Starting phenix.real_space_refine on Mon Mar 18 19:20:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn2_14799/03_2024/7zn2_14799.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn2_14799/03_2024/7zn2_14799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn2_14799/03_2024/7zn2_14799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn2_14799/03_2024/7zn2_14799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn2_14799/03_2024/7zn2_14799.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn2_14799/03_2024/7zn2_14799.pdb" } resolution = 4.29 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= 0.004 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 227 5.16 5 C 56490 2.51 5 N 14939 2.21 5 O 17737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 1093": "OE1" <-> "OE2" Residue "c GLU 425": "OE1" <-> "OE2" Residue "c ASP 581": "OD1" <-> "OD2" Residue "c TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 695": "OE1" <-> "OE2" Residue "c PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 632": "OD1" <-> "OD2" Residue "e PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 303": "OD1" <-> "OD2" Residue "e TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 114": "OE1" <-> "OE2" Residue "b PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 306": "OD1" <-> "OD2" Residue "b GLU 425": "OE1" <-> "OE2" Residue "b TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 499": "OE1" <-> "OE2" Residue "b PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 4": "OE1" <-> "OE2" Residue "R GLU 95": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "a GLU 32": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 95": "OE1" <-> "OE2" Residue "S GLU 129": "OE1" <-> "OE2" Residue "N GLU 4": "OE1" <-> "OE2" Residue "N GLU 95": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "Y GLU 32": "OE1" <-> "OE2" Residue "O GLU 4": "OE1" <-> "OE2" Residue "O GLU 95": "OE1" <-> "OE2" Residue "O GLU 129": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 348": "OE1" <-> "OE2" Residue "C TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "W GLU 32": "OE1" <-> "OE2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 40": "OE1" <-> "OE2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "Z GLU 40": "OE1" <-> "OE2" Residue "Z GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 89393 Number of models: 1 Model: "" Number of chains: 36 Chain: "d" Number of atoms: 7576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7576 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 36, 'TRANS': 912} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "j" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 328 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "h" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 328 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "i" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 328 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "c" Number of atoms: 7576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7576 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 36, 'TRANS': 912} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "f" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5143 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 34, 'TRANS': 634} Chain breaks: 2 Chain: "e" Number of atoms: 5163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5163 Classifications: {'peptide': 671} Link IDs: {'PTRANS': 34, 'TRANS': 636} Chain breaks: 2 Chain: "g" Number of atoms: 4546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4546 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 26, 'TRANS': 562} Chain breaks: 2 Chain: "b" Number of atoms: 7576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7576 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 36, 'TRANS': 912} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "I" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "a" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Q" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "S" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "F" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "N" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "H" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "X" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Y" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "M" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "O" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "E" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "C" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "J" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "L" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "G" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "W" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "U" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "K" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "D" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "A" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "B" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "P" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "T" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "V" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Z" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Time building chain proxies: 35.59, per 1000 atoms: 0.40 Number of scatterers: 89393 At special positions: 0 Unit cell: (282.359, 185.087, 298.571, 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 227 16.00 O 17737 8.00 N 14939 7.00 C 56490 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS d 316 " - pdb=" SG CYS d 327 " distance=2.03 Simple disulfide: pdb=" SG CYS c 316 " - pdb=" SG CYS c 327 " distance=2.03 Simple disulfide: pdb=" SG CYS b 316 " - pdb=" SG CYS b 327 " distance=2.03 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: 27.63 Conformation dependent library (CDL) restraints added in 11.8 seconds 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21304 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 169 sheets defined 11.9% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.52 Creating SS restraints... Processing helix chain 'd' and resid 5 through 15 Processing helix chain 'd' and resid 85 through 96 Processing helix chain 'd' and resid 162 through 167 removed outlier: 3.531A pdb=" N ASP d 166 " --> pdb=" O TYR d 163 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG d 167 " --> pdb=" O ASP d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 179 Processing helix chain 'd' and resid 318 through 325 Processing helix chain 'd' and resid 338 through 343 removed outlier: 4.170A pdb=" N ALA d 342 " --> pdb=" O MET d 338 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA d 343 " --> pdb=" O HIS d 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 338 through 343' Processing helix chain 'd' and resid 380 through 389 Processing helix chain 'd' and resid 392 through 399 Processing helix chain 'd' and resid 401 through 406 removed outlier: 3.844A pdb=" N TRP d 405 " --> pdb=" O PRO d 402 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP d 406 " --> pdb=" O GLU d 403 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 470 Processing helix chain 'd' and resid 478 through 482 removed outlier: 3.501A pdb=" N PHE d 482 " --> pdb=" O LEU d 479 " (cutoff:3.500A) Processing helix chain 'd' and resid 483 through 495 Processing helix chain 'd' and resid 502 through 506 Processing helix chain 'd' and resid 509 through 513 removed outlier: 3.503A pdb=" N GLY d 513 " --> pdb=" O ARG d 510 " (cutoff:3.500A) Processing helix chain 'd' and resid 536 through 549 removed outlier: 3.525A pdb=" N SER d 547 " --> pdb=" O GLY d 543 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE d 548 " --> pdb=" O ILE d 544 " (cutoff:3.500A) Processing helix chain 'd' and resid 587 through 592 Processing helix chain 'd' and resid 616 through 623 Processing helix chain 'd' and resid 639 through 654 Processing helix chain 'd' and resid 907 through 914 removed outlier: 3.591A pdb=" N ASN d 911 " --> pdb=" O LEU d 907 " (cutoff:3.500A) Processing helix chain 'j' and resid 1105 through 1113 removed outlier: 4.121A pdb=" N LEU j1109 " --> pdb=" O SER j1105 " (cutoff:3.500A) Processing helix chain 'h' and resid 1105 through 1113 removed outlier: 4.089A pdb=" N LEU h1109 " --> pdb=" O SER h1105 " (cutoff:3.500A) Processing helix chain 'i' and resid 1105 through 1113 removed outlier: 4.108A pdb=" N LEU i1109 " --> pdb=" O SER i1105 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 15 Processing helix chain 'c' and resid 85 through 96 Processing helix chain 'c' and resid 161 through 167 removed outlier: 3.886A pdb=" N ARG c 167 " --> pdb=" O ASP c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 174 through 180 Processing helix chain 'c' and resid 318 through 325 removed outlier: 3.842A pdb=" N SER c 322 " --> pdb=" O ASP c 318 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP c 323 " --> pdb=" O GLU c 319 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR c 324 " --> pdb=" O THR c 320 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG c 325 " --> pdb=" O ASP c 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 318 through 325' Processing helix chain 'c' and resid 337 through 341 removed outlier: 3.649A pdb=" N ARG c 340 " --> pdb=" O THR c 337 " (cutoff:3.500A) Processing helix chain 'c' and resid 380 through 389 Processing helix chain 'c' and resid 392 through 399 Processing helix chain 'c' and resid 459 through 468 Processing helix chain 'c' and resid 478 through 482 Processing helix chain 'c' and resid 483 through 494 Processing helix chain 'c' and resid 509 through 513 removed outlier: 3.862A pdb=" N GLY c 513 " --> pdb=" O ARG c 510 " (cutoff:3.500A) Processing helix chain 'c' and resid 536 through 549 removed outlier: 3.541A pdb=" N SER c 547 " --> pdb=" O GLY c 543 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE c 548 " --> pdb=" O ILE c 544 " (cutoff:3.500A) Processing helix chain 'c' and resid 576 through 578 No H-bonds generated for 'chain 'c' and resid 576 through 578' Processing helix chain 'c' and resid 587 through 592 Processing helix chain 'c' and resid 616 through 623 Processing helix chain 'c' and resid 639 through 654 Processing helix chain 'c' and resid 665 through 669 Processing helix chain 'c' and resid 907 through 913 Processing helix chain 'c' and resid 914 through 921 removed outlier: 3.676A pdb=" N LEU c 918 " --> pdb=" O ASP c 914 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 90 Processing helix chain 'f' and resid 258 through 264 Processing helix chain 'f' and resid 302 through 305 Processing helix chain 'f' and resid 325 through 330 removed outlier: 3.639A pdb=" N ASN f 329 " --> pdb=" O ASN f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 579 through 592 Processing helix chain 'f' and resid 661 through 667 Processing helix chain 'f' and resid 669 through 673 Processing helix chain 'e' and resid 83 through 90 Processing helix chain 'e' and resid 258 through 264 Processing helix chain 'e' and resid 325 through 330 Processing helix chain 'e' and resid 579 through 591 Processing helix chain 'e' and resid 662 through 668 Processing helix chain 'g' and resid 83 through 90 Processing helix chain 'g' and resid 258 through 265 Processing helix chain 'g' and resid 302 through 305 Processing helix chain 'g' and resid 325 through 330 removed outlier: 4.353A pdb=" N ASN g 329 " --> pdb=" O ASN g 325 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU g 330 " --> pdb=" O SER g 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 325 through 330' Processing helix chain 'g' and resid 579 through 591 removed outlier: 3.722A pdb=" N ALA g 583 " --> pdb=" O ASN g 579 " (cutoff:3.500A) Processing helix chain 'g' and resid 661 through 667 Processing helix chain 'g' and resid 669 through 673 removed outlier: 3.580A pdb=" N GLY g 672 " --> pdb=" O ASN g 669 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 15 Processing helix chain 'b' and resid 85 through 96 Processing helix chain 'b' and resid 161 through 166 removed outlier: 3.543A pdb=" N ASP b 166 " --> pdb=" O TYR b 163 " (cutoff:3.500A) Processing helix chain 'b' and resid 174 through 180 Processing helix chain 'b' and resid 196 through 202 removed outlier: 3.669A pdb=" N GLN b 200 " --> pdb=" O PRO b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 318 through 326 Processing helix chain 'b' and resid 338 through 343 removed outlier: 4.361A pdb=" N ALA b 342 " --> pdb=" O MET b 338 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA b 343 " --> pdb=" O HIS b 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 338 through 343' Processing helix chain 'b' and resid 380 through 389 Processing helix chain 'b' and resid 392 through 399 Processing helix chain 'b' and resid 401 through 410 removed outlier: 4.035A pdb=" N TRP b 405 " --> pdb=" O PRO b 402 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP b 406 " --> pdb=" O GLU b 403 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N SER b 407 " --> pdb=" O TYR b 404 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG b 408 " --> pdb=" O TRP b 405 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS b 410 " --> pdb=" O SER b 407 " (cutoff:3.500A) Processing helix chain 'b' and resid 459 through 469 Processing helix chain 'b' and resid 478 through 482 removed outlier: 3.649A pdb=" N PHE b 482 " --> pdb=" O LEU b 479 " (cutoff:3.500A) Processing helix chain 'b' and resid 483 through 494 Processing helix chain 'b' and resid 502 through 506 removed outlier: 3.578A pdb=" N GLN b 506 " --> pdb=" O THR b 503 " (cutoff:3.500A) Processing helix chain 'b' and resid 509 through 513 removed outlier: 3.509A pdb=" N GLY b 513 " --> pdb=" O ARG b 510 " (cutoff:3.500A) Processing helix chain 'b' and resid 536 through 549 removed outlier: 3.587A pdb=" N SER b 547 " --> pdb=" O GLY b 543 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE b 548 " --> pdb=" O ILE b 544 " (cutoff:3.500A) Processing helix chain 'b' and resid 587 through 592 Processing helix chain 'b' and resid 603 through 606 Processing helix chain 'b' and resid 616 through 623 Processing helix chain 'b' and resid 639 through 654 Processing helix chain 'b' and resid 682 through 685 Processing helix chain 'b' and resid 724 through 729 Processing helix chain 'b' and resid 907 through 914 Processing helix chain 'b' and resid 915 through 921 Processing helix chain 'R' and resid 3 through 7 removed outlier: 3.971A pdb=" N VAL R 7 " --> pdb=" O GLU R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 92 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 76 through 83 Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.596A pdb=" N ILE I 204 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 16 Processing helix chain 'a' and resid 58 through 76 Processing helix chain 'a' and resid 83 through 87 Processing helix chain 'Q' and resid 81 through 91 Processing helix chain 'S' and resid 81 through 92 removed outlier: 3.653A pdb=" N LYS S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 7 No H-bonds generated for 'chain 'F' and resid 5 through 7' Processing helix chain 'F' and resid 91 through 100 Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 192 through 201 Processing helix chain 'F' and resid 275 through 287 removed outlier: 3.521A pdb=" N LEU F 287 " --> pdb=" O LEU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 346 removed outlier: 4.254A pdb=" N GLY F 346 " --> pdb=" O LEU F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 369 Processing helix chain 'N' and resid 3 through 7 removed outlier: 3.973A pdb=" N VAL N 7 " --> pdb=" O GLU N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 92 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 76 through 83 Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.596A pdb=" N ILE H 204 " --> pdb=" O ILE H 201 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 76 Processing helix chain 'Y' and resid 12 through 16 Processing helix chain 'Y' and resid 58 through 76 Processing helix chain 'Y' and resid 83 through 87 Processing helix chain 'M' and resid 81 through 91 Processing helix chain 'O' and resid 81 through 92 removed outlier: 3.654A pdb=" N LYS O 91 " --> pdb=" O THR O 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 7 No H-bonds generated for 'chain 'E' and resid 5 through 7' Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'E' and resid 185 through 190 Processing helix chain 'E' and resid 192 through 201 Processing helix chain 'E' and resid 275 through 287 removed outlier: 3.520A pdb=" N LEU E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 346 removed