Starting phenix.real_space_refine on Tue Mar 19 03:19:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2y_31670/03_2024/7v2y_31670.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2y_31670/03_2024/7v2y_31670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2y_31670/03_2024/7v2y_31670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2y_31670/03_2024/7v2y_31670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2y_31670/03_2024/7v2y_31670.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2y_31670/03_2024/7v2y_31670.pdb" } resolution = 3.4 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= 0.006 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 93 5.16 5 C 14736 2.51 5 N 3862 2.21 5 O 4406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 5": "OE1" <-> "OE2" Residue "A GLU 6": "OE1" <-> "OE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A ASP 470": "OD1" <-> "OD2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ASP 593": "OD1" <-> "OD2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B ASP 225": "OD1" <-> "OD2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B ASP 464": "OD1" <-> "OD2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 496": "OE1" <-> "OE2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 523": "OD1" <-> "OD2" Residue "B PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "B PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 700": "OD1" <-> "OD2" Residue "B ASP 720": "OD1" <-> "OD2" Residue "B GLU 771": "OE1" <-> "OE2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "B TYR 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 813": "OD1" <-> "OD2" Residue "B ASP 860": "OD1" <-> "OD2" Residue "B GLU 884": "OE1" <-> "OE2" Residue "B ARG 895": "NH1" <-> "NH2" Residue "B ARG 908": "NH1" <-> "NH2" Residue "B ASP 912": "OD1" <-> "OD2" Residue "B GLU 919": "OE1" <-> "OE2" Residue "B PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 959": "OD1" <-> "OD2" Residue "B TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 965": "OE1" <-> "OE2" Residue "B ARG 966": "NH1" <-> "NH2" Residue "B ASP 992": "OD1" <-> "OD2" Residue "B GLU 1009": "OE1" <-> "OE2" Residue "B GLU 1024": "OE1" <-> "OE2" Residue "B ASP 1045": "OD1" <-> "OD2" Residue "B PHE 1051": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1102": "OE1" <-> "OE2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "B ASP 1109": "OD1" <-> "OD2" Residue "B ASP 1112": "OD1" <-> "OD2" Residue "B ASP 1131": "OD1" <-> "OD2" Residue "B GLU 1135": "OE1" <-> "OE2" Residue "B ARG 1142": "NH1" <-> "NH2" Residue "B GLU 1171": "OE1" <-> "OE2" Residue "B ARG 1178": "NH1" <-> "NH2" Residue "B ARG 1195": "NH1" <-> "NH2" Residue "B GLU 1210": "OE1" <-> "OE2" Residue "B GLU 1212": "OE1" <-> "OE2" Residue "B GLU 1220": "OE1" <-> "OE2" Residue "B GLU 1230": "OE1" <-> "OE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C ASP 94": "OD1" <-> "OD2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ASP 208": "OD1" <-> "OD2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C ASP 302": "OD1" <-> "OD2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 341": "OD1" <-> "OD2" Residue "C TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 360": "OD1" <-> "OD2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 9": "OD1" <-> "OD2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E ASP 39": "OD1" <-> "OD2" Residue "E ASP 45": "OD1" <-> "OD2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E ASP 136": "OD1" <-> "OD2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E ASP 166": "OD1" <-> "OD2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "E ASP 179": "OD1" <-> "OD2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F GLU 149": "OE1" <-> "OE2" Residue "F TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 176": "OE1" <-> "OE2" Residue "F ASP 182": "OD1" <-> "OD2" Residue "F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 218": "OD1" <-> "OD2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F ARG 228": "NH1" <-> "NH2" Residue "F PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 240": "OD1" <-> "OD2" Residue "F PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F ASP 303": "OD1" <-> "OD2" Residue "F PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 343": "OE1" <-> "OE2" Residue "F PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 415": "OD1" <-> "OD2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 424": "OE1" <-> "OE2" Residue "F PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23097 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4942 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 22, 'TRANS': 570} Chain breaks: 1 Chain: "B" Number of atoms: 9958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1226, 9958 Classifications: {'peptide': 1226} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1191} Chain breaks: 1 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 333, 2606 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "D" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1106 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "E" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1459 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "F" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3026 