Starting phenix.real_space_refine on Tue Apr 16 20:23:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlz_21845/04_2024/6wlz_21845_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlz_21845/04_2024/6wlz_21845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlz_21845/04_2024/6wlz_21845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlz_21845/04_2024/6wlz_21845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlz_21845/04_2024/6wlz_21845_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlz_21845/04_2024/6wlz_21845_updated.pdb" } resolution = 2.9 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= 0.004 sd= 0.095 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 214 5.16 5 C 25708 2.51 5 N 7002 2.21 5 O 7731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 58": "OE1" <-> "OE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A ASP 607": "OD1" <-> "OD2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ASP 349": "OD1" <-> "OD2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B ASP 488": "OD1" <-> "OD2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B ASP 600": "OD1" <-> "OD2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B ASP 607": "OD1" <-> "OD2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ASP 349": "OD1" <-> "OD2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C ASP 419": "OD1" <-> "OD2" Residue "C ASP 466": "OD1" <-> "OD2" Residue "C PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C ASP 517": "OD1" <-> "OD2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 562": "OD1" <-> "OD2" Residue "C ASP 576": "OD1" <-> "OD2" Residue "C ASP 600": "OD1" <-> "OD2" Residue "C PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ASP 247": "OD1" <-> "OD2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "D TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 330": "OD1" <-> "OD2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E ASP 117": "OD1" <-> "OD2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "E PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E ASP 360": "OD1" <-> "OD2" Residue "E TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 431": "OD1" <-> "OD2" Residue "E ASP 447": "OD1" <-> "OD2" Residue "E PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 460": "NH1" <-> "NH2" Residue "E TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F ASP 117": "OD1" <-> "OD2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 239": "OE1" <-> "OE2" Residue "F ASP 247": "OD1" <-> "OD2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F ASP 299": "OD1" <-> "OD2" Residue "F GLU 316": "OE1" <-> "OE2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F ASP 359": "OD1" <-> "OD2" Residue "F ASP 360": "OD1" <-> "OD2" Residue "F GLU 408": "OE1" <-> "OE2" Residue "F GLU 442": "OE1" <-> "OE2" Residue "F ASP 448": "OD1" <-> "OD2" Residue "F ARG 460": "NH1" <-> "NH2" Residue "F TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 16": "OE1" <-> "OE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "X ASP 48": "OD1" <-> "OD2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X ASP 79": "OD1" <-> "OD2" Residue "X GLU 90": "OE1" <-> "OE2" Residue "X TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 170": "OE1" <-> "OE2" Residue "X GLU 173": "OE1" <-> "OE2" Residue "X ASP 194": "OD1" <-> "OD2" Residue "X GLU 195": "OE1" <-> "OE2" Residue "X GLU 209": "OE1" <-> "OE2" Residue "X GLU 220": "OE1" <-> "OE2" Residue "X ASP 221": "OD1" <-> "OD2" Residue "X ASP 244": "OD1" <-> "OD2" Residue "Y GLU 16": "OE1" <-> "OE2" Residue "Y TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y ASP 51": "OD1" <-> "OD2" Residue "Y PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 63": "OE1" <-> "OE2" Residue "Y GLU 67": "OE1" <-> "OE2" Residue "Y ASP 79": "OD1" <-> "OD2" Residue "Y GLU 173": "OE1" <-> "OE2" Residue "Y GLU 191": "OE1" <-> "OE2" Residue "Y GLU 210": "OE1" <-> "OE2" Residue "Y ASP 231": "OD1" <-> "OD2" Residue "Y ASP 244": "OD1" <-> "OD2" Residue "Z ASP 37": "OD1" <-> "OD2" Residue "Z GLU 47": "OE1" <-> "OE2" Residue "Z GLU 63": "OE1" <-> "OE2" Residue "Z ASP 79": "OD1" <-> "OD2" Residue "Z GLU 109": "OE1" <-> "OE2" Residue "Z ASP 125": "OD1" <-> "OD2" Residue "Z ASP 138": "OD1" <-> "OD2" Residue "Z GLU 170": "OE1" <-> "OE2" Residue "Z GLU 173": "OE1" <-> "OE2" Residue "Z ASP 194": "OD1" <-> "OD2" Residue "Z GLU 195": "OE1" <-> "OE2" Residue "Z GLU 220": "OE1" <-> "OE2" Residue "Z ASP 221": "OD1" <-> "OD2" Residue "Z ASP 244": "OD1" <-> "OD2" Residue "Z ASP 261": "OD1" <-> "OD2" Residue "Z GLU 269": "OE1" <-> "OE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 44": "NH1" <-> "NH2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "J ASP 164": "OD1" <-> "OD2" Residue "J TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 175": "OE1" <-> "OE2" Residue "J ASP 226": "OD1" <-> "OD2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 31": "NH1" <-> "NH2" Residue "M ARG 32": "NH1" <-> "NH2" Residue "M GLU 43": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M ARG 48": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M ARG 66": "NH1" <-> "NH2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M ARG 89": "NH1" <-> "NH2" Residue "M GLU 112": "OE1" <-> "OE2" Residue "G ASP 38": "OD1" <-> "OD2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 71": "OE1" <-> "OE2" Residue "G PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G GLU 214": "OE1" <-> "OE2" Residue "I ARG 44": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 108": "OD1" <-> "OD2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "I GLU 175": "OE1" <-> "OE2" Residue "I ASP 201": "OD1" <-> "OD2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L ARG 48": "NH1" <-> "NH2" Residue "L ARG 51": "NH1" <-> "NH2" Residue "L PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 66": "NH1" <-> "NH2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L ARG 89": "NH1" <-> "NH2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L ASP 97": "OD1" <-> "OD2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "L GLU 112": "OE1" <-> "OE2" Residue "H GLU 37": "OE1" <-> "OE2" Residue "H GLU 41": "OE1" <-> "OE2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H ASP 93": "OD1" <-> "OD2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 176": "OD1" <-> "OD2" Residue "K ARG 28": "NH1" <-> "NH2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K ARG 32": "NH1" <-> "NH2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K ARG 48": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K ARG 66": "NH1" <-> "NH2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 109": "OE1" <-> "OE2" Residue "K GLU 112": "OE1" <-> "OE2" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N GLU 27": "OE1" <-> "OE2" Residue "N PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 40": "OE1" <-> "OE2" Residue "N ASP 42": "OD1" <-> "OD2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N GLU 72": "OE1" <-> "OE2" Residue "N GLU 95": "OE1" <-> "OE2" Residue "N TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 99": "OD1" <-> "OD2" Residue "N ARG 107": "NH1" <-> "NH2" Residue "N ARG 110": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40657 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4652 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "C" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3600 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "E" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3589 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3596 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2110 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2136 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 257} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2105 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1570 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "M" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 744 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "G" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1713 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1570 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "L" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 744 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "H" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1570 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "K" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 744 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "N" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.54, per 1000 atoms: 0.53 Number of scatterers: 40657 At special positions: 0 Unit cell: (165.24, 179.28, 183.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 214 16.00 P 2 15.00 O 7731 8.00 N 7002 7.00 C 25708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.97 Conformation dependent library (CDL) restraints added in 7.4 seconds 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9628 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 169 helices and 35 sheets defined 45.2% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 38.05 Creating SS restraints... Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.675A pdb=" N SER A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.994A pdb=" N SER A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.942A pdb=" N GLU A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 320 through 323 No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.908A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.567A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 388 removed outlier: 3.516A pdb=" N SER A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.962A pdb=" N LYS A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 493 removed outlier: 3.641A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.873A pdb=" N LEU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 557 Processing helix chain 'A' and resid 568 through 571 No H-bonds generated for 'chain 'A' and resid 568 through 571' Processing helix chain 'A' and resid 577 through 580 No H-bonds generated for 'chain 'A' and resid 577 through 580' Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'B' and resid 106 through 112 removed outlier: 4.048A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 265 Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.554A pdb=" N GLU B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 351 through 365 removed outlier: 3.683A pdb=" N ALA B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.640A pdb=" N TYR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 428 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 473 through 488 removed outlier: 3.800A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 503 through 518 removed outlier: 3.944A pdb=" N LYS B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 557 removed outlier: 3.625A pdb=" N MET B 544 " --> pdb=" O MET B 540 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 555 " --> pdb=" O ALA B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 removed outlier: 3.534A pdb=" N GLU B 572 " --> pdb=" O SER B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 582 Processing helix chain 'B' and resid 584 through 586 No H-bonds generated for 'chain 'B' and resid 584 through 586' Processing helix chain 'B' and resid 594 through 613 Processing helix chain 'C' and resid 106 through 112 removed outlier: 