outlier: 4.257A pdb=" N GLY E 346 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 369 Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.685A pdb=" N TRP C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.829A pdb=" N ILE C 189 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'J' and resid 3 through 7 removed outlier: 3.972A pdb=" N VAL J 7 " --> pdb=" O GLU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 92 Processing helix chain 'L' and resid 81 through 91 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 76 through 83 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.594A pdb=" N ILE G 204 " --> pdb=" O ILE G 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 16 Processing helix chain 'W' and resid 58 through 76 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'U' and resid 81 through 91 Processing helix chain 'K' and resid 81 through 92 removed outlier: 3.654A pdb=" N LYS K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 7 No H-bonds generated for 'chain 'D' and resid 5 through 7' Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.521A pdb=" N LEU D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 removed outlier: 4.255A pdb=" N GLY D 346 " --> pdb=" O LEU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 369 Processing helix chain 'A' and resid 91 through 100 removed outlier: 3.687A pdb=" N TRP A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.829A pdb=" N ILE A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'B' and resid 91 through 100 removed outlier: 3.684A pdb=" N TRP B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.829A pdb=" N ILE B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'P' and resid 81 through 91 Processing helix chain 'T' and resid 81 through 91 Processing helix chain 'V' and resid 58 through 76 Processing helix chain 'Z' and resid 58 through 76 Processing sheet with id=AA1, first strand: chain 'd' and resid 17 through 28 removed outlier: 4.515A pdb=" N THR d 37 " --> pdb=" O LEU d 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 37 through 42 current: chain 'd' and resid 76 through 82 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 76 through 82 current: chain 'd' and resid 128 through 143 removed outlier: 5.587A pdb=" N ILE d 135 " --> pdb=" O SER d 159 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER d 159 " --> pdb=" O ILE d 135 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY d 137 " --> pdb=" O ASN d 157 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL d 153 " --> pdb=" O LYS d 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 151 through 160 current: chain 'b' and resid 658 through 664 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 658 through 664 current: chain 'b' and resid 686 through 698 removed outlier: 6.641A pdb=" N VAL b 707 " --> pdb=" O ASP b 694 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL b 696 " --> pdb=" O ASN b 705 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN b 705 " --> pdb=" O VAL b 696 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 704 through 710 current: chain 'a' and resid 38 through 41 Processing sheet with id=AA2, first strand: chain 'd' and resid 48 through 50 Processing sheet with id=AA3, first strand: chain 'd' and resid 66 through 69 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 66 through 69 current: chain 'd' and resid 658 through 664 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 658 through 664 current: chain 'd' and resid 686 through 698 removed outlier: 5.638A pdb=" N VAL d 693 " --> pdb=" O GLN d 709 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN d 709 " --> pdb=" O VAL d 693 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 704 through 709 current: chain 'c' and resid 38 through 42 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 38 through 42 current: chain 'c' and resid 53 through 57 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 53 through 57 current: chain 'c' and resid 76 through 82 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 76 through 82 current: chain 'c' and resid 128 through 135 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 128 through 135 current: chain 'c' and resid 151 through 159 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 151 through 159 current: chain 'Y' and resid 38 through 41 Processing sheet with id=AA4, first strand: chain 'd' and resid 210 through 213 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 210 through 213 current: chain 'd' and resid 249 through 259 WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 1086 through 1091 current: chain 'j' and resid 1123 through 1125 Processing sheet with id=AA5, first strand: chain 'd' and resid 225 through 226 removed outlier: 4.402A pdb=" N TYR d 225 " --> pdb=" O LYS d 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'd' and resid 266 through 267 Processing sheet with id=AA7, first strand: chain 'd' and resid 270 through 274 removed outlier: 3.536A pdb=" N ASP d 306 " --> pdb=" O GLU d 436 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLN d 438 " --> pdb=" O PHE d 304 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE d 304 " --> pdb=" O GLN d 438 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 277 through 282 removed outlier: 6.413A pdb=" N ALA d 295 " --> pdb=" O PRO d 277 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE d 279 " --> pdb=" O VAL d 293 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA d 415 " --> pdb=" O PHE d 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'd' and resid 444 through 445 Processing sheet with id=AB1, first strand: chain 'd' and resid 550 through 554 Processing sheet with id=AB2, first strand: chain 'd' and resid 595 through 602 removed outlier: 3.857A pdb=" N LYS d 608 " --> pdb=" O ASP d 602 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL i1098 " --> pdb=" O SER d 611 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR d 613 " --> pdb=" O VAL i1098 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 742 through 745 removed outlier: 3.655A pdb=" N LYS d 743 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER d 762 " --> pdb=" O LYS d 743 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR d 745 " --> pdb=" O GLU d 760 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU d 760 " --> pdb=" O THR d 745 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP d 763 " --> pdb=" O MET d 798 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'd' and resid 785 through 788 removed outlier: 3.685A pdb=" N ALA d 777 " --> pdb=" O GLU d 813 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU d 813 " --> pdb=" O ALA d 777 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA d 810 " --> pdb=" O VAL d 831 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL d 831 " --> pdb=" O ALA d 810 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL d 827 " --> pdb=" O LEU d 814 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 845 through 847 Processing sheet with id=AB6, first strand: chain 'd' and resid 892 through 898 removed outlier: 3.532A pdb=" N ARG d 894 " --> pdb=" O ILE d 885 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG d 932 " --> pdb=" O GLU d 884 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'j' and resid 1097 through 1099 removed outlier: 4.262A pdb=" N LYS b 608 " --> pdb=" O ASP b 602 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'h' and resid 1086 through 1092 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 1086 through 1092 current: chain 'b' and resid 249 through 258 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'h' and resid 1097 through 1099 Processing sheet with id=AC1, first strand: chain 'h' and resid 1118 through 1120 Processing sheet with id=AC2, first strand: chain 'i' and resid 1086 through 1087 removed outlier: 3.506A pdb=" N GLN i1087 " --> pdb=" O GLU c 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'i' and resid 1090 through 1092 removed outlier: 6.322A pdb=" N LEU i1091 " --> pdb=" O ASN c 258 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'i' and resid 1118 through 1119 Processing sheet with id=AC5, first strand: chain 'c' and resid 66 through 69 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 66 through 69 current: chain 'c' and resid 657 through 664 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 657 through 664 current: chain 'c' and resid 686 through 698 removed outlier: 7.285A pdb=" N PHE c 690 " --> pdb=" O TYR c 711 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR c 711 " --> pdb=" O PHE c 690 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL c 707 " --> pdb=" O ASP c 694 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL c 696 " --> pdb=" O ASN c 705 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN c 705 " --> pdb=" O VAL c 696 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 704 through 711 current: chain 'b' and resid 37 through 42 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 37 through 42 current: chain 'b' and resid 53 through 57 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 53 through 57 current: chain 'b' and resid 76 through 82 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 76 through 82 current: chain 'b' and resid 128 through 143 removed outlier: 4.429A pdb=" N ASN b 157 " --> pdb=" O THR b 136 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY b 138 " --> pdb=" O THR b 155 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR b 155 " --> pdb=" O GLY b 138 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE b 140 " --> pdb=" O VAL b 153 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL b 153 " --> pdb=" O ILE b 140 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP b 142 " --> pdb=" O THR b 151 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR b 151 " --> pdb=" O ASP b 142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG X 30 " --> pdb=" O GLY b 150 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER b 152 " --> pdb=" O ARG X 30 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLU X 32 " --> pdb=" O SER b 152 " (cutoff:3.500A) removed outlier: 12.057A pdb=" N ILE b 154 " --> pdb=" O GLU X 32 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 38 through 41 current: chain 'W' and resid 38 through 41 Processing sheet with id=AC6, first strand: chain 'c' and resid 265 through 268 removed outlier: 3.988A pdb=" N THR c 529 " --> pdb=" O TYR c 268 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 271 through 274 Processing sheet with id=AC8, first strand: chain 'c' and resid 276 through 282 removed outlier: 6.620A pdb=" N VAL c 293 " --> pdb=" O ILE c 278 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA c 280 " --> pdb=" O TYR c 291 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR c 291 " --> pdb=" O ALA c 280 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR c 282 " --> pdb=" O ILE c 289 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE c 289 " --> pdb=" O THR c 282 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR c 422 " --> pdb=" O ASP c 365 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP c 365 " --> pdb=" O THR c 422 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 444 through 445 Processing sheet with id=AD1, first strand: chain 'c' and resid 550 through 555 removed outlier: 3.769A pdb=" N LEU c 555 " --> pdb=" O GLU c 558 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU c 558 " --> pdb=" O LEU c 555 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 731 through 734 removed outlier: 3.672A pdb=" N GLU b 899 " --> pdb=" O ASP c 731 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE b 885 " --> pdb=" O LEU b 893 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER b 895 " --> pdb=" O LEU b 883 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU b 883 " --> pdb=" O SER b 895 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG b 897 " --> pdb=" O TYR b 881 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR b 881 " --> pdb=" O ARG b 897 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU b 899 " --> pdb=" O ILE b 879 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE b 879 " --> pdb=" O GLU b 899 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 743 through 745 Processing sheet with id=AD4, first strand: chain 'c' and resid 785 through 788 removed outlier: 4.280A pdb=" N TYR c 773 " --> pdb=" O VAL c 817 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL c 817 " --> pdb=" O TYR c 773 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU c 813 " --> pdb=" O ALA c 777 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 846 through 847 Processing sheet with id=AD6, first strand: chain 'c' and resid 893 through 899 removed outlier: 3.509A pdb=" N ILE c 885 " --> pdb=" O LEU c 893 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER c 895 " --> pdb=" O LEU c 883 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU c 883 " --> pdb=" O SER c 895 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG c 897 " --> pdb=" O TYR c 881 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR c 881 " --> pdb=" O ARG c 897 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLU c 899 " --> pdb=" O ILE c 879 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE c 879 " --> pdb=" O GLU c 899 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 16 through 18 Processing sheet with id=AD8, first strand: chain 'f' and resid 46 through 52 removed outlier: 3.873A pdb=" N GLY f 36 " --> pdb=" O TYR f 78 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'f' and resid 71 through 72 removed outlier: 3.989A pdb=" N PHE f 101 " --> pdb=" O TYR f 71 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'f' and resid 108 through 116 removed outlier: 6.506A pdb=" N ASP f 131 " --> pdb=" O THR f 110 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA f 112 " --> pdb=" O TYR f 129 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR f 129 " --> pdb=" O ALA f 112 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N CYS f 114 " --> pdb=" O ILE f 127 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE f 127 " --> pdb=" O CYS f 114 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'f' and resid 153 through 157 removed outlier: 5.639A pdb=" N LYS f 155 " --> pdb=" O LEU f 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU f 143 " --> pdb=" O LYS f 155 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR f 138 " --> pdb=" O GLN f 182 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN f 182 " --> pdb=" O TYR f 138 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR f 140 " --> pdb=" O SER f 180 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'f' and resid 173 through 175 Processing sheet with id=AE4, first strand: chain 'f' and resid 217 through 222 removed outlier: 4.044A pdb=" N ASN f 217 " --> pdb=" O ASP f 239 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN f 237 " --> pdb=" O VAL f 219 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'f' and resid 250 through 257 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 271 through 274 current: chain 'f' and resid 307 through 309 Processing sheet with id=AE6, first strand: chain 'f' and resid 331 through 335 removed outlier: 6.410A pdb=" N ILE f 340 " --> pdb=" O LEU f 355 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU f 355 " --> pdb=" O ILE f 340 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY f 342 " --> pdb=" O THR f 353 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'f' and resid 376 through 379 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 384 through 387 current: chain 'f' and resid 428 through 433 removed outlier: 3.535A pdb=" N GLY f 431 " --> pdb=" O LYS f 440 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 457 through 459 current: chain 'f' and resid 627 through 629 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 627 through 629 current: chain 'f' and resid 676 through 679 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 684 through 687 current: chain 'e' and resid 339 through 346 removed outlier: 6.998A pdb=" N ILE e 340 " --> pdb=" O LEU e 355 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU e 355 " --> pdb=" O ILE e 340 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY e 342 " --> pdb=" O THR e 353 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE e 376 " --> pdb=" O ILE e 365 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 384 through 393 current: chain 'e' and resid 427 through 433 removed outlier: 3.739A pdb=" N GLY e 427 " --> pdb=" O GLY e 444 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS e 438 " --> pdb=" O ASP e 433 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 