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 15, 'TRANS': 360} Chain breaks: 1 Time building chain proxies: 11.66, per 1000 atoms: 0.50 Number of scatterers: 23097 At special positions: 0 Unit cell: (220.18, 149.33, 119.9, 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 93 16.00 O 4406 8.00 N 3862 7.00 C 14736 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: 7.88 Conformation dependent library (CDL) restraints added in 4.2 seconds 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5506 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 14 sheets defined 55.4% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 removed outlier: 3.615A pdb=" N SER A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 13 " --> pdb=" O GLN A 9 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 removed outlier: 3.679A pdb=" N ILE A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N HIS A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.645A pdb=" N PHE A 46 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.816A pdb=" N LYS A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 79 removed outlier: 3.707A pdb=" N LEU A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 106 removed outlier: 4.117A pdb=" N GLU A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 131 removed outlier: 3.606A pdb=" N THR A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.590A pdb=" N LYS A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 removed outlier: 3.619A pdb=" N SER A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.016A pdb=" N LYS A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 153' Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.680A pdb=" N ASP A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.583A pdb=" N GLU A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 266 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.758A pdb=" N PHE A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.917A pdb=" N ASP A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.563A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 321 removed outlier: 3.596A pdb=" N SER A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A 312 " --> pdb=" O MET A 308 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 316 " --> pdb=" O THR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.586A pdb=" N MET A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 360 removed outlier: 4.052A pdb=" N GLN A 357 " --> pdb=" O TRP A 353 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 388 removed outlier: 3.790A pdb=" N TYR A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 415 removed outlier: 3.827A pdb=" N ILE A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A 405 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 407 " --> pdb=" O CYS A 403 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 415 " --> pdb=" O ASN A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.600A pdb=" N GLY A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.568A pdb=" N LYS A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 488 " --> pdb=" O LYS A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 removed outlier: 3.640A pdb=" N ASN A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 565 removed outlier: 3.752A pdb=" N VAL A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.900A pdb=" N SER B 8 " --> pdb=" O GLN B 4 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 removed outlier: 3.648A pdb=" N SER B 41 " --> pdb=" O TRP B 37 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 42 " --> pdb=" O PRO B 38 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 49 " --> pdb=" O CYS B 45 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 72 removed outlier: 3.554A pdb=" N GLU B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 removed outlier: 3.737A pdb=" N GLU B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 100 " --> pdb=" O HIS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 121 through 130 removed outlier: 3.788A pdb=" N THR B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 removed outlier: 3.505A pdb=" N PHE B 140 " --> pdb=" O HIS B 136 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.821A pdb=" N HIS B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 192 removed outlier: 3.507A pdb=" N GLN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 4.279A pdb=" N GLU B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.914A pdb=" N ASP B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.652A pdb=" N ALA B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 282 removed outlier: 3.589A pdb=" N ILE B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 307 removed outlier: 3.628A pdb=" N TYR B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 304 " --> pdb=" O MET B 300 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 306 " --> pdb=" O CYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 317 removed outlier: 3.583A pdb=" N ASP B 317 " --> pdb=" O TYR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 343 removed outlier: 4.039A pdb=" N GLU B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 removed outlier: 