4.129A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 287 through 290 No H-bonds generated for 'chain 'C' and resid 287 through 290' Processing helix chain 'C' and resid 305 through 308 removed outlier: 3.802A pdb=" N ARG C 308 " --> pdb=" O ILE C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 305 through 308' Processing helix chain 'C' and resid 321 through 340 removed outlier: 3.741A pdb=" N GLU C 324 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 325 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 326 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR C 328 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 331 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 332 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 334 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU C 335 " --> pdb=" O THR C 332 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 336 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE C 337 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG C 338 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP C 339 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 378 through 388 removed outlier: 4.462A pdb=" N ARG C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 473 through 496 removed outlier: 3.685A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 removed outlier: 3.519A pdb=" N GLU C 510 " --> pdb=" O LYS C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 557 removed outlier: 3.737A pdb=" N PHE C 547 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR C 548 " --> pdb=" O MET C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 576 through 586 removed outlier: 3.858A pdb=" N LYS C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 614 removed outlier: 3.547A pdb=" N ILE C 597 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 605 " --> pdb=" O TYR C 601 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 269 through 287 removed outlier: 3.584A pdb=" N ILE D 272 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Proline residue: D 275 - end of helix removed outlier: 4.214A pdb=" N ALA D 278 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 279 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 280 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR D 281 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA D 282 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 283 " --> pdb=" O THR D 280 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 285 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA D 286 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR D 287 " --> pdb=" O PHE D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 removed outlier: 3.758A pdb=" N ALA D 304 " --> pdb=" O MET D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.743A pdb=" N THR D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 364 through 370 Processing helix chain 'D' and resid 415 through 438 removed outlier: 4.064A pdb=" N MET D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 461 Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.383A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 503 removed outlier: 3.580A pdb=" N GLU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 238 through 250 Processing helix chain 'E' and resid 270 through 288 Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 300 through 314 removed outlier: 3.728A pdb=" N ARG E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 327 through 335 removed outlier: 3.718A pdb=" N ILE E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 371 removed outlier: 3.729A pdb=" N TYR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 385 No H-bonds generated for 'chain 'E' and resid 382 through 385' Processing helix chain 'E' and resid 402 through 405 No H-bonds generated for 'chain 'E' and resid 402 through 405' Processing helix chain 'E' and resid 415 through 439 removed outlier: 3.971A pdb=" N ALA E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 461 Processing helix chain 'E' and resid 473 through 486 removed outlier: 4.596A pdb=" N ILE E 486 " --> pdb=" O GLN E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 238 through 248 Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'F' and resid 274 through 287 Processing helix chain 'F' and resid 300 through 314 removed outlier: 3.664A pdb=" N ARG F 314 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 327 through 335 removed outlier: 3.838A pdb=" N THR F 333 " --> pdb=" O THR F 329 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 364 through 370 Processing helix chain 'F' and resid 381 through 384 No H-bonds generated for 'chain 'F' and resid 381 through 384' Processing helix chain 'F' and resid 415 through 439 removed outlier: 3.558A pdb=" N ALA F 434 " --> pdb=" O LYS F 430 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA F 437 " --> pdb=" O GLN F 433 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 443 No H-bonds generated for 'chain 'F' and resid 441 through 443' Processing helix chain 'F' and resid 446 through 461 removed outlier: 3.693A pdb=" N LEU F 450 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN F 456 " --> pdb=" O LEU F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 486 removed outlier: 4.553A pdb=" N ILE F 486 " --> pdb=" O GLN F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 503 removed outlier: 3.890A pdb=" N GLU F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 36 removed outlier: 4.020A pdb=" N VAL X 23 " --> pdb=" O HIS X 19 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA X 30 " --> pdb=" O ILE X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 48 No H-bonds generated for 'chain 'X' and resid 