457 through 459 current: chain 'e' and resid 627 through 629 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 627 through 629 current: chain 'e' and resid 677 through 678 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 677 through 678 current: chain 'g' and resid 339 through 345 removed outlier: 3.588A pdb=" N PHE g 354 " --> pdb=" O GLY g 342 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE g 344 " --> pdb=" O GLN g 352 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLN g 352 " --> pdb=" O ILE g 344 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE g 363 " --> pdb=" O PHE g 378 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE g 376 " --> pdb=" O ILE g 365 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 384 through 387 current: chain 'g' and resid 427 through 431 removed outlier: 3.545A pdb=" N GLY g 427 " --> pdb=" O GLY g 444 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 456 through 459 current: chain 'g' and resid 627 through 629 Processing sheet with id=AE8, first strand: chain 'f' and resid 484 through 488 removed outlier: 3.877A pdb=" N TYR f 487 " --> pdb=" O ILE f 521 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE f 521 " --> pdb=" O TYR f 487 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'f' and resid 528 through 529 removed outlier: 3.556A pdb=" N GLN f 534 " --> pdb=" O ASP f 529 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'f' and resid 567 through 572 Processing sheet with id=AF2, first strand: chain 'e' and resid 12 through 17 Processing sheet with id=AF3, first strand: chain 'e' and resid 47 through 53 removed outlier: 4.024A pdb=" N ARG e 37 " --> pdb=" O PHE e 52 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'e' and resid 71 through 73 Processing sheet with id=AF5, first strand: chain 'e' and resid 109 through 113 removed outlier: 6.718A pdb=" N ASP e 131 " --> pdb=" O THR e 110 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA e 112 " --> pdb=" O TYR e 129 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR e 129 " --> pdb=" O ALA e 112 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'e' and resid 138 through 145 removed outlier: 7.056A pdb=" N CYS e 139 " --> pdb=" O VAL e 158 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL e 158 " --> pdb=" O CYS e 139 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE e 141 " --> pdb=" O TYR e 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 154 through 159 current: chain 'e' and resid 191 through 192 Processing sheet with id=AF7, first strand: chain 'e' and resid 216 through 222 removed outlier: 4.237A pdb=" N ILE e 218 " --> pdb=" O GLN e 237 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN e 237 " --> pdb=" O ILE e 218 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE e 220 " --> pdb=" O ARG e 235 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG e 235 " --> pdb=" O PHE e 220 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'e' and resid 248 through 257 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 270 through 274 current: chain 'e' and resid 308 through 309 Processing sheet with id=AF9, first strand: chain 'e' and resid 481 through 482 removed outlier: 3.514A pdb=" N GLN e 534 " --> pdb=" O ASP e 529 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 485 through 486 removed outlier: 4.005A pdb=" N PHE e 485 " --> pdb=" O CYS e 523 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS e 523 " --> pdb=" O PHE e 485 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 567 through 572 removed outlier: 3.599A pdb=" N ASP e 599 " --> pdb=" O TRP e 617 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR e 611 " --> pdb=" O LYS e 605 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 12 through 14 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 12 through 14 current: chain 'g' and resid 21 through 26 Processing sheet with id=AG4, first strand: chain 'g' and resid 46 through 53 removed outlier: 3.633A pdb=" N GLY g 36 " --> pdb=" O TYR g 78 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 108 through 116 removed outlier: 5.363A pdb=" N ILE g 109 " --> pdb=" O THR g 133 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR g 133 " --> pdb=" O ILE g 109 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'g' and resid 138 through 139 removed outlier: 3.643A pdb=" N TYR g 138 " --> pdb=" O GLN g 182 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR g 190 " --> pdb=" O LEU g 185 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'g' and resid 141 through 145 removed outlier: 7.006A pdb=" N ILE g 141 " --> pdb=" O TYR g 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 154 through 157 current: chain 'g' and resid 197 through 198 Processing sheet with id=AG8, first strand: chain 'g' and resid 217 through 223 removed outlier: 3.689A pdb=" N ASN g 217 " --> pdb=" O ASP g 239 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA g 223 " --> pdb=" O ASP g 233 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 252 through 257 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 270 through 273 current: chain 'g' and resid 307 through 309 Processing sheet with id=AH1, first strand: chain 'g' and resid 567 through 572 removed outlier: 4.170A pdb=" N LYS g 605 " --> pdb=" O THR g 611 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR g 611 " --> pdb=" O LYS g 605 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'g' and resid 675 through 678 removed outlier: 3.612A pdb=" N ILE g 678 " --> pdb=" O TYR g 684 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 266 through 268 Processing sheet with id=AH4, first strand: chain 'b' and resid 270 through 274 removed outlier: 6.552A pdb=" N GLN b 438 " --> pdb=" O PHE b 304 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE b 304 " --> pdb=" O GLN b 438 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 277 through 282 removed outlier: 6.569A pdb=" N VAL b 293 " --> pdb=" O ILE b 278 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA b 280 " --> pdb=" O TYR b 291 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR b 291 " --> pdb=" O ALA b 280 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR b 282 " --> pdb=" O ILE b 289 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE b 289 " --> pdb=" O THR b 282 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA b 415 " --> pdb=" O PHE b 296 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN b 355 " --> pdb=" O THR b 370 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 444 through 445 Processing sheet with id=AH7, first strand: chain 'b' and resid 550 through 555 removed outlier: 3.806A pdb=" N LEU b 555 " --> pdb=" O GLU b 558 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU b 558 " --> pdb=" O LEU b 555 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'b' and resid 740 through 745 removed outlier: 3.847A pdb=" N PHE b 742 " --> pdb=" O SER b 762 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER b 762 " --> pdb=" O PHE b 742 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR b 744 " --> pdb=" O GLU b 760 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU b 760 " --> pdb=" O TYR b 744 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 785 through 788 Processing sheet with id=AI1, first strand: chain 'b' and resid 845 through 847 Processing sheet with id=AI2, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.339A pdb=" N LEU R 10 " --> pdb=" O TYR R 133 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER R 135 " --> pdb=" O LEU R 10 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL R 12 " --> pdb=" O SER R 135 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL R 111 " --> pdb=" O ILE R 127 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU R 129 " --> pdb=" O TYR R 109 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR R 109 " --> pdb=" O GLU R 129 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS R 131 " --> pdb=" O GLY R 107 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY R 107 " --> pdb=" O LYS R 131 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR R 133 " --> pdb=" O LEU R 105 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU R 105 " --> pdb=" O TYR R 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER R 135 " --> pdb=" O GLN R 103 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN R 103 " --> pdb=" O SER R 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP R 110 " --> pdb=" O SER R 49 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE R 50 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.784A pdb=" N LEU R 80 " --> pdb=" O TYR R 18 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL R 75 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER R 77 " --> pdb=" O ILE R 68 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE R 68 " --> pdb=" O SER R 77 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 25 through 27 Processing sheet with id=AI5, first strand: chain 'I' and resid 2 through 3 removed outlier: 3.577A pdb=" N LYS H 230 " --> pdb=" O PHE I 2 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 9 through 15 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 18 through 21 current: chain 'I' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 62 through 68 current: chain 'I' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 90 through 92 current: chain 'I' and resid 115 through 131 removed outlier: 6.411A pdb=" N GLY I 141 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL I 127 " --> pdb=" O ASN I 139 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN I 139 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE I 129 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE I 137 " --> pdb=" O PHE I 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 137 through 143 current: chain 'I' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 177 through 178 current: chain 'I' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 213 through 227 current: chain 'I' and resid 255 through 269 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 275 through 282 current: chain 'G' and resid 52 through 59 Processing sheet with id=AI7, first strand: chain 'I' and resid 31 through 39 removed outlier: 4.643A pdb=" N SER I 33 " --> pdb=" O ASP I 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA I 57 " --> pdb=" O GLN I 35 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE I 37 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE I 55 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR I 39 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N SER I 53 " --> pdb=" O THR I 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 52 through 59 current: chain 'H' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 18 through 21 current: chain 'H' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 62 through 68 current: chain 'H' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 90 through 92 current: chain 'H' and resid 115 through 131 removed outlier: 6.408A pdb=" N GLY H 141 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 127 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN H 139 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE H 129 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE H 137 " --> pdb=" O PHE H 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 137 through 143 current: chain 'H' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 177 through 178 current: chain 'H' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 213 through 227 current: chain 'H' and resid 255 through 269 Processing sheet with id=AI8, first strand: chain 'a' and resid 79 through 81 removed outlier: 5.239A pdb=" N TRP a 48 " --> pdb=" O GLU a 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN a 25 " --> pdb=" O TYR a 47 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER a 19 " --> pdb=" O SER a 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL a 20 " --> pdb=" O LEU Z 187 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR Z 186 " --> pdb=" O SER Z 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER Z 194 " --> pdb=" O THR Z 186 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'a' and resid 92 through 93 Processing sheet with id=AJ1, first strand: chain 'a' and resid 108 through 112 removed outlier: 7.158A pdb=" N VAL a 147 " --> pdb=" O SER a 143 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER a 143 " --> pdb=" O VAL a 147 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN a 149 " --> pdb=" O PHE a 141 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE a 141 " --> pdb=" O ASN a 149 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER a 151 " --> pdb=" O THR a 139 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'a' and resid 182 through 183 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 182 through 183 current: chain 'a' and resid 193 through 194 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 193 through 194 current: chain 'V' and resid 47 through 53 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 47 through 53 current: chain 'V' and resid 173 through 177 Processing sheet with id=AJ3, first strand: chain 'Q' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU Q 10 " --> pdb=" O TYR Q 133 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N SER Q 135 " --> pdb=" O LEU Q 10 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL Q 12 " --> pdb=" O SER Q 135 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG Q 126 " --> pdb=" O ILE Q 113 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE Q 113 " --> pdb=" O ARG Q 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET Q 128 " --> pdb=" O VAL Q 111 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY Q 130 " --> pdb=" O TYR Q 109 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE Q 134 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU Q 105 " --> pdb=" O ILE Q 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA Q 62 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Q' and resid 18 through 23 removed outlier: 7.475A pdb=" N VAL Q 75 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL Q 69 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Q' and resid 25 through 28 removed outlier: 3.814A pdb=" N THR Q 35 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'S' and resid 10 through 13 removed outlier: 6.412A pdb=" N LEU S 10 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER S 135 " --> pdb=" O LEU S 10 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL S 12 " --> pdb=" O SER S 135 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL S 111 " --> pdb=" O ILE S 127 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU S 129 " --> pdb=" O TYR S 109 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR S 109 " --> pdb=" O GLU S 129 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS S 131 " --> pdb=" O GLY S 107 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY S 107 " --> pdb=" O LYS S 131 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR S 133 " --> pdb=" O LEU S 105 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU S 105 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER S 135 " --> pdb=" O GLN S 103 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN S 103 " --> pdb=" O SER S 135 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP S 110 " --> pdb=" O SER S 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER S 49 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.751A pdb=" N TYR S 18 " --> pdb=" O LEU S 80 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 26 through 28 removed outlier: 3.730A pdb=" N LYS S 37 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP S 28 " --> pdb=" O THR S 35 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 9 through 14 removed outlier: 4.239A pdb=" N ILE F 11 " --> pdb=" O ILE F 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 28 current: chain 'F' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 75 current: chain 'F' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 119 through 122 current: chain 'F' and resid 143 through 159 removed outlier: 5.644A pdb=" N ILE F 152 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN F 172 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN F 158 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG F 166 " --> pdb=" O ASN F 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 166 through 173 current: chain 'F' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 221 through 222 current: chain 'F' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 260 through 268 current: chain 'F' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 