4.276A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.699A pdb=" N GLN B 426 " --> pdb=" O HIS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 431 removed outlier: 3.725A pdb=" N LEU B 431 " --> pdb=" O PRO B 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 428 through 431' Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.809A pdb=" N LEU B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 438 " --> pdb=" O GLU B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 438' Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.702A pdb=" N VAL B 444 " --> pdb=" O TYR B 440 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 3.655A pdb=" N SER B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 463 removed outlier: 3.601A pdb=" N GLU B 461 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.741A pdb=" N TYR B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 541 Processing helix chain 'B' and resid 542 through 560 removed outlier: 3.628A pdb=" N LEU B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 552 " --> pdb=" O LYS B 548 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 removed outlier: 3.993A pdb=" N TRP B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.906A pdb=" N ARG B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.560A pdb=" N SER B 596 " --> pdb=" O PRO B 592 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 597 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 601 " --> pdb=" O GLU B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 625 through 640 removed outlier: 3.764A pdb=" N LYS B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 631 " --> pdb=" O PRO B 627 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 636 " --> pdb=" O PHE B 632 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 665 removed outlier: 4.527A pdb=" N ARG B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 657 " --> pdb=" O LYS B 653 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 661 " --> pdb=" O ARG B 657 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 676 Processing helix chain 'B' and resid 683 through 691 removed outlier: 3.532A pdb=" N VAL B 688 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 694 No H-bonds generated for 'chain 'B' and resid 692 through 694' Processing helix chain 'B' and resid 697 through 711 removed outlier: 3.587A pdb=" N VAL B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 742 removed outlier: 3.886A pdb=" N LYS B 740 " --> pdb=" O ALA B 736 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 741 " --> pdb=" O GLY B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 758 removed outlier: 3.504A pdb=" N LYS B 756 " --> pdb=" O THR B 752 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 757 " --> pdb=" O TYR B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 776 removed outlier: 3.599A pdb=" N VAL B 766 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 771 " --> pdb=" O SER B 767 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 774 " --> pdb=" O LYS B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 793 Processing helix chain 'B' and resid 797 through 807 removed outlier: 3.703A pdb=" N GLN B 801 " --> pdb=" O SER B 797 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS B 805 " --> pdb=" O GLN B 801 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 807 " --> pdb=" O ALA B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 828 removed outlier: 3.536A pdb=" N SER B 818 " --> pdb=" O ASN B 814 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 824 " --> pdb=" O ARG B 820 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN B 828 " --> pdb=" O PHE B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 845 removed outlier: 3.624A pdb=" N ILE B 835 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 836 " --> pdb=" O SER B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 877 removed outlier: 3.634A pdb=" N SER B 868 " --> pdb=" O THR B 864 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 871 " --> pdb=" O TRP B 867 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 872 " --> pdb=" O SER B 868 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 886 removed outlier: 3.970A pdb=" N ASN B 885 " --> pdb=" O ALA B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 893 removed outlier: 3.653A pdb=" N ASN B 893 " --> pdb=" O PHE B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 916 removed outlier: 3.586A pdb=" N PHE B 904 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 906 " --> pdb=" O TRP B 902 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP B 909 " --> pdb=" O HIS B 905 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR B 910 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN B 913 " --> pdb=" O ASP B 909 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN B 914 " --> pdb=" O TYR B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 927 removed outlier: 4.251A pdb=" N ASP B 924 " --> pdb=" O ASN B 920 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 925 " --> pdb=" O PHE B 921 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 926 " --> pdb=" O SER B 922 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 927 " --> pdb=" O ILE B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 