45 through 48' Processing helix chain 'X' and resid 54 through 57 No H-bonds generated for 'chain 'X' and resid 54 through 57' Processing helix chain 'X' and resid 62 through 70 Processing helix chain 'X' and resid 78 through 97 removed outlier: 3.867A pdb=" N LEU X 86 " --> pdb=" O SER X 82 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE X 87 " --> pdb=" O ARG X 83 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU X 88 " --> pdb=" O ARG X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 117 Processing helix chain 'X' and resid 125 through 141 Processing helix chain 'X' and resid 147 through 166 removed outlier: 3.584A pdb=" N GLN X 165 " --> pdb=" O MET X 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 174 through 186 removed outlier: 4.077A pdb=" N LYS X 180 " --> pdb=" O ASN X 176 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 206 Processing helix chain 'X' and resid 219 through 233 Processing helix chain 'X' and resid 243 through 250 removed outlier: 3.635A pdb=" N SER X 250 " --> pdb=" O LEU X 246 " (cutoff:3.500A) Processing helix chain 'X' and resid 257 through 271 Processing helix chain 'Y' and resid 15 through 36 Processing helix chain 'Y' and resid 43 through 48 Processing helix chain 'Y' and resid 50 through 57 removed outlier: 4.744A pdb=" N TRP Y 55 " --> pdb=" O ASP Y 51 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA Y 56 " --> pdb=" O VAL Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 62 through 71 Processing helix chain 'Y' and resid 78 through 97 removed outlier: 3.911A pdb=" N ILE Y 87 " --> pdb=" O ARG Y 83 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU Y 88 " --> pdb=" O ARG Y 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 116 removed outlier: 4.076A pdb=" N GLU Y 109 " --> pdb=" O LEU Y 105 " (cutoff:3.500A) Processing helix chain 'Y' and resid 121 through 123 No H-bonds generated for 'chain 'Y' and resid 121 through 123' Processing helix chain 'Y' and resid 126 through 139 Processing helix chain 'Y' and resid 147 through 166 Processing helix chain 'Y' and resid 173 through 186 Processing helix chain 'Y' and resid 195 through 205 removed outlier: 4.400A pdb=" N PHE Y 200 " --> pdb=" O GLN Y 196 " (cutoff:3.500A) Processing helix chain 'Y' and resid 219 through 228 removed outlier: 4.016A pdb=" N ILE Y 224 " --> pdb=" O GLU Y 220 " (cutoff:3.500A) Processing helix chain 'Y' and resid 241 through 251 removed outlier: 3.828A pdb=" N LEU Y 249 " --> pdb=" O LYS Y 245 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER Y 250 " --> pdb=" O LEU Y 246 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER Y 251 " --> pdb=" O SER Y 247 " (cutoff:3.500A) Processing helix chain 'Y' and resid 257 through 272 removed outlier: 3.742A pdb=" N LYS Y 268 " --> pdb=" O ASP Y 264 " (cutoff:3.500A) Processing helix chain 'Z' and resid 15 through 36 removed outlier: 4.073A pdb=" N VAL Z 23 " --> pdb=" O HIS Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 48 Processing helix chain 'Z' and resid 54 through 57 No H-bonds generated for 'chain 'Z' and resid 54 through 57' Processing helix chain 'Z' and resid 62 through 71 removed outlier: 3.640A pdb=" N GLU Z 67 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 97 removed outlier: 3.739A pdb=" N ILE Z 87 " --> pdb=" O ARG Z 83 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU Z 88 " --> pdb=" O ARG Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 116 Processing helix chain 'Z' and resid 121 through 123 No H-bonds generated for 'chain 'Z' and resid 121 through 123' Processing helix chain 'Z' and resid 125 through 142 removed outlier: 3.968A pdb=" N LEU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASN Z 142 " --> pdb=" O ASP Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 161 Processing helix chain 'Z' and resid 173 through 187 Processing helix chain 'Z' and resid 193 through 205 removed outlier: 3.704A pdb=" N TYR Z 197 " --> pdb=" O ILE Z 193 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS Z 198 " --> pdb=" O ASP Z 194 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS Z 205 " --> pdb=" O LYS Z 201 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 235 removed outlier: 3.821A pdb=" N ALA Z 233 " --> pdb=" O MET Z 229 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET Z 234 " --> pdb=" O ILE Z 230 " (cutoff:3.500A) Proline residue: Z 235 - end of helix Processing helix chain 'Z' and resid 258 through 271 removed outlier: 3.696A pdb=" N ASN Z 270 " --> pdb=" O ILE Z 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 107 removed outlier: 4.117A pdb=" N LYS J 52 " --> pdb=" O THR J 48 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS J 69 " --> pdb=" O GLU J 65 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG J 87 " --> pdb=" O VAL J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 127 removed outlier: 3.671A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY J 118 " --> pdb=" O VAL J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 159 removed outlier: 3.531A pdb=" N PHE J 141 " --> pdb=" O LYS J 138 " (cutoff:3.500A) Proline residue: J 142 - end of helix removed outlier: 4.167A pdb=" N LYS J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN J 149 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS J 150 " --> pdb=" O ALA J 147 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.901A pdb=" N ALA J 158 " --> pdb=" O TYR J 155 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR J 159 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 206 removed outlier: 3.872A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 216 Processing helix chain 'M' and resid 29 through 103 removed outlier: 5.251A pdb=" N GLU