309 through 319 current: chain 'F' and resid 331 through 338 Processing sheet with id=AK1, first strand: chain 'F' and resid 40 through 44 removed outlier: 3.918A pdb=" N SER F 64 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR F 43 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN F 62 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'F' and resid 79 through 80 Processing sheet with id=AK3, first strand: chain 'F' and resid 238 through 239 Processing sheet with id=AK4, first strand: chain 'F' and resid 378 through 382 removed outlier: 3.557A pdb=" N ALA F 378 " --> pdb=" O THR F 403 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR F 380 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU F 401 " --> pdb=" O THR F 380 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'F' and resid 389 through 390 removed outlier: 3.916A pdb=" N LEU F 390 " --> pdb=" O THR F 459 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL F 440 " --> pdb=" O ILE F 458 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 396 through 397 Processing sheet with id=AK7, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.339A pdb=" N LEU N 10 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER N 135 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL N 12 " --> pdb=" O SER N 135 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL N 111 " --> pdb=" O ILE N 127 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU N 129 " --> pdb=" O TYR N 109 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR N 109 " --> pdb=" O GLU N 129 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS N 131 " --> pdb=" O GLY N 107 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY N 107 " --> pdb=" O LYS N 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR N 133 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU N 105 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER N 135 " --> pdb=" O GLN N 103 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN N 103 " --> pdb=" O SER N 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP N 110 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE N 50 " --> pdb=" O VAL N 61 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.786A pdb=" N LEU N 80 " --> pdb=" O TYR N 18 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL N 75 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER N 77 " --> pdb=" O ILE N 68 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE N 68 " --> pdb=" O SER N 77 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AL1, first strand: chain 'H' and resid 31 through 39 removed outlier: 4.643A pdb=" N SER H 33 " --> pdb=" O ASP H 59 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA H 57 " --> pdb=" O GLN H 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE H 37 " --> pdb=" O ILE H 55 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE H 55 " --> pdb=" O PHE H 37 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR H 39 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N SER H 53 " --> pdb=" O THR H 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 52 through 59 current: chain 'G' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 21 current: chain 'G' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 62 through 68 current: chain 'G' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 92 current: chain 'G' and resid 115 through 131 removed outlier: 6.407A pdb=" N GLY G 141 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL G 127 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN G 139 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE G 129 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE G 137 " --> pdb=" O PHE G 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 137 through 143 current: chain 'G' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 177 through 178 current: chain 'G' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 213 through 227 current: chain 'G' and resid 255 through 269 Processing sheet with id=AL2, first strand: chain 'X' and resid 19 through 25 removed outlier: 3.530A pdb=" N ASN X 25 " --> pdb=" O TYR X 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 47 through 53 current: chain 'X' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 197 through 202 current: chain 'W' and resid 193 through 194 Processing sheet with id=AL3, first strand: chain 'X' and resid 108 through 112 removed outlier: 6.966A pdb=" N VAL X 147 " --> pdb=" O SER X 143 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER X 143 " --> pdb=" O VAL X 147 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN X 149 " --> pdb=" O PHE X 141 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE X 141 " --> pdb=" O ASN X 149 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER X 151 " --> pdb=" O THR X 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS X 128 " --> pdb=" O VAL X 167 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'X' and resid 193 through 194 removed outlier: 3.505A pdb=" N SER X 194 " --> pdb=" O THR X 186 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR X 186 " --> pdb=" O SER X 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL Y 20 " --> pdb=" O LEU X 187 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER Y 19 " --> pdb=" O SER Y 53 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN Y 25 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP Y 48 " --> pdb=" O GLU Y 202 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'Y' and resid 92 through 93 Processing sheet with id=AL6, first strand: chain 'Y' and resid 108 through 112 removed outlier: 7.157A pdb=" N VAL Y 147 " --> pdb=" O SER Y 143 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N SER Y 143 " --> pdb=" O VAL Y 147 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN Y 149 " --> pdb=" O PHE Y 141 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE Y 141 " --> pdb=" O ASN Y 149 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER Y 151 " --> pdb=" O THR Y 139 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'Y' and resid 182 through 183 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 182 through 183 current: chain 'Y' and resid 193 through 194 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 193 through 194 current: chain 'Z' and resid 47 through 53 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 47 through 53 current: chain 'Z' and resid 173 through 177 Processing sheet with id=AL8, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.527A pdb=" N LEU M 10 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER M 135 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL M 12 " --> pdb=" O SER M 135 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG M 126 " --> pdb=" O ILE M 113 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE M 113 " --> pdb=" O ARG M 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET M 128 " --> pdb=" O VAL M 111 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY M 130 " --> pdb=" O TYR M 109 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE M 134 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU M 105 " --> pdb=" O ILE M 134 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA M 62 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'M' and resid 18 through 23 removed outlier: 7.473A pdb=" N VAL M 75 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL M 69 " --> pdb=" O VAL M 75 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'M' and resid 25 through 28 removed outlier: 3.813A pdb=" N THR M 35 " --> pdb=" O ASP M 28 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.412A pdb=" N LEU O 10 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER O 135 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL O 12 " --> pdb=" O SER O 135 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL O 111 " --> pdb=" O ILE O 127 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU O 129 " --> pdb=" O TYR O 109 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR O 109 " --> pdb=" O GLU O 129 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS O 131 " --> pdb=" O GLY O 107 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY O 107 " --> pdb=" O LYS O 131 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR O 133 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU O 105 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER O 135 " --> pdb=" O GLN O 103 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN O 103 " --> pdb=" O SER O 135 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP O 110 " --> pdb=" O SER O 49 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER O 49 " --> pdb=" O ASP O 110 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'O' and resid 18 through 23 removed outlier: 3.751A pdb=" N TYR O 18 " --> pdb=" O LEU O 80 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'O' and resid 26 through 28 removed outlier: 3.733A pdb=" N LYS O 37 " --> pdb=" O ASP O 26 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP O 28 " --> pdb=" O THR O 35 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'E' and resid 9 through 14 removed outlier: 4.239A pdb=" N ILE E 11 " --> pdb=" O ILE E 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 28 current: chain 'E' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 75 current: chain 'E' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 119 through 122 current: chain 'E' and resid 143 through 159 removed outlier: 5.644A pdb=" N ILE E 152 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN E 172 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN E 158 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG E 166 " --> pdb=" O ASN E 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 166 through 173 current: chain 'E' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 221 through 222 current: chain 'E' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 260 through 268 current: chain 'E' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 309 through 319 current: chain 'E' and resid 331 through 338 Processing sheet with id=AM6, first strand: chain 'E' and resid 40 through 44 removed outlier: 3.918A pdb=" N SER E 64 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR E 43 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN E 62 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'E' and resid 79 through 80 Processing sheet with id=AM8, first strand: chain 'E' and resid 238 through 239 Processing sheet with id=AM9, first strand: chain 'E' and resid 378 through 382 removed outlier: 3.557A pdb=" N ALA E 378 " --> pdb=" O THR E 403 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR E 380 " --> pdb=" O GLU E 401 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU E 401 " --> pdb=" O THR E 380 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'E' and resid 389 through 390 removed outlier: 3.915A pdb=" N LEU E 390 " --> pdb=" O THR E 459 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL E 440 " --> pdb=" O ILE E 458 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'E' and resid 396 through 397 Processing sheet with id=AN3, first strand: chain 'C' and resid 9 through 14 removed outlier: 3.582A pdb=" N VAL C 13 " --> pdb=" O GLN C 26 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN C 26 " --> pdb=" O VAL C 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 75 current: chain 'C' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 119 through 122 current: chain 'C' and resid 143 through 160 removed outlier: 5.714A pdb=" N ILE C 152 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN C 172 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG C 166 " --> pdb=" O ASN C 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 166 through 173 current: chain 'C' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 268 current: chain 'C' and resid 307 through 319 Processing sheet with id=AN4, first strand: chain 'C' and resid 40 through 46 removed outlier: 6.773A pdb=" N ASN C 41 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AN6, first strand: chain 'C' and resid 237 through 239 removed outlier: 4.150A pdb=" N THR C 238 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'C' and resid 378 through 382 removed outlier: 3.893A pdb=" N ALA C 378 " --> pdb=" O THR C 403 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 380 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 401 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.913A pdb=" N LEU C 390 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS C 456 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 442 " --> pdb=" O LYS C 456 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 440 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'C' and resid 395 through 397 Processing sheet with id=AO1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.338A pdb=" N LEU J 10 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER J 135 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL J 12 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL J 111 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU J 129 " --> pdb=" O TYR J 109 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR J 109 " --> pdb=" O GLU J 129 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS J 131 " --> pdb=" O GLY J 107 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY J 107 " --> pdb=" O LYS J 131 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR J 133 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU J 105 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER J 135 " --> pdb=" O GLN J 103 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN J 103 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP J 110 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE J 50 " --> pdb=" O VAL J 61 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'J' and resid 18 through 23 removed outlier: 3.784A pdb=" N LEU J 80 " --> pdb=" O TYR J 18 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL J 75 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER J 77 " --> pdb=" O ILE J 68 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE J 68 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'J' and resid 25 through 27 Processing sheet with id=AO4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.503A pdb=" N LEU L 10 " --> pdb=" O TYR L 133 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N SER L 135 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL L 12 " --> pdb=" O SER L 135 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER L 124 " --> pdb=" O ARG L 115 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ARG L 115 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG L 126 " --> pdb=" O ILE L 113 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE L 113 " --> pdb=" O ARG L 126 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET L 128 " --> pdb=" O VAL L 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL L 111 " --> pdb=" O MET L 128 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE L 134 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU L 105 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER L 49 " --> pdb=" O ASP L 110 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N PHE L 44 " --> pdb=" O ILE L 68 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE L 68 " --> pdb=" O PHE L 44 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU L 46 " --> pdb=" O THR L 66 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR L 66 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY L 48 " --> pdb=" O PHE L 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA L 62 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR L 66 " --> pdb=" O SER L 79 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER L 79 " --> pdb=" O THR L 66 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE L 68 " --> pdb=" O SER L 77 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER L 77 " --> pdb=" O ILE L 68 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AO6, first strand: chain 'W' and resid 79 through 81 removed outlier: 5.238A pdb=" N TRP W 48 " --> pdb=" O GLU W 202 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN W 25 " --> pdb=" O TYR W 47 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER W 19 " --> pdb=" O SER W 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL W 20 " --> pdb=" O LEU V 187 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR V 186 " --> pdb=" O SER V 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER V 194 " --> pdb=" O THR V 186 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'W' and resid 92 through 93 Processing sheet with