951 removed outlier: 3.918A pdb=" N THR B 947 " --> pdb=" O ASP B 943 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TRP B 949 " --> pdb=" O PHE B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 974 removed outlier: 3.895A pdb=" N ARG B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 967 " --> pdb=" O TYR B 963 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 970 " --> pdb=" O ARG B 966 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 974 " --> pdb=" O LEU B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 1019 removed outlier: 4.023A pdb=" N LYS B 983 " --> pdb=" O SER B 979 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 992 " --> pdb=" O ASN B 988 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 994 " --> pdb=" O ILE B 990 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B1009 " --> pdb=" O LYS B1005 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B1010 " --> pdb=" O LYS B1006 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN B1016 " --> pdb=" O SER B1012 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1034 Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'B' and resid 1042 through 1047 removed outlier: 3.564A pdb=" N LEU B1047 " --> pdb=" O PRO B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1052 Processing helix chain 'B' and resid 1052 through 1057 removed outlier: 3.642A pdb=" N PHE B1057 " --> pdb=" O ILE B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1071 removed outlier: 3.652A pdb=" N MET B1063 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B1064 " --> pdb=" O GLU B1060 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR B1068 " --> pdb=" O SER B1064 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS B1069 " --> pdb=" O ILE B1065 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B1070 " --> pdb=" O LEU B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1079 removed outlier: 3.682A pdb=" N LEU B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1107 removed outlier: 3.511A pdb=" N GLY B1091 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B1092 " --> pdb=" O GLY B1088 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B1094 " --> pdb=" O LEU B1090 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B1096 " --> pdb=" O LEU B1092 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B1100 " --> pdb=" O ASP B1096 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B1104 " --> pdb=" O LYS B1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1134 removed outlier: 3.549A pdb=" N LYS B1117 " --> pdb=" O GLN B1113 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS B1122 " --> pdb=" O LEU B1118 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B1123 " --> pdb=" O TYR B1119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B1124 " --> pdb=" O GLU B1120 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B1130 " --> pdb=" O THR B1126 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B1131 " --> pdb=" O GLU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1151 removed outlier: 3.638A pdb=" N ASN B1143 " --> pdb=" O MET B1139 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS B1150 " --> pdb=" O GLU B1146 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B1151 " --> pdb=" O PHE B1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1175 removed outlier: 3.616A pdb=" N ILE B1162 " --> pdb=" O VAL B1158 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR B1167 " --> pdb=" O GLN B1163 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR B1168 " --> pdb=" O LEU B1164 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B1169 " --> pdb=" O VAL B1165 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU B1170 " --> pdb=" O TYR B1166 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B1172 " --> pdb=" O THR B1168 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B1173 " --> pdb=" O LEU B1169 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN B1175 " --> pdb=" O GLU B1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 1181 through 1193 removed outlier: 3.536A pdb=" N SER B1185 " --> pdb=" O ILE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1196 No H-bonds generated for 'chain 'B' and resid 1194 through 1196' Processing helix chain 'B' and resid 1211 through 1232 removed outlier: 3.609A pdb=" N MET B1221 " --> pdb=" O ARG B1217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN B1228 " --> pdb=" O GLU B1224 " (cutoff:3.500A) Processing helix chain 'B' and resid 1241 through 1255 removed outlier: 3.605A pdb=" N ASN B1249 " --> pdb=" O GLN B1245 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS B1250 " --> pdb=" O LEU B1246 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER B1251 " --> pdb=" O GLU B1247 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 56 removed outlier: 3.502A pdb=" N SER C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'D' and resid 4 through 9 removed outlier: 3.515A pdb=" N ASP D 9 " --> pdb=" O GLN D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 removed outlier: 3.809A pdb=" N LYS D 14 " --> pdb=" O GLN D 10 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 15 " --> pdb=" O VAL D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 