M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS M 56 " --> pdb=" O GLU M 52 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER M 68 " --> pdb=" O GLY M 64 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG M 92 " --> pdb=" O PHE M 88 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASP M 93 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLU M 94 " --> pdb=" O GLN M 90 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL M 95 " --> pdb=" O ASN M 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 75 removed outlier: 4.008A pdb=" N ASN G 31 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU G 71 " --> pdb=" O PHE G 67 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA G 72 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 85 Processing helix chain 'G' and resid 129 through 174 Processing helix chain 'G' and resid 176 through 215 removed outlier: 3.614A pdb=" N ILE G 187 " --> pdb=" O THR G 183 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG G 196 " --> pdb=" O ASP G 192 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU G 198 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU G 214 " --> pdb=" O LYS G 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 104 removed outlier: 3.668A pdb=" N VAL I 83 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS I 104 " --> pdb=" O GLN I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 127 removed outlier: 3.745A pdb=" N GLN I 113 " --> pdb=" O THR I 109 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 196 through 203 Processing helix chain 'I' and resid 208 through 216 removed outlier: 3.546A pdb=" N GLY I 213 " --> pdb=" O PRO I 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 90 removed outlier: 3.725A pdb=" N SER L 68 " --> pdb=" O GLY L 64 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN L 78 " --> pdb=" O GLU L 74 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN L 85 " --> pdb=" O MET L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 103 Processing helix chain 'H' and resid 35 through 106 removed outlier: 5.364A pdb=" N LYS H 52 " --> pdb=" O THR H 48 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE H 53 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N MET H 54 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU H 55 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN H 67 " --> pdb=" O GLN H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 127 removed outlier: 3.935A pdb=" N VAL H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 121 " --> pdb=" O ASP H 117 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 157 removed outlier: 3.680A pdb=" N ALA H 146 " --> pdb=" O PRO H 142 " (cutoff:3.500A) Proline residue: H 153 - end of helix Processing helix chain 'H' and resid 196 through 204 Processing helix chain 'H' and resid 208 through 216 Processing helix chain 'K' and resid 31 through 89 removed outlier: 4.363A pdb=" N ALA K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU K 38 " --> pdb=" O LYS K 34 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN K 41 " --> pdb=" O LYS K 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE K 55 " --> pdb=" O ARG K 51 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS K 56 " --> pdb=" O GLU K 52 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER K 68 " --> pdb=" O GLY K 64 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER K 70 " --> pdb=" O ARG K 66 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 103 Processing helix chain 'N' and resid 14 through 23 Processing helix chain 'N' and resid 45 through 57 Processing helix chain 'N' and resid 68 through 71 No H-bonds generated for 'chain 'N' and resid 68 through 71' Processing helix chain 'N' and resid 75 through 79 Processing sheet with id= A, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.590A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 28 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= C, first strand: chain 'A' and resid 183 through 185 removed outlier: 4.929A pdb=" N ASP A 134 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 166 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE A 155 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N HIS A 164 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 146 through 148 removed outlier: 6.611A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 219 through 221 removed outlier: 3.746A pdb=" N GLU A 219 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A 391 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 271 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N MET A 347 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ASP A 349 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL A 275 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 406 through 409 removed outlier: 6.997A pdb=" N VAL A 431 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 295 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 20 through 25 removed outlier: 6.653A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 56 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN B 65 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B 54 " --> pdb=" O GLN B 65 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= J, first strand: chain 'B' and resid 183 through 185 removed outlier: 4.990A pdb=" N ASP B 134 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS B 164 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.179A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 219 through 221 removed outlier: 3.615A pdb=" N GLU B 219 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASP B 349 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 275 