id=AO8, first strand: chain 'W' and resid 108 through 112 removed outlier: 7.156A pdb=" N VAL W 147 " --> pdb=" O SER W 143 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER W 143 " --> pdb=" O VAL W 147 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN W 149 " --> pdb=" O PHE W 141 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE W 141 " --> pdb=" O ASN W 149 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER W 151 " --> pdb=" O THR W 139 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU U 10 " --> pdb=" O TYR U 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER U 135 " --> pdb=" O LEU U 10 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL U 12 " --> pdb=" O SER U 135 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG U 126 " --> pdb=" O ILE U 113 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE U 113 " --> pdb=" O ARG U 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET U 128 " --> pdb=" O VAL U 111 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY U 130 " --> pdb=" O TYR U 109 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE U 134 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU U 105 " --> pdb=" O ILE U 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA U 62 " --> pdb=" O ILE U 50 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'U' and resid 18 through 23 removed outlier: 7.474A pdb=" N VAL U 75 " --> pdb=" O VAL U 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL U 69 " --> pdb=" O VAL U 75 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.814A pdb=" N THR U 35 " --> pdb=" O ASP U 28 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.415A pdb=" N LEU K 10 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER K 135 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL K 12 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL K 111 " --> pdb=" O ILE K 127 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU K 129 " --> pdb=" O TYR K 109 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR K 109 " --> pdb=" O GLU K 129 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS K 131 " --> pdb=" O GLY K 107 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY K 107 " --> pdb=" O LYS K 131 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR K 133 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU K 105 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER K 135 " --> pdb=" O GLN K 103 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN K 103 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP K 110 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER K 49 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'K' and resid 18 through 23 removed outlier: 3.750A pdb=" N TYR K 18 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'K' and resid 26 through 28 removed outlier: 3.731A pdb=" N LYS K 37 " --> pdb=" O ASP K 26 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP K 28 " --> pdb=" O THR K 35 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'D' and resid 9 through 14 removed outlier: 4.239A pdb=" N ILE D 11 " --> pdb=" O ILE D 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 28 current: chain 'D' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 75 current: chain 'D' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 119 through 122 current: chain 'D' and resid 143 through 159 removed outlier: 5.642A pdb=" N ILE D 152 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN D 172 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN D 158 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG D 166 " --> pdb=" O ASN D 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 166 through 173 current: chain 'D' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 221 through 222 current: chain 'D' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 260 through 268 current: chain 'D' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 309 through 319 current: chain 'D' and resid 331 through 338 Processing sheet with id=AP7, first strand: chain 'D' and resid 40 through 44 removed outlier: 3.918A pdb=" N SER D 64 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR D 43 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN D 62 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'D' and resid 79 through 80 Processing sheet with id=AP9, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AQ1, first strand: chain 'D' and resid 378 through 382 removed outlier: 3.557A pdb=" N ALA D 378 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 380 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 401 " --> pdb=" O THR D 380 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.916A pdb=" N LEU D 390 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 440 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AQ4, first strand: chain 'A' and resid 9 through 14 removed outlier: 3.583A pdb=" N VAL A 13 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 26 " --> pdb=" O VAL A 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 75 current: chain 'A' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 119 through 122 current: chain 'A' and resid 143 through 160 removed outlier: 5.713A pdb=" N ILE A 152 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN A 172 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG A 166 " --> pdb=" O ASN A 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 268 current: chain 'A' and resid 307 through 319 Processing sheet with id=AQ5, first strand: chain 'A' and resid 40 through 46 removed outlier: 6.773A pdb=" N ASN A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AQ7, first strand: chain 'A' and resid 237 through 239 removed outlier: 4.150A pdb=" N THR A 238 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'A' and resid 378 through 382 removed outlier: 3.892A pdb=" N ALA A 378 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 380 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 401 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.912A pdb=" N LEU A 390 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS A 456 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 442 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 440 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'A' and resid 395 through 397 Processing sheet with id=AR2, first strand: chain 'B' and resid 9 through 14 removed outlier: 3.583A pdb=" N VAL B 13 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 26 " --> pdb=" O VAL B 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 75 current: chain 'B' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 119 through 122 current: chain 'B' and resid 143 through 160 removed outlier: 5.716A pdb=" N ILE B 152 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN B 172 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG B 166 " --> pdb=" O ASN B 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 173 current: chain 'B' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 260 through 268 current: chain 'B' and resid 307 through 319 Processing sheet with id=AR3, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.772A pdb=" N ASN B 41 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AR5, first strand: chain 'B' and resid 237 through 239 removed outlier: 4.149A pdb=" N THR B 238 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'B' and resid 378 through 382 removed outlier: 3.893A pdb=" N ALA B 378 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 380 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 401 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.914A pdb=" N LEU B 390 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS B 456 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 442 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 440 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'B' and resid 395 through 397 Processing sheet with id=AR9, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.544A pdb=" N SER P 124 " --> pdb=" O ARG P 115 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ARG P 115 " --> pdb=" O SER P 124 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG P 126 " --> pdb=" O ILE P 113 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE P 113 " --> pdb=" O ARG P 126 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET P 128 " --> pdb=" O VAL P 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL P 111 " --> pdb=" O MET P 128 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE P 134 " --> pdb=" O LEU P 105 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU P 105 " --> pdb=" O ILE P 134 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER P 49 " --> pdb=" O ASP P 110 " (cutoff:3.500A) removed outlier: 10.081A pdb=" N PHE P 44 " --> pdb=" O ILE P 68 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE P 68 " --> pdb=" O PHE P 44 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU P 46 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR P 66 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY P 48 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA P 62 " --> pdb=" O ILE P 50 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR P 66 " --> pdb=" O SER P 79 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N SER P 79 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE P 68 " --> pdb=" O SER P 77 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER P 77 " --> pdb=" O ILE P 68 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'P' and resid 25 through 26 Processing sheet with id=AS2, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.505A pdb=" N LEU T 10 " --> pdb=" O TYR T 133 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER T 135 " --> pdb=" O LEU T 10 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL T 12 " --> pdb=" O SER T 135 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER T 124 " --> pdb=" O ARG T 115 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG T 115 " --> pdb=" O SER T 124 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG T 126 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE T 113 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET T 128 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL T 111 " --> pdb=" O MET T 128 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE T 134 " --> pdb=" O LEU T 105 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU T 105 " --> pdb=" O ILE T 134 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER T 49 " --> pdb=" O ASP T 110 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N PHE T 44 " --> pdb=" O ILE T 68 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE T 68 " --> pdb=" O PHE T 44 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU T 46 " --> pdb=" O THR T 66 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N THR T 66 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY T 48 " --> pdb=" O PHE T 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA T 62 " --> pdb=" O ILE T 50 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR T 66 " --> pdb=" O SER T 79 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER T 79 " --> pdb=" O THR T 66 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE T 68 " --> pdb=" O SER T 77 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER T 77 " --> pdb=" O ILE T 68 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'T' and resid 25 through 26 Processing sheet with id=AS4, first strand: chain 'V' and resid 29 through 32 Processing sheet with id=AS5, first strand: chain 'V' and resid 108 through 112 removed outlier: 6.966A pdb=" N VAL V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER V 143 " --> pdb=" O VAL V 147 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN V 149 " --> pdb=" O PHE V 141 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE V 141 " --> pdb=" O ASN V 149 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER V 151 " --> pdb=" O THR V 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS V 128 " --> pdb=" O VAL V 167 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'Z' and resid 29 through 32 Processing sheet with id=AS7, first strand: chain 'Z' and resid 108 through 112 removed outlier: 6.966A pdb=" N VAL Z 147 " --> pdb=" O SER Z 143 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER Z 143 " --> pdb=" O VAL Z 147 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN Z 149 " --> pdb=" O PHE Z 141 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE Z 141 " --> pdb=" O ASN Z 149 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER Z 151 " --> pdb=" O THR Z 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS Z 128 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) 1854 hydrogen bonds defined for protein. 4908 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: 54.34 Time building geometry restraints manager: 30.47 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: 29369 1.34 - 1.46: 20087 1.46 - 1.58: 41297 1.58 - 1.70: 0 1.70 - 1.81: 419 Bond restraints: 91172 Sorted by residual: bond pdb=" N VAL Z 41 " pdb=" CA VAL Z 41 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.23e+00 bond pdb=" N VAL V 41 " pdb=" CA VAL V 41 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.12e+00 bond pdb=" N VAL X 41 " pdb=" CA VAL X 41 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.09e+00 bond pdb=" N VAL V 38 " pdb=" CA VAL V 38 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 7.82e+00 bond pdb=" N THR L 66 " pdb=" CA THR L 66 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.74e+00 ... (remaining 91167 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.56: 2283 106.56 - 113.46: 50324 113.46 - 120.35: 31281 120.35 - 127.25: 39241 127.25 - 134.14: 793 Bond angle restraints: 123922 Sorted by residual: angle pdb=" CA PRO T 33 " pdb=" N PRO T 33 " pdb=" CD PRO T 33 " ideal model delta sigma weight residual 112.00 105.03 6.97 1.40e+00 5.10e-01 2.48e+01 angle pdb=" CA PRO L 33 " pdb=" N PRO L 33 " pdb=" CD PRO L 33 " ideal model delta sigma weight residual 112.00 105.06 6.94 1.40e+00 5.10e-01 2.46e+01 angle pdb=" CA PRO P 33 " pdb=" N PRO P 33 " pdb=" CD PRO P 33 " ideal model delta sigma weight residual 112.00 105.08 6.92 1.40e+00 5.10e-01 2.44e+01 angle pdb=" N TYR e 487 " pdb=" CA TYR e 487 " pdb=" C TYR e 487 " ideal model delta sigma weight residual 111.71 116.95 -5.24 1.34e+00 5.57e-01 1.53e+01 angle pdb=" N TYR e 487 " pdb=" CA TYR e 487 " pdb=" CB TYR e 487 " ideal model delta sigma weight residual 111.66 105.87 5.79 1.56e+00 4.11e-01 1.38e+01 ... (remaining 123917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 49889 17.91 - 35.82: 3882 35.82 - 53.73: 596 53.73 - 71.64: 84 71.64 - 89.55: 65 Dihedral angle restraints: 54516 sinusoidal: 21233 harmonic: 33283 Sorted by residual: dihedral pdb=" CB CYS b 316 " pdb=" SG CYS b 316 " pdb=" SG CYS b 327 " pdb=" CB CYS b 327 " ideal model delta sinusoidal sigma weight residual 93.00 25.78 67.22 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS c 316 " pdb=" SG CYS c 316 " pdb=" SG CYS c 327 " pdb=" CB CYS c 327 " ideal model delta sinusoidal sigma weight residual 93.00 35.73 57.27 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS d 316 " pdb=" SG CYS d 316 " pdb=" SG CYS d 327 " pdb=" CB CYS d 327 " ideal model delta sinusoidal sigma weight residual 93.00 39.01 53.99 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 54513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 10006 0.039 - 0.077: 2522 0.077 - 0.116: 1308 0.116 - 0.155: 273 0.155 - 0.193: 17 Chirality restraints: 14126 Sorted by residual: chirality pdb=" CA ILE L 78 " pdb=" N ILE L 78 " pdb=" C ILE L 78 " pdb=" CB ILE L 78 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA ILE T 78 " pdb=" N ILE T 78 " pdb=" C ILE T 78 " pdb=" CB ILE T 78 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CA ILE P 78 " pdb=" N ILE P 78 " pdb=" C ILE P 78 " pdb=" CB ILE P 78 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 14123 not shown) Planarity restraints: 16035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 32 " 0.076 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO L 33 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO L 33 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO L 33 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR P 32 " -0.076 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO P 33 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO P 33 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO P 33 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR T 32 " -0.076 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO T 33 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO T 33 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO T 33 " -0.060 5.00e-02 4.00e+02 ... (remaining 16032 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 1257 2.62 - 3.19: 81280 3.19 - 3.76: 134619 3.76 - 4.33: 196428 4.33 - 4.90: 323708 Nonbonded interactions: 737292 Sorted by model distance: nonbonded pdb=" OG1 THR c 337 " pdb=" O GLN c 349 " model vdw 2.048 2.440 nonbonded pdb=" O VAL b 855 " pdb=" OG1 THR b 856 " model vdw 2.063 2.440 nonbonded pdb=" O ILE f 474 " pdb=" OG SER g 193 " model vdw 2.069 2.440 nonbonded pdb=" O LEU c 555 " pdb=" OG SER c 556 " model vdw 2.078 2.440 nonbonded pdb=" OD1 ASP c 302 " pdb=" NZ LYS c 441 " model vdw 2.080 2.520 ... (remaining 737287 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' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = (chain 'L' and resid 2 through 140) selection = (chain 'M' and resid 2 through 140) selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 2 through 140) selection = (chain 'Q' and resid 2 through 140) selection = chain 'R' selection = chain 'S' selection = (chain 'T' and resid 2 through 140) selection = (chain 'U' and resid 2 through 140) } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = (chain 'e' and (resid 1 through 223 or resid 232 through 469 or resid 562 throug \ h 688)) selection = (chain 'f' and (resid 1 through 469 or resid 562 through 688)) selection = (chain 'g' and (resid 1 through 223 or resid 232 through 688)) } ncs_group { reference = chain 'h' selection = chain 'i' selection = chain 'j' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.060 Extract box with map and model: 12.090 Check model and map are aligned: 0.970 Set scattering table: 0.600 Process input model: 206.100 Find NCS groups from input model: 4.530 Set up NCS constraints: 0.790 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: 0.030 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 229.