10 through 15' Processing helix chain 'D' and resid 21 through 44 removed outlier: 3.713A pdb=" N ASP D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER D 40 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 100 removed outlier: 3.816A pdb=" N PHE D 72 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 73 " --> pdb=" O HIS D 69 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 138 removed outlier: 4.057A pdb=" N ILE D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 112 " --> pdb=" O PRO D 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 113 " --> pdb=" O ASP D 109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL D 133 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 37 removed outlier: 3.567A pdb=" N GLU E 16 " --> pdb=" O SER E 12 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN E 18 " --> pdb=" O CYS E 14 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU E 22 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 53 removed outlier: 4.326A pdb=" N LEU E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS E 53 " --> pdb=" O GLU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 84 removed outlier: 3.559A pdb=" N LEU E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG E 59 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 62 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 104 removed outlier: 3.900A pdb=" N ILE E 100 " --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 109 through 119 removed outlier: 3.747A pdb=" N ASP E 113 " --> pdb=" O HIS E 109 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 162 removed outlier: 4.075A pdb=" N ILE E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 162 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 removed outlier: 4.044A pdb=" N ALA E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN E 173 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN E 180 " --> pdb=" O ASN E 176 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE E 181 " --> pdb=" O TYR E 177 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS E 182 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA E 184 " --> pdb=" O GLN E 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 68 removed outlier: 3.529A pdb=" N PHE F 67 " --> pdb=" O PHE F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 81 removed outlier: 4.208A pdb=" N ILE F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP F 79 " --> pdb=" O ARG F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 98 removed outlier: 3.867A pdb=" N THR F 92 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE F 93 " --> pdb=" O GLN F 89 " (cutoff:3.500A) Proline residue: F 94 - end of helix removed outlier: 4.092A pdb=" N HIS F 98 " --> pdb=" O PRO F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 124 removed outlier: 4.551A pdb=" N PHE F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL F 117 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER F 119 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 151 removed outlier: 3.787A pdb=" N ALA F 143 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR F 144 " --> pdb=" O ARG F 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'F' and resid 181 through 184 Processing helix chain 'F' and resid 191 through 200 removed outlier: 4.568A pdb=" N ALA F 197 " --> pdb=" O GLY F 193 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F 198 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL F 199 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG F 200 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 222 removed outlier: 3.553A pdb=" N GLU F 222 " --> pdb=" O ASP F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 236 removed outlier: 3.569A pdb=" N ARG F 228 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU F 232 " --> pdb=" O ARG F 228 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE F 233 " --> pdb=" O ASP F 229 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 removed outlier: 3.809A pdb=" N ARG F 259 " --> pdb=" O ARG F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 302 removed outlier: 3.871A pdb=" N ASP F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 328 removed outlier: 3.679A pdb=" N GLU F 321 " --> pdb=" O THR F 317 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS F 324 " --> pdb=" O ASN F 320 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA F 328 " --> pdb=" O LYS F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 354 removed outlier: 3.559A pdb=" N ALA F 347 " --> pdb=" O GLU F 343 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR F 349 " --> pdb=" O ARG F 345 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE F 352 " --> pdb=" O ARG F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 368 removed outlier: 3.582A pdb=" N PHE F 366 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY F 367 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG F 368 " --> pdb=" O VAL F 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 363 through 368' Processing helix chain 'F' and resid 389 through 394 Processing helix chain 'F' and resid 398 through 402 removed outlier: 4.181A pdb=" N GLY F 401 " --> pdb=" O GLY F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 