Starting phenix.real_space_refine on Fri Mar 22 19:29:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ptj_20471/03_2024/6ptj_20471.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ptj_20471/03_2024/6ptj_20471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ptj_20471/03_2024/6ptj_20471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ptj_20471/03_2024/6ptj_20471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ptj_20471/03_2024/6ptj_20471.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ptj_20471/03_2024/6ptj_20471.pdb" } resolution = 3.8 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= 0.001 sd= 0.007 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 146 5.16 5 C 21918 2.51 5 N 5844 2.21 5 O 6453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 22": "NH1" <-> "NH2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "C ASP 5": "OD1" <-> "OD2" Residue "C PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 6": "OD1" <-> "OD2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "c GLU 10": "OE1" <-> "OE2" Residue "c ARG 68": "NH1" <-> "NH2" Residue "c ARG 69": "NH1" <-> "NH2" Residue "c ARG 117": "NH1" <-> "NH2" Residue "c ASP 150": "OD1" <-> "OD2" Residue "c GLU 154": "OE1" <-> "OE2" Residue "c GLU 157": "OE1" <-> "OE2" Residue "c TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 226": "NH1" <-> "NH2" Residue "c GLU 238": "OE1" <-> "OE2" Residue "c ARG 307": "NH1" <-> "NH2" Residue "c ASP 323": "OD1" <-> "OD2" Residue "c TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 393": "OD1" <-> "OD2" Residue "c ARG 398": "NH1" <-> "NH2" Residue "c ARG 406": "NH1" <-> "NH2" Residue "c PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 411": "NH1" <-> "NH2" Residue "c PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 472": "NH1" <-> "NH2" Residue "c TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 535": "OD1" <-> "OD2" Residue "c ARG 547": "NH1" <-> "NH2" Residue "c ARG 587": "NH1" <-> "NH2" Residue "c ASP 617": "OD1" <-> "OD2" Residue "c ARG 634": "NH1" <-> "NH2" Residue "2 GLU 217": "OE1" <-> "OE2" Residue "2 ARG 224": "NH1" <-> "NH2" Residue "2 GLU 243": "OE1" <-> "OE2" Residue "2 PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 308": "OE1" <-> "OE2" Residue "2 ARG 319": "NH1" <-> "NH2" Residue "2 TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 413": "OD1" <-> "OD2" Residue "2 ASP 416": "OD1" <-> "OD2" Residue "2 ARG 459": "NH1" <-> "NH2" Residue "3 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 108": "NH1" <-> "NH2" Residue "3 GLU 126": "OE1" <-> "OE2" Residue "3 ARG 208": "NH1" <-> "NH2" Residue "3 ARG 224": "NH1" <-> "NH2" Residue "3 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 263": "OE1" <-> "OE2" Residue "3 ASP 290": "OD1" <-> "OD2" Residue "3 ARG 291": "NH1" <-> "NH2" Residue "3 PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 178": "NH1" <-> "NH2" Residue "4 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 210": "OD1" <-> "OD2" Residue "4 TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 234": "NH1" <-> "NH2" Residue "4 GLU 255": "OE1" <-> "OE2" Residue "4 GLU 267": "OE1" <-> "OE2" Residue "4 ASP 292": "OD1" <-> "OD2" Residue "4 GLU 297": "OE1" <-> "OE2" Residue "4 GLU 316": "OE1" <-> "OE2" Residue "4 ARG 373": "NH1" <-> "NH2" Residue "4 ARG 388": "NH1" <-> "NH2" Residue "4 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 421": "OD1" <-> "OD2" Residue "4 ARG 428": "NH1" <-> "NH2" Residue "5 GLU 37": "OE1" <-> "OE2" Residue "5 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 81": "OD1" <-> "OD2" Residue "5 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 152": "OD1" <-> "OD2" Residue "5 GLU 246": "OE1" <-> "OE2" Residue "5 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 252": "OD1" <-> "OD2" Residue "5 GLU 263": "OE1" <-> "OE2" Residue "5 ASP 279": "OD1" <-> "OD2" Residue "5 TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 338": "OE1" <-> "OE2" Residue "6 ARG 112": "NH1" <-> "NH2" Residue "6 ARG 137": "NH1" <-> "NH2" Residue "6 TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 172": "OE1" <-> "OE2" Residue "6 ARG 176": "NH1" <-> "NH2" Residue "6 ARG 186": "NH1" <-> "NH2" Residue "6 ARG 190": "NH1" <-> "NH2" Residue "6 ARG 275": "NH1" <-> "NH2" Residue "6 ARG 277": "NH1" <-> "NH2" Residue "6 ARG 280": "NH1" <-> "NH2" Residue "6 GLU 303": "OE1" <-> "OE2" Residue "6 ARG 360": "NH1" <-> "NH2" Residue "6 ARG 375": "NH1" <-> "NH2" Residue "6 ARG 382": "NH1" <-> "NH2" Residue "6 ASP 384": "OD1" <-> "OD2" Residue "6 PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 406": "OD1" <-> "OD2" Residue "6 ARG 446": "NH1" <-> "NH2" Residue "6 ASP 447": "OD1" <-> "OD2" Residue "7 ASP 81": "OD1" <-> "OD2" Residue "7 ASP 84": "OD1" <-> "OD2" Residue "7 ASP 100": "OD1" <-> "OD2" Residue "7 ASP 101": "OD1" <-> "OD2" Residue "7 ASP 136": "OD1" <-> "OD2" Residue "7 GLU 151": "OE1" <-> "OE2" Residue "7 ARG 152": "NH1" <-> "NH2" Residue "7 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 199": "NH1" <-> "NH2" Residue "7 TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 214": "NH1" <-> "NH2" Residue "7 ARG 216": "NH1" <-> "NH2" Residue "7 ASP 250": "OD1" <-> "OD2" Residue "7 GLU 256": "OE1" <-> "OE2" Residue "7 TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 373": "OE1" <-> "OE2" Residue "E TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 530": "OD1" <-> "OD2" Residue "E ASP 535": "OD1" <-> "OD2" Residue "E PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 