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 : 0.003 0.077 91172 Z= 0.195 Angle : 0.518 7.645 123922 Z= 0.290 Chirality : 0.045 0.193 14126 Planarity : 0.004 0.111 16035 Dihedral : 13.117 89.547 33203 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: -1.30 (0.08), residues: 11397 helix: 0.51 (0.16), residues: 1145 sheet: -0.67 (0.08), residues: 3967 loop : -1.24 (0.07), residues: 6285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP e 507 HIS 0.006 0.001 HIS A 129 PHE 0.015 0.001 PHE H 92 TYR 0.022 0.001 TYR c 409 ARG 0.009 0.000 ARG F 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1777 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1777 time to evaluate : 8.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 124 THR cc_start: 0.7877 (p) cc_final: 0.7654 (t) REVERT: d 583 ASP cc_start: 0.7636 (t0) cc_final: 0.6946 (t0) REVERT: d 627 ASP cc_start: 0.8356 (t0) cc_final: 0.8126 (t0) REVERT: j 1112 LEU cc_start: 0.7993 (mp) cc_final: 0.7505 (mp) REVERT: h 1090 THR cc_start: 0.7793 (m) cc_final: 0.7350 (t) REVERT: h 1122 ASN cc_start: 0.8330 (m-40) cc_final: 0.7989 (t0) REVERT: i 1100 VAL cc_start: 0.9035 (m) cc_final: 0.8792 (p) REVERT: c 599 SER cc_start: 0.7363 (m) cc_final: 0.7040 (p) REVERT: c 790 LEU cc_start: 0.8052 (pt) cc_final: 0.7617 (pp) REVERT: c 892 MET cc_start: 0.5664 (tpt) cc_final: 0.5225 (tpt) REVERT: e 78 TYR cc_start: 0.6914 (p90) cc_final: 0.6697 (p90) REVERT: e 190 THR cc_start: 0.7697 (p) cc_final: 0.7446 (t) REVERT: g 567 MET cc_start: 0.1021 (mmt) cc_final: 0.0453 (tpt) REVERT: b 251 LYS cc_start: 0.4634 (tttt) cc_final: 0.4158 (tptt) REVERT: b 314 MET cc_start: 0.6972 (mtm) cc_final: 0.5866 (mtp) REVERT: b 368 ILE cc_start: 0.8869 (mt) cc_final: 0.8669 (mt) REVERT: b 511 TYR cc_start: 0.7476 (m-80) cc_final: 0.7042 (m-80) REVERT: b 803 ILE cc_start: 0.8098 (pt) cc_final: 0.7889 (pt) REVERT: R 127 ILE cc_start: 0.8895 (pt) cc_final: 0.8574 (pt) REVERT: R 129 GLU cc_start: 0.6593 (tt0) cc_final: 0.6187 (mt-10) REVERT: I 38 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8098 (ptmm) REVERT: I 107 MET cc_start: 0.8264 (ttp) cc_final: 0.8006 (ttm) REVERT: I 238 LEU cc_start: 0.8986 (mt) cc_final: 0.8360 (pp) REVERT: a 178 MET cc_start: 0.8355 (mmp) cc_final: 0.8066 (mmm) REVERT: Q 6 ARG cc_start: 0.5198 (mmt90) cc_final: 0.4595 (mmt180) REVERT: Q 128 MET cc_start: 0.6791 (mtp) cc_final: 0.6579 (mtt) REVERT: S 5 ASN cc_start: 0.8135 (m-40) cc_final: 0.7845 (m-40) REVERT: S 6 ARG cc_start: 0.7617 (mtm180) cc_final: 0.6487 (mmt180) REVERT: S 9 ASP cc_start: 0.7945 (m-30) cc_final: 0.7734 (p0) REVERT: S 100 ASN cc_start: 0.8958 (t0) cc_final: 0.8046 (t0) REVERT: F 63 ASP cc_start: 0.7164 (p0) cc_final: 0.6914 (t70) REVERT: F 77 LEU cc_start: 0.8306 (mt) cc_final: 0.7926 (mp) REVERT: F 91 ASP cc_start: 0.8638 (p0) cc_final: 0.8402 (p0) REVERT: F 313 VAL cc_start: 0.7776 (t) cc_final: 0.7439 (t) REVERT: N 29 ASP cc_start: 0.6942 (m-30) cc_final: 0.5705 (p0) REVERT: H 59 ASP cc_start: 0.8290 (t0) cc_final: 0.8053 (t0) REVERT: H 210 ASN cc_start: 0.7491 (m-40) cc_final: 0.7285 (m-40) REVERT: X 66 ASP cc_start: 0.7271 (p0) cc_final: 0.6977 (t0) REVERT: Y 7 TYR cc_start: 0.8066 (m-10) cc_final: 0.7241 (m-80) REVERT: M 21 LEU cc_start: 0.8563 (tp) cc_final: 0.7821 (mp) REVERT: O 9 ASP cc_start: 0.7367 (m-30) cc_final: 0.7105 (p0) REVERT: O 35 THR cc_start: 0.5659 (m) cc_final: 0.4462 (m) REVERT: O 73 GLN cc_start: 0.7340 (tp40) cc_final: 0.7017 (tp40) REVERT: O 105 LEU cc_start: 0.7956 (tp) cc_final: 0.7615 (tt) REVERT: E 206 ASN cc_start: 0.8523 (m-40) cc_final: 0.8240 (m110) REVERT: E 268 TYR cc_start: 0.6833 (m-80) cc_final: 0.6445 (m-80) REVERT: E 405 SER cc_start: 0.9072 (m) cc_final: 0.8669 (p) REVERT: C 32 ASP cc_start: 0.6997 (p0) cc_final: 0.6698 (t0) REVERT: C 156 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7679 (tm-30) REVERT: C 209 THR cc_start: 0.7986 (m) cc_final: 0.7654 (m) REVERT: C 360 THR cc_start: 0.8821 (p) cc_final: 0.8555 (t) REVERT: J 100 ASN cc_start: 0.8360 (t0) cc_final: 0.8147 (t0) REVERT: J 127 ILE cc_start: 0.8656 (pt) cc_final: 0.8288 (pt) REVERT: J 128 MET cc_start: 0.7909 (mmm) cc_final: 0.7619 (mmm) REVERT: G 32 THR cc_start: 0.8337 (p) cc_final: 0.8129 (p) REVERT: G 146 LYS cc_start: 0.7875 (tttt) cc_final: 0.7660 (ttpt) REVERT: G 218 MET cc_start: 0.7669 (mtp) cc_final: 0.7151 (mtm) REVERT: G 244 THR cc_start: 0.7719 (p) cc_final: 0.7421 (p) REVERT: W 193 TYR cc_start: 0.7379 (m-80) cc_final: 0.6912 (m-10) REVERT: U 22 MET cc_start: 0.7154 (mtp) cc_final: 0.6589 (mmp) REVERT: U 78 ILE cc_start: 0.8649 (pt) cc_final: 0.8296 (mm) REVERT: U 105 LEU cc_start: 0.8603 (tp) cc_final: 0.8370 (tt) REVERT: K 25 MET cc_start: 0.7496 (ttt) cc_final: 0.7191 (ttm) REVERT: K 46 LEU cc_start: 0.7610 (mp) cc_final: 0.7353 (mp) REVERT: K 88 ILE cc_start: 0.8193 (mt) cc_final: 0.7984 (tt) REVERT: D 83 ASN cc_start: 0.5521 (m-40) cc_final: 0.5271 (m-40) REVERT: D 160 ASP cc_start: 0.7647 (t0) cc_final: 0.6767 (t0) REVERT: D 245 MET cc_start: 0.8456 (mtp) cc_final: 0.8167 (mtp) REVERT: A 120 MET cc_start: 0.5995 (ptm) cc_final: 0.5538 (pmm) REVERT: A 136 ILE cc_start: 0.9389 (mm) cc_final: 0.9097 (tp) REVERT: A 304 ASP cc_start: 0.7381 (m-30) cc_final: 0.6854 (p0) REVERT: A 405 SER cc_start: 0.7913 (m) cc_final: 0.7550 (t) REVERT: B 156 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6402 (tm-30) REVERT: B 159 VAL cc_start: 0.8194 (t) cc_final: 0.7964 (t) REVERT: B 168 THR cc_start: 0.8033 (m) cc_final: 0.7773 (m) REVERT: B 199 ILE cc_start: 0.8895 (mt) cc_final: 0.8646 (pt) REVERT: B 217 ASP cc_start: 0.7440 (m-30) cc_final: 0.7167 (t0) REVERT: P 1 MET cc_start: 0.3625 (tpt) cc_final: 0.3341 (tpp) REVERT: P 37 LYS cc_start: 0.8519 (ptpp) cc_final: 0.8224 (tmtt) REVERT: P 91 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7870 (tppp) REVERT: V 126 LEU cc_start: 0.8484 (mt) cc_final: 0.8179 (mt) REVERT: Z 1 MET cc_start: 0.6952 (ptm) cc_final: 0.6703 (ptm) REVERT: Z 41 VAL cc_start: 0.8122 (t) cc_final: 0.7790 (t) REVERT: Z 135 VAL cc_start: 0.9071 (t) cc_final: 0.8809 (p) outliers start: 0 outliers final: 0 residues processed: 1777 average time/residue: 0.8877 time to fit residues: 2700.3288 Evaluate side-chains 720 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 720 time to evaluate : 7.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1130 random chunks: chunk 954 optimal weight: 0.0570 chunk 856 optimal weight: 5.9990 chunk 475 optimal weight: 8.9990 chunk 292 optimal weight: 7.9990 chunk 577 optimal weight: 10.0000 chunk 457 optimal weight: 0.9990 chunk 885 optimal weight: 4.9990 chunk 342 optimal weight: 10.0000 chunk 538 optimal weight: 1.9990 chunk 659 optimal weight: 7.9990 chunk 1026 optimal weight: 0.3980 overall best weight: 1.6904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 789 GLN d 820 ASN j1103 GLN j1122 ASN ** i1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 770 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 417 GLN f 448 GLN ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 291 HIS ** e 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 469 ASN g 182 GLN ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 398 ASN I 35 GLN I 49 ASN I 121 ASN I 216 ASN I 269 ASN ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN H 216 ASN E 31 GLN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 ASN G 113 ASN G 216 ASN W 108 GLN W 149 ASN K 103 GLN D 26 GLN D 31 GLN D 236 ASN B 175 GLN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 100 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 91172 Z= 0.200 Angle : 0.541 11.554 123922 Z= 0.287 Chirality : 0.046 0.260 14126 Planarity : 0.004 0.064 16035 Dihedral : 4.358 59.992 12463 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.10 % Allowed : 3.73 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.08), residues: 11397 helix: 0.66 (0.16), residues: 1158 sheet: -0.56 (0.08), residues: 4108 loop : -1.07 (0.07), residues: 6131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G 81 HIS 0.005 0.001 HIS B 113 PHE 0.038 0.001 PHE X 141 TYR 0.023 0.001 TYR f 199 ARG 0.046 0.001 ARG Z 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 947 time to evaluate : 7.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 1090 THR cc_start: 0.7813 (m) cc_final: 0.7522 (t) REVERT: h 1102 MET cc_start: 0.6008 (mtt) cc_final: 0.5788 (mtt) REVERT: h 1122 ASN cc_start: 0.8348 (m-40) cc_final: 0.7901 (t0) REVERT: i 1100 VAL cc_start: 0.9027 (m) cc_final: 0.8804 (p) REVERT: c 599 SER cc_start: 0.7406 (m) cc_final: 0.6907 (p) REVERT: c 790 LEU cc_start: 0.8098 (pt) cc_final: 0.7897 (pp) REVERT: c 892 MET cc_start: 0.6050 (tpt) cc_final: 0.5785 (tpt) REVERT: e 432 MET cc_start: 0.2924 (tpt) cc_final: 0.1189 (ttt) REVERT: e 482 GLN cc_start: 0.8255 (tm-30) cc_final: 0.8038 (tm-30) REVERT: g 1 MET cc_start: 0.2233 (mmm) cc_final: -0.0598 (ttp) REVERT: g 103 MET cc_start: 0.3599 (tpp) cc_final: 0.3109 (mmt) REVERT: b 214 ILE cc_start: 0.7777 (pt) cc_final: 0.7470 (pt) REVERT: b 246 TYR cc_start: 0.7561 (p90) cc_final: 0.7295 (p90) REVERT: b 251 LYS cc_start: 0.4664 (tttt) cc_final: 0.4178 (tptt) REVERT: b 915 PHE cc_start: 0.7810 (m-10) cc_final: 0.7604 (m-10) REVERT: R 128 MET cc_start: 0.8699 (mmm) cc_final: 0.8118 (mmm) REVERT: I 82 MET cc_start: 0.8569 (ttp) cc_final: 0.8249 (ttm) REVERT: a 78 TYR cc_start: 0.7117 (m-10) cc_final: 0.6859 (m-10) REVERT: a 80 ASP cc_start: 0.8126 (m-30) cc_final: 0.7776 (m-30) REVERT: Q 20 LEU cc_start: 0.8300 (tp) cc_final: 0.8064 (tp) REVERT: Q 25 MET cc_start: 0.5637 (tpt) cc_final: 0.5405 (tpt) REVERT: S 6 ARG cc_start: 0.7557 (mtm180) cc_final: 0.6370 (mmt180) REVERT: S 22 MET cc_start: 0.7825 (mtm) cc_final: 0.6866 (mtm) REVERT: S 26 ASP cc_start: 0.6465 (t0) cc_final: 0.6167 (t70) REVERT: S 29 ASP cc_start: 0.6073 (t0) cc_final: 0.5865 (t70) REVERT: F 91 ASP cc_start: 0.8717 (p0) cc_final: 0.8381 (p0) REVERT: H 59 ASP cc_start: 0.8422 (t0) cc_final: 0.8092 (t0) REVERT: X 31 ASP cc_start: 0.7109 (t70) cc_final: 0.6703 (m-30) REVERT: M 21 LEU cc_start: 0.8447 (tp) cc_final: 0.7932 (mp) REVERT: O 105 LEU cc_start: 0.8237 (tp) cc_final: 0.7809 (tt) REVERT: E 206 ASN cc_start: 0.8725 (m-40) cc_final: 0.8310 (m110) REVERT: E 268 TYR cc_start: 0.6857 (m-80) cc_final: 0.6513 (m-10) REVERT: E 405 SER cc_start: 0.9042 (m) cc_final: 0.8604 (p) REVERT: C 32 ASP cc_start: 0.6958 (p0) cc_final: 0.6729 (p0) REVERT: C 159 VAL cc_start: 0.6780 (t) cc_final: 0.6577 (t) REVERT: C 360 THR cc_start: 0.8829 (p) cc_final: 0.8546 (t) REVERT: J 9 ASP cc_start: 0.7588 (m-30) cc_final: 0.7213 (p0) REVERT: J 128 MET cc_start: 0.8005 (mmm) cc_final: 0.7534 (mmm) REVERT: L 94 LYS cc_start: 0.8010 (tptt) cc_final: 0.6983 (tptm) REVERT: G 73 LEU cc_start: 0.9159 (mt) cc_final: 0.8914 (mt) REVERT: G 107 MET cc_start: 0.7030 (ttm) cc_final: 0.6413 (ttp) REVERT: G 218 MET cc_start: 0.7712 (mtp) cc_final: 0.7154 (mtm) REVERT: W 71 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7125 (mm-30) REVERT: U 22 MET cc_start: 0.7196 (mtp) cc_final: 0.6744 (mmp) REVERT: U 41 LEU cc_start: 0.8557 (tp) cc_final: 0.8139 (tp) REVERT: U 78 ILE cc_start: 0.8692 (pt) cc_final: 0.8398 (mm) REVERT: K 9 ASP cc_start: 0.8003 (m-30) cc_final: 0.7779 (m-30) REVERT: K 25 MET cc_start: 0.7393 (ttt) cc_final: 0.7124 (ttm) REVERT: D 83 ASN cc_start: 0.5594 (m-40) cc_final: 0.5364 (m-40) REVERT: D 192 ASP cc_start: 0.6918 (p0) cc_final: 0.6690 (p0) REVERT: D 216 MET cc_start: 0.7703 (mmm) cc_final: 0.7421 (tpp) REVERT: A 120 MET cc_start: 0.6049 (ptm) cc_final: 0.5534 (pmm) REVERT: A 304 ASP cc_start: 0.7217 (m-30) cc_final: 0.7015 (p0) REVERT: A 405 SER cc_start: 0.8107 (m) cc_final: 0.7832 (t) REVERT: B 199 ILE cc_start: 0.8886 (mt) cc_final: 0.8633 (pt) REVERT: B 233 ILE cc_start: 0.8302 (mp) cc_final: 0.8054 (mp) REVERT: T 129 GLU cc_start: 0.7641 (pm20) cc_final: 0.7282 (pm20) REVERT: Z 1 MET cc_start: 0.7236 (ptm) cc_final: 0.6858 (ptm) outliers start: 10 outliers final: 4 residues processed: 955 average time/residue: 0.8133 time to fit residues: 1363.2144 Evaluate side-chains 612 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 608 time to evaluate : 7.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1130 random chunks: chunk 570 optimal weight: 4.9990 chunk 318 optimal weight: 0.9980 chunk 854 optimal weight: 3.9990 chunk 698 optimal weight: 6.9990 chunk 283 optimal weight: 20.0000 chunk 1028 optimal weight: 9.9990 chunk 1110 optimal weight: 3.9990 chunk 915 optimal weight: 3.9990 chunk 1019 optimal weight: 2.9990 chunk 350 optimal weight: 40.0000 chunk 824 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 800 GLN d 889 GLN j1122 ASN ** i1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 770 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN g 25 GLN ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 185 ASN b 528 ASN b 540 ASN I 49 ASN I 113 ASN ** I 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN H 45 HIS H 49 ASN H 113 ASN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 269 ASN Y 25 ASN Y 51 ASN Y 104 GLN M 73 GLN E 182 GLN C 174 ASN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN J 100 ASN ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 ASN ** D 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 ASN Z 188 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 91172 Z= 0.263 Angle : 0.555 12.005 123922 Z= 0.293 Chirality : 0.046 0.230 14126 Planarity : 0.004 0.064 16035 Dihedral : 4.520 68.259 12463 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: -1.06 (0.08), residues: 11397 helix: 0.53 (0.16), residues: 1176 sheet: -0.52 (0.08), residues: 3999 loop : -1.03 (0.07), residues: 6222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 95 HIS 0.006 0.001 HIS A 20 PHE 0.029 0.002 PHE X 17 TYR 0.027 0.002 TYR a 136 ARG 0.013 0.001 ARG L 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 783 time to evaluate : 7.