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 406 through 410 removed outlier: 6.810A pdb=" N VAL B 431 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N TRP B 433 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 295 through 298 Processing sheet with id= O, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.425A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= Q, first strand: chain 'C' and resid 183 through 185 removed outlier: 4.779A pdb=" N ASP C 134 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.469A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 219 through 221 removed outlier: 3.572A pdb=" N GLU C 219 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 271 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N MET C 347 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 273 " --> pdb=" O MET C 347 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASP C 349 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL C 275 " --> pdb=" O ASP C 349 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 245 through 249 removed outlier: 6.547A pdb=" N ILE C 406 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE C 248 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY C 408 " --> pdb=" O ILE C 248 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 295 through 297 Processing sheet with id= V, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.131A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 120 through 123 Processing sheet with id= X, first strand: chain 'D' and resid 131 through 133 removed outlier: 8.101A pdb=" N PHE D 132 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU D 259 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE D 351 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE D 191 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.267A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP E 61 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL E 50 " --> pdb=" O ASP E 61 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= AA, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.722A pdb=" N ARG E 130 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N CYS E 258 " --> pdb=" O PHE E 227 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N HIS E 292 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL E 230 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU E 294 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA E 232 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE E 296 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 351 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE E 191 " --> pdb=" O LEU E 354 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.848A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU F 88 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AD, first strand: chain 'F' and resid 130 through 133 removed outlier: 3.605A pdb=" N ARG F 130 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE F 351 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE F 191 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 164 through 167 Processing sheet with id= AF, first strand: chain 'G' and resid 95 through 101 Processing sheet with id= AG, first strand: chain 'I' and resid 164 through 167 Processing sheet with id= AH, first strand: chain 'H' and resid 164 through 167 Processing sheet with id= AI, first strand: chain 'N' and resid 87 through 91 removed outlier: 7.867A pdb=" N LEU N 7 " --> pdb=" O GLY N 62 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE N 64 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA N 9 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE N 66 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE N 11 " --> pdb=" O ILE N 66 " (cutoff:3.500A) 1779 hydrogen bonds defined for protein. 5181 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.18 Time building geometry restraints manager: 16.38 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: 13437 1.34 - 1.46: 5623 1.46 - 1.57: 21921 1.57 - 1.69: 3 1.69 - 1.81: 374 Bond restraints: 41358 Sorted by residual: bond pdb=" C ARG D 120 " pdb=" N THR D 121 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.07e-02 2.33e+03 1.01e+01 bond pdb=" N GLN D 156 " pdb=" CA GLN D 156 " ideal model delta sigma weight residual 1.457 1.432 0.024 1.41e-02 5.03e+03 3.02e+00 bond pdb=" CA PRO B 169 " pdb=" C PRO B 169 " ideal model delta sigma weight residual 1.514 1.505 0.009 5.50e-03 3.31e+04 2.63e+00 bond pdb=" C GLN Y 207 " pdb=" O GLN Y 207 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.28e+00 bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.82e+00 ... (remaining 41353 not shown) Histogram of bond angle deviations from ideal: 98.70 - 106.16: 984 106.16 - 113.61: 23165 113.61 - 121.06: 20800 121.06 - 128.52: 10717 128.52 - 135.97: 173 Bond angle restraints: 55839 Sorted by residual: angle pdb=" C LYS L 34 " pdb=" N GLN L 35 " pdb=" CA GLN L 35 " ideal model delta sigma weight residual 121.14 113.09 8.05 1.75e+00 3.27e-01 2.12e+01 angle pdb=" CA GLN L 35 " pdb=" CB GLN L 35 " pdb=" CG GLN L 35 " ideal model delta sigma weight residual 114.10 121.34 -7.24 2.00e+00 2.50e-01 1.31e+01 angle pdb=" N ILE C 102 " pdb=" CA ILE C 102 " pdb=" C ILE C 102 " ideal model delta sigma weight residual 112.98 108.87 4.11 1.25e+00 6.40e-01 1.08e+01 angle pdb=" N VAL E 438 " pdb=" CA VAL E 438 " pdb=" C VAL E 438 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.06e+01 angle pdb=" N ILE C 94 " pdb=" CA ILE C 94 " pdb=" C ILE C 94 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.06e+01 ... (remaining 55834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 24297 33.88 - 67.76: 1066 67.76 - 101.65: 96 101.65 - 