694": "OD1" <-> "OD2" Residue "E ASP 739": "OD1" <-> "OD2" Residue "E GLU 814": "OE1" <-> "OE2" Residue "E GLU 826": "OE1" <-> "OE2" Residue "E GLU 842": "OE1" <-> "OE2" Residue "E GLU 846": "OE1" <-> "OE2" Residue "E TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 851": "OE1" <-> "OE2" Residue "E GLU 853": "OE1" <-> "OE2" Residue "E GLU 888": "OE1" <-> "OE2" Residue "E GLU 919": "OE1" <-> "OE2" Residue "E GLU 923": "OE1" <-> "OE2" Residue "F TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 490": "OD1" <-> "OD2" Residue "F GLU 541": "OE1" <-> "OE2" Residue "F ASP 560": "OD1" <-> "OD2" Residue "F TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 675": "OD1" <-> "OD2" Residue "F PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 714": "OE1" <-> "OE2" Residue "F GLU 736": "OE1" <-> "OE2" Residue "F GLU 824": "OE1" <-> "OE2" Residue "F GLU 826": "OE1" <-> "OE2" Residue "F GLU 835": "OE1" <-> "OE2" Residue "F GLU 853": "OE1" <-> "OE2" Residue "F PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 892": "OD1" <-> "OD2" Residue "G TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 509": "OE1" <-> "OE2" Residue "G TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 519": "OD1" <-> "OD2" Residue "G ASP 530": "OD1" <-> "OD2" Residue "G GLU 541": "OE1" <-> "OE2" Residue "G TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 654": "OE1" <-> "OE2" Residue "G PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 715": "OE1" <-> "OE2" Residue "G GLU 727": "OE1" <-> "OE2" Residue "G TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 775": "OE1" <-> "OE2" Residue "G GLU 814": "OE1" <-> "OE2" Residue "G GLU 842": "OE1" <-> "OE2" Residue "G TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 876": "OD1" <-> "OD2" Residue "G GLU 880": "OE1" <-> "OE2" Residue "G TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34361 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1696 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1557 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "C" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1288 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 148} Chain breaks: 3 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: "D" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1891 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain breaks: 3 Chain: "c" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4482 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 15, 'TRANS': 537} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "2" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2025 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 247} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "3" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2139 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain breaks: 3 Chain: "4" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2299 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "5" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2006 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 12, 'TRANS': 239} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2081 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 13, 'TRANS': 259} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "7" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2615 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 3 Chain: "E" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3408 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 400} Chain breaks: 2 Chain: "F" Number of atoms: 3472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 431, 3464 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 431, 3464 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 407} Chain breaks: 1 bond proxies already assigned to first conformer: 3541 Chain: "G" Number of atoms: 3402 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 423, 3394 Classifications: {'peptide': 423} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 399} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 423, 3394 Classifications: {'peptide': 423} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 399} Chain breaks: 2 bond proxies already assigned to first conformer: 3470 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AASN F 753 " occ=0.35 ... (14 atoms not shown) pdb=" ND2BASN F 753 " occ=0.65 residue: pdb=" N AASN G 753 " occ=0.38 ... (14 atoms not shown) pdb=" ND2BASN G 753 " occ=0.62 Time building chain proxies: 20.58, per 1000 atoms: 0.60 Number of scatterers: 34361 At special positions: 0 Unit cell: (221.244, 182.58, 200.838, 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 146 16.00 O 6453 8.00 N 5844 7.00 C 21918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 7 265 " - pdb=" SG CYS 7 289 " distance=2.02 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: 12.02 Conformation dependent library (CDL) restraints added in 6.5 seconds 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8178 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 48 sheets defined 30.