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 245 TYR cc_start: 0.7891 (t80) cc_final: 0.7683 (t80) REVERT: d 823 ARG cc_start: 0.4791 (ptm160) cc_final: 0.4358 (ptm160) REVERT: j 1102 MET cc_start: 0.6087 (ptp) cc_final: 0.5559 (ptp) REVERT: h 1122 ASN cc_start: 0.8040 (m-40) cc_final: 0.7775 (t0) REVERT: c 448 ASP cc_start: 0.8355 (p0) cc_final: 0.8101 (p0) REVERT: c 790 LEU cc_start: 0.8084 (pt) cc_final: 0.7870 (pp) REVERT: c 892 MET cc_start: 0.6443 (tpt) cc_final: 0.6078 (tpt) REVERT: f 432 MET cc_start: 0.4668 (tpt) cc_final: 0.3679 (tpt) REVERT: e 482 GLN cc_start: 0.8559 (tm-30) cc_final: 0.7694 (tm-30) REVERT: b 214 ILE cc_start: 0.8163 (pt) cc_final: 0.7869 (pt) REVERT: b 217 LYS cc_start: 0.8165 (tmtt) cc_final: 0.7727 (mttp) REVERT: b 915 PHE cc_start: 0.7910 (m-10) cc_final: 0.7571 (m-10) REVERT: R 128 MET cc_start: 0.7676 (mmm) cc_final: 0.6253 (mtt) REVERT: I 82 MET cc_start: 0.8515 (ttp) cc_final: 0.8025 (ttm) REVERT: I 238 LEU cc_start: 0.8861 (mt) cc_final: 0.8645 (mt) REVERT: Q 1 MET cc_start: 0.3848 (tpp) cc_final: 0.3537 (ppp) REVERT: Q 64 PHE cc_start: 0.7450 (m-80) cc_final: 0.6773 (m-80) REVERT: S 22 MET cc_start: 0.7884 (mtm) cc_final: 0.7524 (tpt) REVERT: F 91 ASP cc_start: 0.8305 (p0) cc_final: 0.7922 (p0) REVERT: F 133 MET cc_start: 0.7753 (tpp) cc_final: 0.7513 (tpp) REVERT: H 236 LYS cc_start: 0.8104 (mttp) cc_final: 0.7870 (ptpp) REVERT: X 28 MET cc_start: 0.7963 (ptp) cc_final: 0.7543 (ptt) REVERT: X 31 ASP cc_start: 0.7637 (t70) cc_final: 0.6864 (m-30) REVERT: X 38 VAL cc_start: 0.8986 (t) cc_final: 0.8678 (p) REVERT: M 21 LEU cc_start: 0.8303 (tp) cc_final: 0.7880 (mp) REVERT: O 105 LEU cc_start: 0.8487 (tp) cc_final: 0.8070 (tt) REVERT: E 133 MET cc_start: 0.8664 (tpp) cc_final: 0.8369 (tpp) REVERT: E 268 TYR cc_start: 0.6692 (m-80) cc_final: 0.6180 (m-10) REVERT: E 405 SER cc_start: 0.8767 (m) cc_final: 0.8457 (p) REVERT: J 128 MET cc_start: 0.8185 (mmm) cc_final: 0.7841 (mmm) REVERT: L 94 LYS cc_start: 0.7960 (tptt) cc_final: 0.7134 (tptm) REVERT: W 178 MET cc_start: 0.7487 (mmm) cc_final: 0.7237 (mmm) REVERT: U 22 MET cc_start: 0.7381 (mtp) cc_final: 0.6732 (mmp) REVERT: K 25 MET cc_start: 0.7303 (ttt) cc_final: 0.7063 (ttm) REVERT: K 100 ASN cc_start: 0.8533 (t0) cc_final: 0.7375 (t0) REVERT: D 192 ASP cc_start: 0.7429 (p0) cc_final: 0.7134 (p0) REVERT: D 447 LYS cc_start: 0.8480 (mptt) cc_final: 0.8105 (mttp) REVERT: A 120 MET cc_start: 0.6489 (ptm) cc_final: 0.5478 (pmm) REVERT: A 216 MET cc_start: 0.8195 (mpp) cc_final: 0.7712 (mpp) REVERT: A 325 GLU cc_start: 0.8129 (tp30) cc_final: 0.7822 (tm-30) REVERT: A 405 SER cc_start: 0.8158 (m) cc_final: 0.7836 (p) REVERT: B 199 ILE cc_start: 0.8806 (mt) cc_final: 0.8592 (pt) REVERT: B 233 ILE cc_start: 0.8378 (mp) cc_final: 0.8164 (mp) REVERT: P 127 ILE cc_start: 0.8772 (mm) cc_final: 0.7794 (mm) REVERT: T 20 LEU cc_start: 0.8143 (pp) cc_final: 0.7780 (pp) REVERT: T 129 GLU cc_start: 0.7565 (pm20) cc_final: 0.7093 (pm20) REVERT: Z 1 MET cc_start: 0.7738 (ptm) cc_final: 0.7281 (ptm) outliers start: 10 outliers final: 2 residues processed: 792 average time/residue: 0.7921 time to fit residues: 1108.5906 Evaluate side-chains 525 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 523 time to evaluate : 7.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1130 random chunks: chunk 1015 optimal weight: 20.0000 chunk 772 optimal weight: 10.0000 chunk 533 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 490 optimal weight: 5.9990 chunk 690 optimal weight: 8.9990 chunk 1031 optimal weight: 3.9990 chunk 1092 optimal weight: 3.9990 chunk 539 optimal weight: 4.9990 chunk 977 optimal weight: 0.6980 chunk 294 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 161 GLN d 554 ASN ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 889 GLN j1122 ASN ** i1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 769 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 647 ASN f 648 ASN ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 417 GLN ** e 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 584 ASN b 778 HIS I 161 GLN a 108 GLN ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 103 GLN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 ASN H 192 GLN H 210 ASN O 103 GLN C 182 GLN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 100 ASN V 51 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 91172 Z= 0.200 Angle : 0.512 11.817 123922 Z= 0.269 Chirality : 0.045 0.250 14126 Planarity : 0.004 0.067 16035 Dihedral : 4.409 70.456 12463 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.92 % Favored : 97.06 % Rotamer: Outliers : 0.01 % Allowed : 3.27 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.08), residues: 11397 helix: 0.53 (0.16), residues: 1177 sheet: -0.46 (0.08), residues: 4059 loop : -0.97 (0.07), residues: 6161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP e 240 HIS 0.006 0.001 HIS E 113 PHE 0.015 0.001 PHE X 141 TYR 0.030 0.001 TYR d 44 ARG 0.018 0.000 ARG d 823 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 756 time to evaluate : 7.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 245 TYR cc_start: 0.7891 (t80) cc_final: 0.7690 (t80) REVERT: d 846 ARG cc_start: 0.6709 (mmt180) cc_final: 0.5358 (mmt180) REVERT: c 448 ASP cc_start: 0.8283 (p0) cc_final: 0.8031 (p0) REVERT: f 432 MET cc_start: 0.4696 (tpt) cc_final: 0.3803 (tpt) REVERT: e 567 MET cc_start: 0.6977 (tmm) cc_final: 0.6584 (ppp) REVERT: g 103 MET cc_start: 0.4030 (tpp) cc_final: 0.3433 (mmt) REVERT: b 214 ILE cc_start: 0.8238 (pt) cc_final: 0.8016 (pt) REVERT: b 217 LYS cc_start: 0.8137 (tmtt) cc_final: 0.7789 (mttp) REVERT: b 251 LYS cc_start: 0.5395 (tttt) cc_final: 0.4560 (tptt) REVERT: b 915 PHE cc_start: 0.7745 (m-10) cc_final: 0.7342 (m-10) REVERT: I 82 MET cc_start: 0.8502 (ttp) cc_final: 0.8177 (ttm) REVERT: I 238 LEU cc_start: 0.8936 (mt) cc_final: 0.8682 (mt) REVERT: a 66 ASP cc_start: 0.7363 (t70) cc_final: 0.7104 (t0) REVERT: Q 1 MET cc_start: 0.4222 (tpp) cc_final: 0.3518 (ppp) REVERT: Q 64 PHE cc_start: 0.7452 (m-80) cc_final: 0.6828 (m-80) REVERT: S 22 MET cc_start: 0.7807 (mtm) cc_final: 0.7393 (tpt) REVERT: F 133 MET cc_start: 0.7615 (tpp) cc_final: 0.7308 (tpp) REVERT: N 4 GLU cc_start: 0.8437 (pp20) cc_final: 0.7705 (pp20) REVERT: H 241 ASP cc_start: 0.8079 (t70) cc_final: 0.7828 (t0) REVERT: X 28 MET cc_start: 0.7873 (ptp) cc_final: 0.7451 (ptt) REVERT: X 38 VAL cc_start: 0.9120 (t) cc_final: 0.8820 (p) REVERT: Y 78 TYR cc_start: 0.6896 (m-80) cc_final: 0.6624 (m-10) REVERT: M 8 ILE cc_start: 0.8660 (pt) cc_final: 0.8338 (pt) REVERT: M 21 LEU cc_start: 0.8274 (tp) cc_final: 0.7868 (mp) REVERT: O 105 LEU cc_start: 0.8568 (tp) cc_final: 0.8351 (tt) REVERT: E 268 TYR cc_start: 0.6495 (m-80) cc_final: 0.6137 (m-10) REVERT: E 405 SER cc_start: 0.8765 (m) cc_final: 0.8457 (p) REVERT: C 197 MET cc_start: 0.8145 (mmm) cc_final: 0.7875 (mmm) REVERT: J 37 LYS cc_start: 0.8519 (tmtt) cc_final: 0.8302 (tmtt) REVERT: J 128 MET cc_start: 0.8313 (mmm) cc_final: 0.7848 (mmm) REVERT: G 218 MET cc_start: 0.7831 (mtp) cc_final: 0.7611 (mtm) REVERT: W 21 ASN cc_start: 0.8209 (t0) cc_final: 0.7999 (t0) REVERT: U 41 LEU cc_start: 0.8794 (tp) cc_final: 0.8526 (tp) REVERT: K 9 ASP cc_start: 0.8150 (m-30) cc_final: 0.7898 (m-30) REVERT: K 78 ILE cc_start: 0.8338 (tp) cc_final: 0.7995 (tt) REVERT: D 192 ASP cc_start: 0.7445 (p0) cc_final: 0.7126 (p0) REVERT: D 216 MET cc_start: 0.8066 (mmm) cc_final: 0.7797 (tpp) REVERT: A 120 MET cc_start: 0.6689 (ptm) cc_final: 0.5756 (pmm) REVERT: A 136 ILE cc_start: 0.9306 (mm) cc_final: 0.9084 (tp) REVERT: A 216 MET cc_start: 0.8116 (mpp) cc_final: 0.7637 (mpp) REVERT: A 325 GLU cc_start: 0.8182 (tp30) cc_final: 0.7838 (tm-30) REVERT: A 405 SER cc_start: 0.8143 (m) cc_final: 0.7814 (p) REVERT: B 199 ILE cc_start: 0.8806 (mt) cc_final: 0.8579 (pt) REVERT: T 129 GLU cc_start: 0.7783 (pm20) cc_final: 0.7247 (pm20) REVERT: Z 1 MET cc_start: 0.7914 (ptm) cc_final: 0.7706 (ptp) outliers start: 1 outliers final: 0 residues processed: 757 average time/residue: 0.7946 time to fit residues: 1065.1442 Evaluate side-chains 506 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 7.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1130 random chunks: chunk 909 optimal weight: 6.9990 chunk 620 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 813 optimal weight: 3.9990 chunk 450 optimal weight: 2.9990 chunk 932 optimal weight: 5.9990 chunk 755 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 557 optimal weight: 10.0000 chunk 980 optimal weight: 9.9990 chunk 275 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 339 HIS d 363 ASN ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 789 GLN d 889 GLN j1122 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 108 GLN ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 364 ASN ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN ** g 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 278 GLN ** g 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 339 HIS b 523 GLN b 528 ASN ** b 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 ASN ** a 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 103 GLN F 41 ASN F 66 ASN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 108 GLN E 318 HIS ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 HIS J 5 ASN ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 108 GLN D 31 GLN D 96 HIS D 291 ASN A 318 HIS A 368 ASN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 100 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 91172 Z= 0.275 Angle : 0.547 12.426 123922 Z= 0.287 Chirality : 0.045 0.226 14126 Planarity : 0.004 0.119 16035 Dihedral : 4.547 73.481 12463 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.51 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: -1.00 (0.08), residues: 11397 helix: 0.44 (0.16), residues: 1176 sheet: -0.44 (0.08), residues: 4064 loop : -0.99 (0.07), residues: 6157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP e 507 HIS 0.022 0.002 HIS G 112 PHE 0.017 0.002 PHE K 125 TYR 0.027 0.002 TYR H 118 ARG 0.014 0.001 ARG e 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 708 time to evaluate : 7.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 382 LYS cc_start: 0.3352 (mtmm) cc_final: 0.3053 (mmmt) REVERT: f 435 VAL cc_start: 0.7916 (t) cc_final: 0.7588 (p) REVERT: g 103 MET cc_start: 0.3914 (tpp) cc_final: 0.3336 (tpp) REVERT: b 217 LYS cc_start: 0.8146 (tmtt) cc_final: 0.7762 (mttp) REVERT: I 82 MET cc_start: 0.8504 (ttp) cc_final: 0.8219 (ttm) REVERT: I 238 LEU cc_start: 0.8930 (mt) cc_final: 0.8679 (mt) REVERT: a 66 ASP cc_start: 0.7430 (t70) cc_final: 0.7145 (t0) REVERT: Q 1 MET cc_start: 0.4343 (tpp) cc_final: 0.3767 (ppp) REVERT: S 22 MET cc_start: 0.7878 (mtm) cc_final: 0.7286 (tpt) REVERT: F 133 MET cc_start: 0.7640 (tpp) cc_final: 0.7315 (tpp) REVERT: N 4 GLU cc_start: 0.8262 (pp20) cc_final: 0.8030 (pp20) REVERT: N 22 MET cc_start: 0.5612 (ttm) cc_final: 0.5164 (ttm) REVERT: H 241 ASP cc_start: 0.8234 (t70) cc_final: 0.8002 (t0) REVERT: X 38 VAL cc_start: 0.9152 (t) cc_final: 0.8874 (p) REVERT: M 21 LEU cc_start: 0.8315 (tp) cc_final: 0.7838 (mp) REVERT: O 6 ARG cc_start: 0.7873 (mtm110) cc_final: 0.6643 (mmt180) REVERT: E 245 MET cc_start: 0.8815 (mtt) cc_final: 0.8488 (mtt) REVERT: E 268 TYR cc_start: 0.6487 (m-80) cc_final: 0.6203 (m-10) REVERT: E 405 SER cc_start: 0.8796 (m) cc_final: 0.8441 (p) REVERT: C 120 MET cc_start: 0.4382 (ptt) cc_final: 0.3566 (ptp) REVERT: J 128 MET cc_start: 0.8192 (mmm) cc_final: 0.7914 (mmm) REVERT: L 94 LYS cc_start: 0.8023 (tptt) cc_final: 0.7393 (tptm) REVERT: W 1 MET cc_start: 0.8150 (tpp) cc_final: 0.7851 (tpp) REVERT: W 21 ASN cc_start: 0.8245 (t0) cc_final: 0.8042 (t0) REVERT: U 41 LEU cc_start: 0.8841 (tp) cc_final: 0.8489 (tp) REVERT: K 9 ASP cc_start: 0.8150 (m-30) cc_final: 0.7936 (m-30) REVERT: K 25 MET cc_start: 0.7319 (ttm) cc_final: 0.7020 (ttt) REVERT: D 192 ASP cc_start: 0.7637 (p0) cc_final: 0.7397 (p0) REVERT: D 216 MET cc_start: 0.8118 (mmm) cc_final: 0.7828 (tpp) REVERT: D 447 LYS cc_start: 0.8409 (mttt) cc_final: 0.8082 (mttp) REVERT: A 120 MET cc_start: 0.6703 (ptm) cc_final: 0.5817 (pmm) REVERT: A 216 MET cc_start: 0.8414 (mpp) cc_final: 0.7751 (mpp) REVERT: A 245 MET cc_start: 0.8911 (mtt) cc_final: 0.8605 (mtt) REVERT: A 325 GLU cc_start: 0.8540 (tp30) cc_final: 0.8241 (tm-30) REVERT: A 405 SER cc_start: 0.8344 (m) cc_final: 0.8086 (p) REVERT: B 255 PHE cc_start: 0.7326 (m-10) cc_final: 0.7012 (m-10) REVERT: T 25 MET cc_start: 0.8207 (tpt) cc_final: 0.7910 (tpt) REVERT: T 129 GLU cc_start: 0.7852 (pm20) cc_final: 0.7299 (pm20) REVERT: Z 1 MET cc_start: 0.8117 (ptm) cc_final: 0.7896 (ptp) outliers start: 0 outliers final: 0 residues processed: 708 average time/residue: 0.8021 time to fit residues: 1006.0782 Evaluate side-chains 487 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 487 time to evaluate : 7.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1130 random chunks: chunk 367 optimal weight: 5.9990 chunk 983 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 641 optimal weight: 0.9980 chunk 269 optimal weight: 10.0000 chunk 1093 optimal weight: 0.8980 chunk 907 optimal weight: 10.0000 chunk 506 optimal weight: 3.9990 chunk 90 optimal weight: 30.0000 chunk 361 optimal weight: 20.0000 chunk 573 optimal weight: 7.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 889 GLN j1122 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 228 GLN c 381 GLN c 446 ASN ** c 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 ASN ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 397 ASN ** e 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN ** g 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 339 HIS b 639 ASN ** b 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 ASN ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 GLN O 140 GLN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 206 ASN ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 ASN G 216 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 91172 Z= 0.320 Angle : 0.588 12.135 123922 Z= 0.308 Chirality : 0.046 0.214 14126 Planarity : 0.004 0.057 16035 Dihedral : 4.778 75.815 12463 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: -1.15 (0.07), residues: 11397 helix: 0.16 (0.15), residues: 1194 sheet: -0.53 (0.08), residues: 4052 loop : -1.07 (0.07), residues: 6151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP e 507 HIS 0.009 0.002 HIS b 339 PHE 0.028 0.002 PHE I 202 TYR 0.027 0.002 TYR E 203 ARG 0.007 0.001 ARG d 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 659 time to evaluate : 8.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 245 TYR cc_start: 0.7771 (t80) cc_final: 0.7426 (t80) REVERT: f 166 MET cc_start: 0.7432 (mpp) cc_final: 0.7170 (mpp) REVERT: f 382 LYS cc_start: 0.3329 (mtmm) cc_final: 0.3018 (mmmt) REVERT: f 435 VAL cc_start: 0.8218 (t) cc_final: 0.7960 (p) REVERT: b 217 LYS cc_start: 0.8182 (tmtt) cc_final: 0.7790 (mttp) REVERT: I 238 LEU cc_start: 0.8957 (mt) cc_final: 0.8701 (mt) REVERT: a 66 ASP cc_start: 0.7477 (t70) cc_final: 0.7171 (t0) REVERT: Q 64 PHE cc_start: 0.7450 (m-80) cc_final: 0.7080 (m-80) REVERT: S 22 MET cc_start: 0.7873 (mtm) cc_final: 0.7284 (tpt) REVERT: N 18 TYR cc_start: 0.7789 (t80) cc_final: 0.7588 (t80) REVERT: N 22 MET cc_start: 0.5491 (ttm) cc_final: 0.4890 (ttp) REVERT: H 158 THR cc_start: 0.8923 (p) cc_final: 0.8617 (m) REVERT: X 38 VAL cc_start: 0.9206 (t) cc_final: 0.8900 (p) REVERT: M 21 LEU cc_start: 0.8335 (tp) cc_final: 0.7956 (mp) REVERT: E 245 MET cc_start: 0.8758 (mtt) cc_final: 0.8431 (mtt) REVERT: E 268 TYR cc_start: 0.6548 (m-80) cc_final: 0.6122 (m-80) REVERT: E 405 SER cc_start: 0.8717 (m) cc_final: 0.8393 (p) REVERT: C 344 ASP cc_start: 0.6494 (p0) cc_final: 0.5979 (p0) REVERT: J 22 MET cc_start: 0.6885 (mtp) cc_final: 0.6260 (mtp) REVERT: J 37 LYS cc_start: 0.8562 (tmtt) cc_final: 0.8310 (tmtt) REVERT: L 20 LEU cc_start: 0.8153 (tp) cc_final: 0.7830 (mm) REVERT: L 94 LYS cc_start: 0.7954 (tptt) cc_final: 0.7507 (tptm) REVERT: W 21 ASN cc_start: 0.8211 (t0) cc_final: 0.8008 (t0) REVERT: K 28 ASP cc_start: 0.6653 (t0) cc_final: 0.6418 (t0) REVERT: D 192 ASP cc_start: 0.7821 (p0) cc_final: 0.7526 (p0) REVERT: D 216 MET cc_start: 0.8272 (mmm) cc_final: 0.7980 (tpp) REVERT: A 405 SER cc_start: 0.8390 (m) cc_final: 0.8130 (p) REVERT: B 1 MET cc_start: 0.7776 (tpp) cc_final: 0.7184 (tmm) REVERT: B 255 PHE cc_start: 0.7475 (m-10) cc_final: 0.7144 (m-10) REVERT: P 1 MET cc_start: 0.4074 (tpt) cc_final: 0.3549 (tpt) REVERT: T 129 GLU cc_start: 0.8009 (pm20) cc_final: 0.7301 (pm20) outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.7893 time to fit residues: 923.4725 Evaluate side-chains 475 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 7.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1130 random chunks: chunk 1054 optimal weight: 0.0370 chunk 123 optimal weight: 10.0000 chunk 622 optimal weight: 10.0000 chunk 798 optimal weight: 1.9990 chunk 618 optimal weight: 9.9990 chunk 920 optimal weight: 9.9990 chunk 610 optimal weight: 2.9990 chunk 1089 optimal weight: 10.0000 chunk 681 optimal weight: 6.9990 chunk 664 optimal weight: 0.9990 chunk 502 optimal weight: 6.