426 removed outlier: 3.730A pdb=" N VAL F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU F 419 " --> pdb=" O ASP F 415 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU F 424 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA2, first strand: chain 'B' and resid 484 through 486 Processing sheet with id=AA3, first strand: chain 'B' and resid 488 through 491 removed outlier: 6.162A pdb=" N TYR B 489 " --> pdb=" O VAL B 505 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 4.737A pdb=" N ARG C 44 " --> pdb=" O HIS C 365 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N HIS C 365 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 353 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.826A pdb=" N LYS C 70 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 115 through 120 removed outlier: 4.574A pdb=" N ASP C 117 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C 131 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE C 137 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR C 154 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU C 139 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 163 through 165 removed outlier: 3.596A pdb=" N THR C 165 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 174 through 175 removed outlier: 3.924A pdb=" N CYS C 197 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 214 through 217 removed outlier: 3.791A pdb=" N SER C 214 " --> pdb=" O GLY C 227 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU C 233 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS C 248 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 235 " --> pdb=" O CYS C 246 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.503A pdb=" N THR C 270 " --> pdb=" O TYR C 278 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR C 278 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 279 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 298 through 302 Processing sheet with id=AB3, first strand: chain 'C' and resid 318 through 320 Processing sheet with id=AB4, first strand: chain 'F' and resid 162 through 165 removed outlier: 6.392A pdb=" N ALA F 163 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL F 133 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA F 190 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL F 135 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL F 134 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASP F 215 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE F 136 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL F 102 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET F 245 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS F 104 " --> pdb=" O MET F 245 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER F 247 " --> pdb=" O CYS F 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 333 through 335 removed outlier: 6.707A pdb=" N ILE F 334 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 309 " --> pdb=" O CYS F 360 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N SER F 362 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE F 311 " --> pdb=" O SER F 362 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE F 310 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA F 431 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR F 285 " --> pdb=" O ALA F 431 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2229 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: 6.81 Time building geometry restraints manager: 8.76 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: 7452 1.34 - 1.46: 4899 1.46 - 1.58: 11053 1.58 - 1.70: 0 1.70 - 1.82: 145 Bond restraints: 23549 Sorted by residual: bond pdb=" C LEU B1183 " pdb=" N PRO B1184 " ideal model delta sigma weight residual 1.337 1.375 -0.038 1.24e-02 6.50e+03 9.35e+00 bond pdb=" C PHE C 346 " pdb=" N TYR C 347 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.37e-02 5.33e+03 7.28e+00 bond pdb=" C THR C 62 " pdb=" N PRO C 63 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 6.94e+00 bond pdb=" C PHE B1155 " pdb=" N PRO B1156 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.60e+00 bond pdb=" C THR C 59 " pdb=" N PRO C 60 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.83e+00 ... (remaining 23544 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.56: 490 106.56 - 113.46: 12930 113.46 - 120.36: 9124 120.36 - 127.26: 9073 127.26 - 134.17: 209 Bond angle restraints: 31826 Sorted by residual: angle pdb=" N VAL B 683 " pdb=" CA VAL B 683 " pdb=" C VAL B 683 " ideal model delta sigma weight residual 113.53 106.07 7.46 9.80e-01 1.04e+00 5.80e+01 angle pdb=" C HIS B 561 " pdb=" N GLY B 562 " pdb=" CA GLY B 562 " ideal model delta sigma weight residual 121.41 132.17 -10.76 1.96e+00 2.60e-01 3.01e+01 angle pdb=" C ILE B 625 " pdb=" N LEU B 626 " pdb=" CA LEU B 626 " ideal model delta sigma weight residual 119.78 126.07 -6.29 1.24e+00 6.50e-01 2.57e+01 angle pdb=" N LYS B 960 " pdb=" CA LYS B 960 " pdb=" C LYS B 960 " ideal model delta sigma weight residual 114.56 108.32 6.24 1.27e+00 6.20e-01 2.42e+01 angle pdb=" C TYR C 168 " pdb=" N ASP C 169 " pdb=" CA ASP C 169 " ideal model delta sigma weight residual 120.68 128.03 -7.35 