135.53: 1 135.53 - 169.41: 1 Dihedral angle restraints: 25461 sinusoidal: 10518 harmonic: 14943 Sorted by residual: dihedral pdb=" O2A ADP C 701 " pdb=" O3A ADP C 701 " pdb=" PA ADP C 701 " pdb=" PB ADP C 701 " ideal model delta sinusoidal sigma weight residual 300.00 130.59 169.41 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA LYS M 34 " pdb=" C LYS M 34 " pdb=" N GLN M 35 " pdb=" CA GLN M 35 " ideal model delta harmonic sigma weight residual 180.00 148.52 31.48 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA ASN L 30 " pdb=" C ASN L 30 " pdb=" N ARG L 31 " pdb=" CA ARG L 31 " ideal model delta harmonic sigma weight residual 180.00 148.60 31.40 0 5.00e+00 4.00e-02 3.94e+01 ... (remaining 25458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4726 0.053 - 0.105: 1345 0.105 - 0.158: 199 0.158 - 0.210: 5 0.210 - 0.263: 1 Chirality restraints: 6276 Sorted by residual: chirality pdb=" CB ILE B 327 " pdb=" CA ILE B 327 " pdb=" CG1 ILE B 327 " pdb=" CG2 ILE B 327 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA GLN L 35 " pdb=" N GLN L 35 " pdb=" C GLN L 35 " pdb=" CB GLN L 35 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA ASN C 397 " pdb=" N ASN C 397 " pdb=" C ASN C 397 " pdb=" CB ASN C 397 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 6273 not shown) Planarity restraints: 7245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR Y 146 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO Y 147 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO Y 147 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO Y 147 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN I 194 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.04e+00 pdb=" C ASN I 194 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN I 194 " -0.015 2.00e-02 2.50e+03 pdb=" N THR I 195 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 363 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO D 364 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 364 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 364 " -0.029 5.00e-02 4.00e+02 ... (remaining 7242 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 945 2.69 - 3.24: 38228 3.24 - 3.79: 61265 3.79 - 4.35: 86712 4.35 - 4.90: 144784 Nonbonded interactions: 331934 Sorted by model distance: nonbonded pdb=" NH2 ARG E 208 " pdb=" O PRO E 467 " model vdw 2.132 2.520 nonbonded pdb=" O ASN E 393 " pdb=" OG SER E 397 " model vdw 2.156 2.440 nonbonded pdb=" OH TYR D 39 " pdb=" OE1 GLU H 210 " model vdw 2.163 2.440 nonbonded pdb=" OE2 GLU B 360 " pdb=" OG1 THR E 329 " model vdw 2.164 2.440 nonbonded pdb=" OG SER F 253 " pdb=" OD1 ASP F 255 " model vdw 2.187 2.440 ... (remaining 331929 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' and (resid 17 through 497 or (resid 498 through 499 and (name N or na \ me CA or name C or name O or name CB )) or resid 500 through 616)) selection = (chain 'C' and (resid 17 through 497 or (resid 498 through 499 and (name N or na \ me CA or name C or name O or name CB )) or resid 500 through 616)) } ncs_group { reference = (chain 'D' and (resid 39 through 314 or (resid 315 and (name N or name CA or nam \ e C or name O or name CB )) or resid 316 through 434 or (resid 435 and (name N o \ r name CA or name C or name O or name CB )) or resid 436 through 440 or (resid 4 \ 41 through 443 and (name N or name CA or name C or name O or name CB )) or resid \ 444 through 506)) selection = (chain 'E' and (resid 39 through 314 or (resid 315 and (name N or name CA or nam \ e C or name O or name CB )) or resid 316 through 506)) selection = (chain 'F' and (resid 39 through 434 or (resid 435 and (name N or name CA or nam \ e C or name O or name CB )) or resid 436 through 440 or (resid 441 through 443 a \ nd (name N or name CA or name C or name O or name CB )) or resid 444 through 506 \ )) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = (chain 'X' and (resid 14 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or resid 102 through 219 or (resid 220 and (name N o \ r name CA or name C or name O or name CB )) or resid 221 through 222 or (resid 2 \ 23 and (name N or name CA or name C or name O or name CB )) or resid 224 through \ 275)) selection = (chain 'Y' and (resid 14 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or resid 102 through 235 or (resid 236 and (name CA \ or name C or name O or name CB or name CG or name CD or name CE or name NZ )) or \ resid 237 through 275)) selection = (chain 'Z' and (resid 14 through 219 or (resid 220 and (name N or name CA or nam \ e C or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N o \ r name CA or name C or name O or name CB )) or resid 224 through 235 or (resid 2 \ 36 and (name CA or name C or name O or name CB or name CG or name CD or name CE \ or name NZ )) or resid 237 through 275)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 11.320 Check model and map are aligned: 0.650 Set scattering table: 0.430 Process input model: 105.870 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 41358 Z= 0.403 Angle : 0.661 11.231 55839 Z= 0.368 Chirality : 0.047 0.263 6276 Planarity : 0.005 0.061 7245 Dihedral : 17.767 169.411 15833 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 7.27 % Allowed : 20.45 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.10), residues: 5098 helix: -1.67 (0.09), residues: 2478 sheet: -1.43 (0.19), residues: 632 loop : -2.74 (0.11), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 450 HIS 0.005 0.001 HIS C 444 PHE 0.020 0.002 PHE I 38 TYR 0.014 0.002 TYR I 56 ARG 0.005 0.000 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 550 time to evaluate : 5.