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 400 ASN ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 889 GLN j1122 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 ASN ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN ** g 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 574 ASN b 207 HIS b 339 HIS ** b 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 849 ASN ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 ASN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 120 GLN ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN A 397 GLN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 100 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 91172 Z= 0.228 Angle : 0.536 12.112 123922 Z= 0.280 Chirality : 0.045 0.208 14126 Planarity : 0.004 0.054 16035 Dihedral : 4.632 75.710 12463 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: -1.08 (0.08), residues: 11397 helix: 0.28 (0.15), residues: 1183 sheet: -0.49 (0.08), residues: 4042 loop : -1.02 (0.07), residues: 6172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP e 287 HIS 0.009 0.001 HIS d 778 PHE 0.024 0.001 PHE d 915 TYR 0.024 0.002 TYR G 274 ARG 0.032 0.001 ARG I 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 7.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 245 TYR cc_start: 0.7864 (t80) cc_final: 0.7511 (t80) REVERT: d 846 ARG cc_start: 0.5190 (mmt180) cc_final: 0.4612 (mmt180) REVERT: f 382 LYS cc_start: 0.3357 (mtmm) cc_final: 0.3111 (mmmt) REVERT: g 1 MET cc_start: 0.3648 (mmm) cc_final: -0.0506 (ttp) REVERT: b 217 LYS cc_start: 0.8210 (tmtt) cc_final: 0.7800 (mttp) REVERT: a 66 ASP cc_start: 0.7332 (t70) cc_final: 0.7002 (t0) REVERT: S 22 MET cc_start: 0.7708 (mtm) cc_final: 0.7193 (tpt) REVERT: F 133 MET cc_start: 0.7936 (tpp) cc_final: 0.7397 (tpp) REVERT: N 54 LEU cc_start: 0.8755 (mt) cc_final: 0.8457 (tp) REVERT: X 38 VAL cc_start: 0.9255 (t) cc_final: 0.8922 (p) REVERT: M 21 LEU cc_start: 0.8403 (tp) cc_final: 0.8018 (mp) REVERT: E 227 THR cc_start: 0.8548 (m) cc_final: 0.8005 (p) REVERT: E 245 MET cc_start: 0.8685 (mtt) cc_final: 0.8328 (mtt) REVERT: E 405 SER cc_start: 0.8753 (m) cc_final: 0.8462 (p) REVERT: C 120 MET cc_start: 0.4372 (ptt) cc_final: 0.3476 (ptp) REVERT: C 344 ASP cc_start: 0.6524 (p0) cc_final: 0.6016 (p0) REVERT: J 127 ILE cc_start: 0.9068 (pt) cc_final: 0.8516 (tt) REVERT: J 128 MET cc_start: 0.8078 (mmm) cc_final: 0.7626 (mmm) REVERT: L 1 MET cc_start: 0.4744 (tpp) cc_final: 0.4478 (tpt) REVERT: L 20 LEU cc_start: 0.8105 (tp) cc_final: 0.7768 (mm) REVERT: L 94 LYS cc_start: 0.8018 (tptt) cc_final: 0.7561 (tptm) REVERT: G 107 MET cc_start: 0.7183 (ttm) cc_final: 0.6816 (ttp) REVERT: K 9 ASP cc_start: 0.8170 (m-30) cc_final: 0.7964 (m-30) REVERT: K 28 ASP cc_start: 0.6629 (t0) cc_final: 0.6428 (t0) REVERT: D 192 ASP cc_start: 0.7690 (p0) cc_final: 0.7366 (p0) REVERT: D 216 MET cc_start: 0.8238 (mmm) cc_final: 0.7926 (tpp) REVERT: D 447 LYS cc_start: 0.8483 (mptt) cc_final: 0.8070 (mttp) REVERT: A 136 ILE cc_start: 0.9185 (mm) cc_final: 0.8948 (tp) REVERT: A 405 SER cc_start: 0.8352 (m) cc_final: 0.8069 (p) REVERT: B 1 MET cc_start: 0.7658 (tpp) cc_final: 0.7178 (tmm) REVERT: B 199 ILE cc_start: 0.8707 (mt) cc_final: 0.8485 (pt) REVERT: B 255 PHE cc_start: 0.7484 (m-10) cc_final: 0.7141 (m-10) REVERT: T 129 GLU cc_start: 0.8090 (pm20) cc_final: 0.7391 (pm20) outliers start: 0 outliers final: 0 residues processed: 668 average time/residue: 0.7808 time to fit residues: 923.6525 Evaluate side-chains 470 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 470 time to evaluate : 7.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1130 random chunks: chunk 673 optimal weight: 6.9990 chunk 434 optimal weight: 9.9990 chunk 650 optimal weight: 0.7980 chunk 328 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 211 optimal weight: 0.0370 chunk 692 optimal weight: 7.9990 chunk 742 optimal weight: 9.9990 chunk 538 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 856 optimal weight: 0.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j1122 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 709 GLN f 94 ASN ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 546 GLN f 682 ASN ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN ** g 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 411 ASN b 339 HIS ** b 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** a 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 ASN ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 91172 Z= 0.165 Angle : 0.511 13.360 123922 Z= 0.266 Chirality : 0.045 0.234 14126 Planarity : 0.003 0.064 16035 Dihedral : 4.460 74.661 12463 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 0.03 % Allowed : 0.90 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.08), residues: 11397 helix: 0.40 (0.16), residues: 1206 sheet: -0.44 (0.08), residues: 3966 loop : -0.96 (0.07), residues: 6225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP c 369 HIS 0.011 0.001 HIS A 113 PHE 0.018 0.001 PHE C 293 TYR 0.022 0.001 TYR R 99 ARG 0.010 0.000 ARG d 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 671 time to evaluate : 8.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 245 TYR cc_start: 0.7836 (t80) cc_final: 0.7492 (t80) REVERT: d 597 GLN cc_start: 0.7243 (tm-30) cc_final: 0.6846 (tm-30) REVERT: d 846 ARG cc_start: 0.5265 (mmt180) cc_final: 0.4943 (mmt180) REVERT: c 547 SER cc_start: 0.8241 (m) cc_final: 0.7970 (p) REVERT: f 382 LYS cc_start: 0.3349 (mtmm) cc_final: 0.3116 (mmmt) REVERT: g 1 MET cc_start: 0.3398 (mmm) cc_final: -0.0933 (ttp) REVERT: b 217 LYS cc_start: 0.8284 (tmtt) cc_final: 0.7813 (mttp) REVERT: I 238 LEU cc_start: 0.8957 (mt) cc_final: 0.8696 (mt) REVERT: a 66 ASP cc_start: 0.7111 (t70) cc_final: 0.6754 (t0) REVERT: S 22 MET cc_start: 0.7607 (mtm) cc_final: 0.7176 (tpt) REVERT: F 133 MET cc_start: 0.7835 (tpp) cc_final: 0.7365 (tpp) REVERT: X 38 VAL cc_start: 0.9276 (t) cc_final: 0.8925 (p) REVERT: X 66 ASP cc_start: 0.7316 (p0) cc_final: 0.6965 (t0) REVERT: M 21 LEU cc_start: 0.8370 (tp) cc_final: 0.7920 (mp) REVERT: E 227 THR cc_start: 0.8683 (m) cc_final: 0.7915 (p) REVERT: E 245 MET cc_start: 0.8633 (mtt) cc_final: 0.8264 (mtt) REVERT: E 405 SER cc_start: 0.8840 (m) cc_final: 0.8539 (p) REVERT: C 120 MET cc_start: 0.4032 (ptt) cc_final: 0.3337 (ptp) REVERT: C 344 ASP cc_start: 0.6496 (p0) cc_final: 0.6045 (p0) REVERT: J 127 ILE cc_start: 0.9081 (pt) cc_final: 0.8516 (tt) REVERT: J 128 MET cc_start: 0.8115 (mmm) cc_final: 0.7695 (mmm) REVERT: L 20 LEU cc_start: 0.8054 (tp) cc_final: 0.7735 (mm) REVERT: L 94 LYS cc_start: 0.7943 (tptt) cc_final: 0.7566 (tptm) REVERT: G 107 MET cc_start: 0.7096 (ttm) cc_final: 0.6689 (ttp) REVERT: K 28 ASP cc_start: 0.6560 (t0) cc_final: 0.6311 (t0) REVERT: D 192 ASP cc_start: 0.7606 (p0) cc_final: 0.7237 (p0) REVERT: D 216 MET cc_start: 0.8181 (mmm) cc_final: 0.7860 (tpp) REVERT: D 447 LYS cc_start: 0.8232 (mptt) cc_final: 0.7886 (mttp) REVERT: A 216 MET cc_start: 0.7695 (mpp) cc_final: 0.7402 (mpp) REVERT: A 268 TYR cc_start: 0.6136 (m-10) cc_final: 0.5785 (m-10) REVERT: A 329 VAL cc_start: 0.6777 (t) cc_final: 0.6275 (t) REVERT: A 405 SER cc_start: 0.8334 (m) cc_final: 0.8058 (p) REVERT: B 1 MET cc_start: 0.7603 (tpp) cc_final: 0.7120 (tmm) REVERT: B 199 ILE cc_start: 0.8750 (mt) cc_final: 0.8549 (pt) REVERT: B 255 PHE cc_start: 0.7376 (m-10) cc_final: 0.7054 (m-10) REVERT: P 1 MET cc_start: 0.3871 (tpt) cc_final: 0.3493 (tpt) outliers start: 3 outliers final: 0 residues processed: 674 average time/residue: 0.8015 time to fit residues: 966.1281 Evaluate side-chains 476 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 476 time to evaluate : 7.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1130 random chunks: chunk 990 optimal weight: 20.0000 chunk 1043 optimal weight: 0.9980 chunk 951 optimal weight: 9.9990 chunk 1014 optimal weight: 0.7980 chunk 610 optimal weight: 2.9990 chunk 442 optimal weight: 7.9990 chunk 796 optimal weight: 1.9990 chunk 311 optimal weight: 1.9990 chunk 917 optimal weight: 6.9990 chunk 959 optimal weight: 3.9990 chunk 1011 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j1122 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 ASN ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN ** g 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 339 HIS b 778 HIS ** b 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 ASN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN D 31 GLN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 91172 Z= 0.181 Angle : 0.517 12.554 123922 Z= 0.268 Chirality : 0.045 0.233 14126 Planarity : 0.004 0.059 16035 Dihedral : 4.416 74.273 12463 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.08), residues: 11397 helix: 0.48 (0.16), residues: 1194 sheet: -0.41 (0.08), residues: 4050 loop : -0.93 (0.07), residues: 6153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP c 369 HIS 0.010 0.001 HIS b 339 PHE 0.016 0.001 PHE g 167 TYR 0.019 0.001 TYR E 268 ARG 0.015 0.000 ARG R 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 7.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 245 TYR cc_start: 0.7736 (t80) cc_final: 0.7402 (t80) REVERT: d 338 MET cc_start: 0.7412 (tpt) cc_final: 0.7056 (tpt) REVERT: d 597 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6849 (tm-30) REVERT: c 338 MET cc_start: 0.8182 (tpt) cc_final: 0.7889 (tpt) REVERT: c 547 SER cc_start: 0.8276 (m) cc_final: 0.7982 (p) REVERT: f 382 LYS cc_start: 0.3370 (mtmm) cc_final: 0.3126 (mmmt) REVERT: g 1 MET cc_start: 0.3571 (mmm) cc_final: -0.0440 (ttp) REVERT: b 217 LYS cc_start: 0.8297 (tmtt) cc_final: 0.8003 (mttp) REVERT: S 8 ILE cc_start: 0.9045 (tt) cc_final: 0.8752 (tt) REVERT: S 22 MET cc_start: 0.7630 (mtm) cc_final: 0.7170 (tpt) REVERT: F 133 MET cc_start: 0.7817 (tpp) cc_final: 0.7368 (tpp) REVERT: X 38 VAL cc_start: 0.9286 (t) cc_final: 0.9055 (p) REVERT: X 66 ASP cc_start: 0.7403 (p0) cc_final: 0.6979 (t0) REVERT: X 178 MET cc_start: 0.8548 (mmm) cc_final: 0.7952 (mmp) REVERT: M 21 LEU cc_start: 0.8455 (tp) cc_final: 0.8000 (mp) REVERT: E 245 MET cc_start: 0.8582 (mtt) cc_final: 0.8111 (mtt) REVERT: E 405 SER cc_start: 0.8806 (m) cc_final: 0.8475 (p) REVERT: C 120 MET cc_start: 0.4182 (ptt) cc_final: 0.3318 (ptp) REVERT: C 344 ASP cc_start: 0.6545 (p0) cc_final: 0.6086 (p0) REVERT: J 127 ILE cc_start: 0.8987 (pt) cc_final: 0.8274 (tt) REVERT: G 107 MET cc_start: 0.6996 (ttm) cc_final: 0.6594 (ttp) REVERT: D 192 ASP cc_start: 0.7669 (p0) cc_final: 0.7402 (p0) REVERT: D 216 MET cc_start: 0.8127 (mmm) cc_final: 0.7805 (tpp) REVERT: D 447 LYS cc_start: 0.8173 (mptt) cc_final: 0.7743 (mttp) REVERT: A 216 MET cc_start: 0.7850 (mpp) cc_final: 0.7508 (mpp) REVERT: A 268 TYR cc_start: 0.5999 (m-10) cc_final: 0.5679 (m-10) REVERT: A 329 VAL cc_start: 0.6414 (t) cc_final: 0.5922 (t) REVERT: A 405 SER cc_start: 0.8360 (m) cc_final: 0.8080 (p) REVERT: B 1 MET cc_start: 0.7651 (tpp) cc_final: 0.7227 (tmm) REVERT: B 255 PHE cc_start: 0.7417 (m-10) cc_final: 0.7109 (m-10) REVERT: P 1 MET cc_start: 0.3578 (tpt) cc_final: 0.3245 (tpt) REVERT: T 20 LEU cc_start: 0.8478 (pp) cc_final: 0.8205 (pp) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.7942 time to fit residues: 907.3878 Evaluate side-chains 473 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 473 time to evaluate : 7.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1130 random chunks: chunk 666 optimal weight: 2.9990 chunk 1073 optimal weight: 7.9990 chunk 655 optimal weight: 5.9990 chunk 509 optimal weight: 0.9980 chunk 746 optimal weight: 8.9990 chunk 1125 optimal weight: 2.9990 chunk 1036 optimal weight: 8.9990 chunk 896 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 692 optimal weight: 0.6980 chunk 549 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 397 GLN ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 778 HIS d 781 HIS j1122 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 ASN ** f 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 74 GLN b 108 GLN b 339 HIS b 636 ASN b 781 HIS ** b 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 ASN ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 GLN C 182 GLN ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 91172 Z= 0.172 Angle : 0.510 12.678 123922 Z= 0.265 Chirality : 0.045 0.225 14126 Planarity : 0.003 0.055 16035 Dihedral : 4.376 74.084 12463 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 0.02 % Allowed : 0.26 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.08), residues: 11397 helix: 0.47 (0.16), residues: 1195 sheet: -0.36 (0.08), residues: 3965 loop : -0.93 (0.07), residues: 6237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP c 369 HIS 0.011 0.001 HIS b 339 PHE 0.016 0.001 PHE g 167 TYR 0.021 0.001 TYR G 274 ARG 0.005 0.000 ARG Z 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22794 Ramachandran restraints generated. 11397 Oldfield, 0 Emsley, 11397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 635 time to evaluate : 7.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 245 TYR cc_start: 0.7754 (t80) cc_final: 0.7418 (t80) REVERT: d 338 MET cc_start: 0.7429 (tpt) cc_final: 0.7078 (tpt) REVERT: d 597 GLN cc_start: 0.7284 (tm-30) cc_final: 0.6841 (tm-30) REVERT: d 781 HIS cc_start: 0.4187 (OUTLIER) cc_final: 0.3508 (m90) REVERT: d 892 MET cc_start: 0.4976 (tpt) cc_final: 0.3026 (tpt) REVERT: c 338 MET cc_start: 0.7981 (tpt) cc_final: 0.7729 (tpt) REVERT: c 547 SER cc_start: 0.8260 (m) cc_final: 0.7992 (p) REVERT: f 166 MET cc_start: 0.7071 (mpp) cc_final: 0.6774 (mpp) REVERT: f 382 LYS cc_start: 0.3377 (mtmm) cc_final: 0.3119 (mmmt) REVERT: e 388 ASP cc_start: 0.3657 (t0) cc_final: 0.3336 (m-30) REVERT: g 1 MET cc_start: 0.3604 (mmm) cc_final: -0.0371 (ttp) REVERT: g 567 MET cc_start: 0.4075 (ttm) cc_final: 0.3642 (ttt) REVERT: b 217 LYS cc_start: 0.8341 (tmtt) cc_final: 0.8028 (mttp) REVERT: S 22 MET cc_start: 0.7727 (mtm) cc_final: 0.7265 (tpt) REVERT: F 133 MET cc_start: 0.7800 (tpp) cc_final: 0.7344 (tpp) REVERT: X 38 VAL cc_start: 0.9380 (t) cc_final: 0.9081 (p) REVERT: X 66 ASP cc_start: 0.7540 (p0) cc_final: 0.7117 (t0) REVERT: M 21 LEU cc_start: 0.8500 (tp) cc_final: 0.8076 (mp) REVERT: E 227 THR cc_start: 0.8426 (p) cc_final: 0.8165 (t) REVERT: E 245 MET cc_start: 0.8532 (mtt) cc_final: 0.8040 (mtt) REVERT: C 120 MET cc_start: 0.4125 (ptt) cc_final: 0.3433 (ptp) REVERT: C 344 ASP cc_start: 0.6638 (p0) cc_final: 0.6107 (p0) REVERT: J 127 ILE cc_start: 0.8739 (pt) cc_final: 0.8172 (tt) REVERT: G 107 MET cc_start: 0.6975 (ttm) cc_final: 0.6575 (ttp) REVERT: D 216 MET cc_start: 0.8068 (mmm) cc_final: 0.7776 (tpp) REVERT: D 447 LYS cc_start: 0.8142 (mptt) cc_final: 0.7689 (mttp) REVERT: A 216 MET cc_start: 0.7766 (mpp) cc_final: 0.7500 (mpp) REVERT: A 268 TYR cc_start: 0.6177 (m-10) cc_final: 0.5896 (m-10) REVERT: A 329 VAL cc_start: 0.6452 (t) cc_final: 0.5969 (t) REVERT: A 405 SER cc_start: 0.8359 (m) cc_final: 0.8087 (p) REVERT: B 1 MET cc_start: 0.7702 (tpp) cc_final: 0.7259 (tmm) REVERT: B 255 PHE cc_start: 0.7433 (m-10) cc_final: 0.7098 (m-10) REVERT: P 1 MET cc_start: 0.3688 (tpt) cc_final: 0.3341 (tpt) REVERT: T 20 LEU cc_start: 0.8317 (pp) cc_final: 0.7875 (pp) REVERT: V 1 MET cc_start: 0.8008 (ppp) cc_final: 0.7384 (ppp) outliers start: 2 outliers final: 0 residues processed: 637 average time/residue: 0.7726 time to fit residues: 877.7991 Evaluate side-chains 464 residues out of total 9913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 463 time to evaluate : 7.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1130 random chunks: chunk 712 optimal weight: 0.0870 chunk 954 optimal weight: 0.0470 chunk 274 optimal weight: 5.9990 chunk 826 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 897 optimal weight: 7.9990 chunk 375 optimal weight: 30.0000 chunk 921 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 639 ASN ** d 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j1122 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 479 GLN ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN g 352 GLN b 339 HIS ** b 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 100 ASN ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.066035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047900 restraints weight = 505078.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.049282 restraints weight = 295107.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049589 restraints weight = 189100.364| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 91172 Z= 0.218 Angle : 0.531 12.903 123922 Z= 0.275 Chirality : 0.045 0.221 14126 Planarity : 0.004 0.057 16035 Dihedral : 4.471 75.038 12463 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.08), residues: 11397 helix: 0.43 (0.16), residues: 1192 sheet: -0.38 (0.08), residues: 3922 loop : -0.95 (0.07), residues: 6283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP c 369 HIS 0.012 0.001 HIS b 339 PHE 0.017 0.001 PHE g 167 TYR 0.020 0.001 TYR G 274 ARG 0.005 0.000 ARG d 930 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18733.67 seconds wall clock time: 335 minutes 33.13 seconds (20133.13 seconds total)