1.52e+00 4.33e-01 2.34e+01 ... (remaining 31821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12459 17.94 - 35.88: 1555 35.88 - 53.82: 267 53.82 - 71.76: 47 71.76 - 89.70: 34 Dihedral angle restraints: 14362 sinusoidal: 5911 harmonic: 8451 Sorted by residual: dihedral pdb=" CA LEU A 335 " pdb=" C LEU A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta harmonic sigma weight residual -180.00 -138.85 -41.15 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA PHE A 437 " pdb=" C PHE A 437 " pdb=" N GLU A 438 " pdb=" CA GLU A 438 " ideal model delta harmonic sigma weight residual -180.00 -146.36 -33.64 0 5.00e+00 4.00e-02 4.53e+01 dihedral pdb=" CA LEU E 124 " pdb=" C LEU E 124 " pdb=" N SER E 125 " pdb=" CA SER E 125 " ideal model delta harmonic sigma weight residual 180.00 148.42 31.58 0 5.00e+00 4.00e-02 3.99e+01 ... (remaining 14359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3085 0.067 - 0.134: 445 0.134 - 0.200: 55 0.200 - 0.267: 8 0.267 - 0.334: 3 Chirality restraints: 3596 Sorted by residual: chirality pdb=" CB ILE C 61 " pdb=" CA ILE C 61 " pdb=" CG1 ILE C 61 " pdb=" CG2 ILE C 61 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB VAL B 257 " pdb=" CA VAL B 257 " pdb=" CG1 VAL B 257 " pdb=" CG2 VAL B 257 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE A 374 " pdb=" CA ILE A 374 " pdb=" CG1 ILE A 374 " pdb=" CG2 ILE A 374 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3593 not shown) Planarity restraints: 4055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 141 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A 142 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 671 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO B 672 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 672 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 672 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 289 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO A 290 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.040 5.00e-02 4.00e+02 ... (remaining 4052 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6445 2.80 - 3.33: 19605 3.33 - 3.85: 35326 3.85 - 4.38: 42188 4.38 - 4.90: 71886 Nonbonded interactions: 175450 Sorted by model distance: nonbonded pdb=" OH TYR B 453 " pdb=" O SER C 284 " model vdw 2.276 2.440 nonbonded pdb=" O ALA B 112 " pdb=" OG1 THR B 116 " model vdw 2.301 2.440 nonbonded pdb=" OG1 THR C 165 " pdb=" O ALA C 178 " model vdw 2.306 2.440 nonbonded pdb=" OH TYR A 365 " pdb=" O LYS D 106 " model vdw 2.311 2.440 nonbonded pdb=" O ASP A 60 " pdb=" OG SER A 63 " model vdw 2.312 2.440 ... (remaining 175445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.38 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 9.740 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 55.760 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23549 Z= 0.306 Angle : 0.961 12.707 31826 Z= 0.564 Chirality : 0.049 0.334 3596 Planarity : 0.006 0.100 4055 Dihedral : 16.295 89.699 8856 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.46 % Favored : 92.43 % Rotamer: Outliers : 0.34 % Allowed : 8.54 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.11 % 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: -6.23 (0.10), residues: 2828 helix: -4.67 (0.05), residues: 1485 sheet: -2.00 (0.35), residues: 195 loop : -3.52 (0.13), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 280 HIS 0.006 0.001 HIS B 211 PHE 0.023 0.002 PHE B 889 TYR 0.028 0.002 TYR B 432 ARG 0.006 0.001 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 437 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.7798 (t0) cc_final: 0.7456 (t0) REVERT: A 308 MET cc_start: 0.7344 (mmt) cc_final: 0.6711 (tmm) REVERT: A 339 MET cc_start: 0.7779 (mtm) cc_final: 0.7397 (mtm) REVERT: A 340 LYS cc_start: 0.7758 (mttm) cc_final: 0.7515 (mtmm) REVERT: A 416 ASP cc_start: 0.7204 (t0) cc_final: 0.6829 (t0) REVERT: A 455 ILE cc_start: 0.8508 (tp) cc_final: 0.8116 (tp) REVERT: A 479 MET cc_start: 0.7800 (mtp) cc_final: 0.7507 (mtp) REVERT: A 553 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7226 (tp30) REVERT: A 578 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7687 (mtp-110) REVERT: B 47 ASP cc_start: 0.7278 (t0) cc_final: 0.6823 (t0) REVERT: B 194 TYR cc_start: 0.8183 (m-10) cc_final: 0.7895 (m-10) REVERT: B 298 MET cc_start: 0.8323 (mmm) cc_final: 0.8073 (tpt) REVERT: B 338 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7723 (tm-30) REVERT: B 542 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7663 (mt) REVERT: B 660 LYS cc_start: 0.7831 (tmmt) cc_final: 0.7568 (ttpt) REVERT: B 802 TYR cc_start: 0.8023 (t80) cc_final: 0.7567 (t80) REVERT: B 937 LEU cc_start: 0.4420 (OUTLIER) cc_final: 0.4200 (pp) REVERT: B 978 MET cc_start: 0.4967 (mtp) cc_final: 0.4003 (pmm) REVERT: B 1117 LYS cc_start: 0.8459 (mmtm) cc_final: 0.8078 (tptm) REVERT: B 1139 MET cc_start: 0.7280 (mmm) cc_final: 0.7070 (mmt) REVERT: D 10 GLN cc_start: 0.8590 (mt0) cc_final: 0.8389 (mt0) REVERT: D 37 LEU cc_start: 0.9140 (tp) cc_final: 0.8926 (tp) REVERT: D 109 ASP cc_start: 0.8357 (t0) cc_final: 0.8156 (t0) REVERT: D 125 GLN cc_start: 0.7770 (mt0) cc_final: 0.7363 (tm-30) REVERT: F 189 VAL cc_start: 0.6627 (m) cc_final: 0.6315 (p) REVERT: F 253 GLU cc_start: 0.5686 (tm-30) cc_final: 0.4848 (pm20) REVERT: F 299 GLN cc_start: 0.7467 (tt0) cc_final: 0.7242 (tm-30) REVERT: F 354 ASP cc_start: 0.7386 (t70) cc_final: 0.7106 (t0) outliers start: 9 outliers final: 3 residues processed: 445 average time/residue: 0.3669 time to fit residues: 246.6096 Evaluate side-chains 318 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 313 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 256 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 309 ASN A 327 ASN A 355 ASN A 407 ASN A 556 GLN B 11 ASN B 121 ASN B 173 ASN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 422 HIS B 590 ASN B 679 ASN B 703 GLN B 762 ASN B 801 GLN B 805 HIS ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN B1061 ASN B1067 ASN ** B1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1163 GLN C 47 HIS C 72 HIS C 193 HIS ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 59 GLN D 88 ASN D 93 GLN E 74 GLN E 79 GLN F 282 GLN F 330 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23549 Z= 0.229 Angle : 0.624 8.371 31826 Z= 0.327 Chirality : 0.043 0.180 3596 Planarity : 0.005 0.077 4055 Dihedral : 5.893 46.615 3074 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.78 % Favored : 92.11 % Rotamer: Outliers : 2.06 % Allowed : 14.10 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.07 % 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: -4.60 (0.12), residues: 2828 helix: -3.02 (0.10), residues: 1492 sheet: -1.49 (0.37), residues: 202 loop : -3.23 (0.15), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 174 HIS 0.010 0.001 HIS B 805 PHE 0.033 0.002 PHE B 948 TYR 0.028 0.002 TYR A 552 ARG 0.005 0.000 ARG B 950 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 346 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.6867 (OUTLIER) cc_final: 0.6377 (m-40) REVERT: A 308 MET cc_start: 0.7276 (mmt) cc_final: 0.6442 (tmm) REVERT: A 340 LYS cc_start: 0.7811 (mttm) cc_final: 0.7549 (mtmm) REVERT: A 382 LEU cc_start: 0.8300 (tt) cc_final: 0.8054 (tp) REVERT: B 47 ASP cc_start: 0.7618 (t0) cc_final: 0.7063 (t0) REVERT: B 194 TYR cc_start: 0.8325 (m-10) cc_final: 0.7673 (m-10) REVERT: B 338 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7162 (tp30) REVERT: B 931 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7297 (tm-30) REVERT: B 937 LEU cc_start: 0.4558 (OUTLIER) cc_final: 0.4220 (pp) REVERT: B 978 MET cc_start: 0.4950 (mtp) cc_final: 0.3977 (pmm) REVERT: B 1116 ARG cc_start: 0.8385 (tpt90) cc_final: 0.7814 (tpt90) REVERT: B 1117 LYS cc_start: 0.8653 (mmtm) cc_final: 0.8302 (tptm) REVERT: B 1139 MET cc_start: 0.7415 (mmm) cc_final: 0.7171 (mmt) REVERT: B 1221 MET cc_start: 0.7662 (mtt) cc_final: 0.7370 (tmm) REVERT: C 320 TYR cc_start: 0.7864 (m-80) cc_final: 0.7634 (m-80) REVERT: C 353 TYR cc_start: 0.4815 (t80) cc_final: 0.4441 (t80) REVERT: D 10 GLN cc_start: 0.8590 (mt0) cc_final: 0.8386 (mt0) REVERT: D 63 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: D 125 GLN cc_start: 0.7580 (mt0) cc_final: 0.7090 (tm-30) REVERT: F 152 ARG cc_start: 0.7486 (ttp-170) cc_final: 0.7155 (tmm-80) REVERT: F 268 ILE cc_start: 0.6391 (mm) cc_final: 0.6008 (pt) REVERT: F 299 GLN cc_start: 0.7626 (tt0) cc_final: 0.7238 (tm-30) REVERT: F 354 ASP cc_start: 0.7097 (t70) cc_final: 0.6740 (t0) outliers start: 54 outliers final: 32 residues processed: 384 average time/residue: 0.3328 time to fit residues: 202.0521 Evaluate side-chains 342 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 307 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 996 THR Chi-restraints excluded: chain B residue 1045 ASP Chi-restraints excluded: chain B residue 1063 MET Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.725 > 50: distance: 42 - 60: 27.168 distance: 46 - 71: 31.873 distance: 52 - 79: 36.936 distance: 56 - 60: 30.346 distance: 60 - 61: 38.466 distance: 61 - 62: 43.833 distance: 61 - 64: 47.850 distance: 62 - 71: 31.926 distance: 64 - 65: 39.435 distance: 65 - 66: 19.714 distance: 65 - 67: 37.961 distance: 66 - 68: 18.645 distance: 67 - 69: 33.234 distance: 68 - 70: 16.655 distance: 69 - 70: 16.964 distance: 71 - 72: 32.055 distance: 75 - 76: 14.765 distance: 76 - 77: 13.176 distance: 76 - 78: 27.574 distance: 80 - 81: 51.917 distance: 80 - 83: 39.840 distance: 81 - 82: 40.246 distance: 81 - 87: 37.302 distance: 87 - 88: 38.693 distance: 88 - 89: 39.534 distance: 88 - 91: 26.743 distance: 89 - 90: 36.963 distance: 89 - 93: 56.462 distance: 91 - 92: 57.702 distance: 95 - 102: 38.869 distance: 97 - 98: 41.249 distance: 98 - 99: 21.935 distance: 99 - 100: 17.420 distance: 99 - 101: 50.460 distance: 104 - 105: 6.412 distance: 104 - 114: 57.167 distance: 107 - 108: 12.154 distance: 107 - 109: 40.046 distance: 108 - 110: 43.943 distance: 109 - 111: 50.198 distance: 110 - 112: 50.131 distance: 111 - 112: 36.486 distance: 115 - 118: 40.063 distance: 116 - 117: 40.310 distance: 124 - 125: 40.708 distance: 124 - 131: 4.239 distance: 127 - 128: 40.579 distance: 131 - 132: 33.896 distance: 132 - 133: 28.227 distance: 133 - 134: 11.468 distance: 133 - 140: 6.949 distance: 135 - 136: 40.454 distance: 136 - 137: 39.864 distance: 140 - 141: 23.798 distance: 142 - 147: 34.051 distance: 144 - 146: 39.697