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7901 (mmt-90) REVERT: A 471 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7173 (pp20) REVERT: A 506 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7590 (mmtp) REVERT: A 578 LEU cc_start: 0.9144 (mt) cc_final: 0.8815 (mt) REVERT: B 161 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8205 (tt) REVERT: B 387 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8313 (tp30) REVERT: B 523 ASN cc_start: 0.7960 (t0) cc_final: 0.7739 (t0) REVERT: B 556 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6634 (pm20) REVERT: B 597 ILE cc_start: 0.7995 (mt) cc_final: 0.7783 (mp) REVERT: C 18 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7287 (t80) REVERT: C 80 LEU cc_start: 0.9031 (tt) cc_final: 0.8776 (tp) REVERT: C 171 ARG cc_start: 0.8167 (mtp180) cc_final: 0.7885 (mtm180) REVERT: C 201 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.5435 (tm-30) REVERT: C 467 LYS cc_start: 0.8734 (tttm) cc_final: 0.8383 (ttmm) REVERT: C 571 ARG cc_start: 0.7512 (tmt-80) cc_final: 0.7293 (tmt-80) REVERT: C 573 HIS cc_start: 0.7357 (t-170) cc_final: 0.6906 (t-170) REVERT: C 574 MET cc_start: 0.8209 (mtm) cc_final: 0.7895 (mtp) REVERT: D 57 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8712 (mt) REVERT: D 238 MET cc_start: 0.8560 (tpp) cc_final: 0.8274 (tpt) REVERT: D 386 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7888 (mtm-85) REVERT: E 169 MET cc_start: 0.9116 (ttt) cc_final: 0.8434 (ttt) REVERT: E 180 MET cc_start: 0.9236 (mtp) cc_final: 0.9018 (mtm) REVERT: E 300 MET cc_start: 0.8479 (mmm) cc_final: 0.8047 (mmm) REVERT: E 342 GLU cc_start: 0.7570 (tt0) cc_final: 0.7308 (pt0) REVERT: E 408 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: E 497 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7406 (tp-100) REVERT: F 137 LYS cc_start: 0.8288 (mttt) cc_final: 0.8054 (mppt) REVERT: F 154 MET cc_start: 0.8239 (mmt) cc_final: 0.7976 (mmm) REVERT: F 237 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8258 (p0) REVERT: F 239 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: F 431 ASP cc_start: 0.7643 (m-30) cc_final: 0.7387 (m-30) REVERT: F 435 MET cc_start: 0.8236 (ttp) cc_final: 0.8036 (ttm) REVERT: X 166 TYR cc_start: 0.7302 (m-80) cc_final: 0.6982 (m-80) REVERT: X 171 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7230 (p0) REVERT: Y 115 MET cc_start: 0.7953 (mtt) cc_final: 0.7667 (mtp) REVERT: Y 244 ASP cc_start: 0.6512 (OUTLIER) cc_final: 0.6133 (p0) REVERT: Z 177 GLN cc_start: 0.6831 (tp40) cc_final: 0.6555 (tp40) REVERT: Z 229 MET cc_start: 0.5280 (tpp) cc_final: 0.5041 (mmm) REVERT: J 54 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.6358 (mtm) REVERT: J 55 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6915 (mt-10) REVERT: J 99 LYS cc_start: 0.8099 (mttt) cc_final: 0.7684 (mtpm) REVERT: J 131 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7700 (ttm-80) REVERT: J 185 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8965 (p0) REVERT: J 198 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8206 (m) REVERT: J 212 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7962 (ttt-90) REVERT: M 85 GLN cc_start: 0.8432 (mp10) cc_final: 0.8220 (mp-120) REVERT: I 89 ASP cc_start: 0.7463 (m-30) cc_final: 0.7090 (m-30) REVERT: I 131 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7655 (mtp85) REVERT: I 139 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: L 74 GLU cc_start: 0.7295 (tt0) cc_final: 0.6728 (tm-30) REVERT: L 79 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6193 (tm-30) REVERT: L 90 GLN cc_start: 0.8061 (mt0) cc_final: 0.7629 (mm110) REVERT: L 102 PHE cc_start: 0.8353 (m-80) cc_final: 0.8018 (m-80) REVERT: H 54 MET cc_start: 0.6678 (ptp) cc_final: 0.6252 (pmt) REVERT: H 97 GLU cc_start: 0.7708 (tp30) cc_final: 0.7375 (tp30) REVERT: H 183 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8718 (mm) REVERT: H 201 ASP cc_start: 0.8117 (t70) cc_final: 0.7911 (t0) REVERT: K 83 ILE cc_start: 0.8309 (mt) cc_final: 0.8056 (mm) REVERT: N 66 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7568 (mm) outliers start: 323 outliers final: 161 residues processed: 836 average time/residue: 1.6306 time to fit residues: 1640.6151 Evaluate side-chains 669 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 486 time to evaluate : 4.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 501 SER Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 237 ASN Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 314 ARG Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain X residue 51 ASP Chi-restraints excluded: chain X residue 126 TYR Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 171 ASP Chi-restraints excluded: chain X residue 250 SER Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 40 ASN Chi-restraints excluded: chain Y residue 126 TYR Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 188 MET Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 244 ASP Chi-restraints excluded: chain Y residue 269 GLU Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 87 ILE Chi-restraints excluded: chain Z residue 162 GLN Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 171 SER Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain M residue 34 LYS Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 139 GLN Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 105 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 429 optimal weight: 20.0000 chunk 385 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 260 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 398 optimal weight: 9.9990 chunk 154 optimal weight: 0.4980 chunk 242 optimal weight: 0.6980 chunk 296 optimal weight: 0.5980 chunk 462 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: