 - 161: 18.247 distance: 161 - 162: 10.180 distance: 161 - 164: 5.536 distance: 162 - 163: 12.700 distance: 162 - 168: 8.959 distance: 163 - 194: 7.445 distance: 164 - 165: 15.169 distance: 164 - 166: 20.803 distance: 165 - 167: 9.838 distance: 168 - 169: 16.887 distance: 169 - 170: 39.995 distance: 169 - 172: 33.193 distance: 170 - 171: 52.297 distance: 170 - 179: 38.854 distance: 171 - 198: 32.886 distance: 172 - 173: 33.418 distance: 173 - 174: 24.826 distance: 174 - 175: 27.104 distance: 175 - 176: 18.267 distance: 176 - 177: 9.469 distance: 176 - 178: 8.463 distance: 179 - 180: 10.625 distance: 180 - 181: 28.066 distance: 180 - 183: 16.572 distance: 181 - 182: 25.097 distance: 181 - 186: 20.751 distance: 183 - 184: 6.595 distance: 183 - 185: 22.311