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 5 through 21 removed outlier: 4.102A pdb=" N LEU A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 52 removed outlier: 3.551A pdb=" N ASN A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 50 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.693A pdb=" N GLU A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 57 " --> pdb=" O TYR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 removed outlier: 4.040A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 104 removed outlier: 3.785A pdb=" N TYR A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 94 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 142 removed outlier: 3.789A pdb=" N LEU A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.512A pdb=" N GLU B 23 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 removed outlier: 3.715A pdb=" N GLN B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 82' Processing helix chain 'B' and resid 99 through 107 removed outlier: 4.362A pdb=" N GLU B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 130 removed outlier: 3.885A pdb=" N LYS B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.815A pdb=" N GLN B 146 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU B 157 " --> pdb=" O GLN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 4.172A pdb=" N GLU B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 11 through 13 No H-bonds generated for 'chain 'C' and resid 11 through 13' Processing helix chain 'C' and resid 81 through 91 removed outlier: 4.361A pdb=" N LYS C 89 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.551A pdb=" N LEU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 133 removed outlier: 4.133A pdb=" N LEU C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 189 removed outlier: 3.638A pdb=" N LYS C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 185 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 11 Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.768A pdb=" N PHE D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 68 " --> pdb=" O MET D 64 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 71 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.747A pdb=" N LYS D 85 " --> pdb=" O GLN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 105 removed outlier: 3.989A pdb=" N SER D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET D 93 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 97 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 128 through 142 removed outlier: 3.636A pdb=" N GLU D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.687A pdb=" N GLN D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 161 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 195 removed outlier: 3.548A pdb=" N ASP D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 187 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 189 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU D 193 " --> pdb=" O ILE D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.928A pdb=" N MET D 202 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 17 removed outlier: 3.673A pdb=" N LYS c 14 " --> pdb=" O GLU c 10 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE c 15 " --> pdb=" O ALA c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 36 through 48 removed outlier: 3.517A pdb=" N ALA c 41 " --> pdb=" O ASP c 37 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR c 42 " --> pdb=" O ALA c 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU c 45 " --> pdb=" O ALA c 41 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU c 47 " --> pdb=" O LYS c 43 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU c 48 " --> pdb=" O MET c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 65 through 72 removed outlier: 3.554A pdb=" N ARG c 69 " --> pdb=" O SER c 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 91 through 97 Processing helix chain 'c' and resid 130 through 135 removed outlier: 3.939A pdb=" N ILE c 134 " --> pdb=" O ASN c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 145 through 150 removed outlier: 3.607A pdb=" N ASP c 149 " --> pdb=" O ASP c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 153 through 161 removed outlier: 3.633A pdb=" N ALA c 158 " --> pdb=" O GLU c 154 " (cutoff:3.500A) Processing helix chain 'c' and resid 219 through 237 removed outlier: 3.524A pdb=" N GLU c 234 " --> pdb=" O ILE c 230 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY c 235 " --> pdb=" O HIS c 231 " (cutoff:3.500A) Processing helix chain 'c' and resid 250 through 263 removed outlier: 3.794A pdb=" N GLN c 254 " --> pdb=" O SER c 250 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR c 256 " --> pdb=" O SER c 252 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA c 261 " --> pdb=" O SER c 257 " (cutoff:3.500A) Processing helix chain 'c' and resid 267 through 275 removed outlier: 4.862A pdb=" N ASN c 273 " --> pdb=" O ASN c 269 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE c 274 " --> pdb=" O LEU c 270 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU c 275 " --> pdb=" O TRP c 271 " (cutoff:3.500A) Processing helix chain 'c' and resid 278 through 283 removed outlier: 4.170A pdb=" N ILE c 282 " --> pdb=" O THR c 278 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA c 283 " --> pdb=" O SER c 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 278 through 283' Processing helix chain 'c' and resid 297 through 302 removed outlier: 3.955A pdb=" N LEU c 302 " --> pdb=" O GLU c 298 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 340 removed outlier: 4.092A pdb=" N TYR c 340 " --> pdb=" O ASP c 336 " (cutoff:3.500A) Processing helix chain 'c' and resid 344 through 349 Processing helix chain 'c' and resid 355 through 367 removed outlier: 3.933A pdb=" N HIS c 360 " --> pdb=" O LYS c 356 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS c 361 " --> pdb=" O LYS c 357 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE c 363 " --> pdb=" O LEU c 359 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG c 365 " --> pdb=" O LYS c 361 " (cutoff:3.500A) Processing helix chain 'c' and resid 371 through 375 Processing helix chain 'c' and resid 376 through 380 removed outlier: 4.071A pdb=" N MET c 380 " --> pdb=" O TRP c 377 " (cutoff:3.500A) Processing helix chain 'c' and resid 381 through 386 removed outlier: 3.733A pdb=" N LYS c 385 " --> pdb=" O ASP c 381 " (cutoff:3.500A) Processing helix chain 'c' and resid 387 through 395 removed outlier: 3.516A pdb=" N ILE c 391 " --> pdb=" O GLU c 387 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP c 393 " --> pdb=" O GLY c 389 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS c 394 " --> pdb=" O ILE c 390 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN c 395 " --> pdb=" O ILE c 391 " (cutoff:3.500A) Processing helix chain 'c' and resid 421 through 430 removed outlier: 3.536A pdb=" N VAL c 425 " --> pdb=" O ALA c 421 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA c 427 " --> pdb=" O GLU c 423 " (cutoff:3.500A) Processing helix chain 'c' and resid 463 through 482 removed outlier: 3.637A pdb=" N THR c 467 " --> pdb=" O ALA c 463 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN c 468 " --> pdb=" O GLN c 464 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU c 469 " --> pdb=" O LYS c 465 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG c 472 " --> pdb=" O ASN c 468 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN c 476 " --> pdb=" O ARG c 472 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP c 478 " --> pdb=" O VAL c 474 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU c 479 " --> pdb=" O SER c 475 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER c 480 " --> pdb=" O ASN c 476 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP c 482 " --> pdb=" O TRP c 478 " (cutoff:3.500A) Processing helix chain 'c' and resid 492 through 497 removed outlier: 4.092A pdb=" N GLN c 497 " --> pdb=" O ASN c 493 " (cutoff:3.500A) Processing helix chain 'c' and resid 509 through 517 removed outlier: 3.857A pdb=" N LEU c 514 " --> pdb=" O GLY c 510 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS c 516 " --> pdb=" O ALA c 512 " (cutoff:3.500A) Processing helix chain 'c' and resid 537 through 540 removed outlier: 3.916A pdb=" N ARG c 540 " --> pdb=" O ASP c 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 537 through 540' Processing helix chain 'c' and resid 541 through 557 removed outlier: 3.544A pdb=" N LEU c 545 " --> pdb=" O ASN c 541 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU c 546 " --> pdb=" O PRO c 542 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG c 547 " --> pdb=" O LEU c 543 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU c 554 " --> pdb=" O ASN c 550 " (cutoff:3.500A) Processing helix chain 'c' and resid 606 through 614 removed outlier: 4.327A pdb=" N ILE c 612 " --> pdb=" O ALA c 608 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR c 613 " --> pdb=" O PHE c 609 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA c 614 " --> pdb=" O GLN c 610 " (cutoff:3.500A) Processing helix chain 'c' and resid 636 through 646 removed outlier: 3.655A pdb=" N PHE c 640 " --> pdb=" O ASP c 636 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU c 642 " --> pdb=" O SER c 638 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS c 643 " --> pdb=" O PRO c 639 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU c 644 " --> pdb=" O PHE c 640 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR c 645 " --> pdb=" O LEU c 641 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU c 646 " --> pdb=" O GLU c 642 " (cutoff:3.500A) Processing helix chain '2' and resid 203 through 212 removed outlier: 3.716A pdb=" N ARG 2 209 " --> pdb=" O ARG 2 205 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU 2 210 " --> pdb=" O THR 2 206 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS 2 212 " --> pdb=" O ALA 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 217 removed outlier: 3.524A pdb=" N LEU 2 216 " --> pdb=" O LYS 2 212 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 251 removed outlier: 3.546A pdb=" N GLU 2 251 " --> pdb=" O ARG 2 247 " (cutoff:3.500A) Processing helix chain '2' and resid 253 through 262 removed outlier: 3.826A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU 2 258 " --> pdb=" O ALA 2 254 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA 2 261 " --> pdb=" O ALA 2 257 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 280 removed outlier: 4.781A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA 2 275 " --> pdb=" O PHE 2 271 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU 2 277 " --> pdb=" O LEU 2 273 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 Processing helix chain '3' and resid 18 through 27 removed outlier: 3.536A pdb=" N GLY 3 22 " --> pdb=" O ASP 3 18 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG 3 24 " --> pdb=" O VAL 3 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG 3 26 " --> pdb=" O GLY 3 22 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 52 removed outlier: 3.508A pdb=" N SER 3 41 " --> pdb=" O SER 3 37 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL 3 42 " --> pdb=" O TYR 3 38 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG 3 43 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER 3 50 " --> pdb=" O GLN 3 46 " (cutoff:3.500A) Processing helix chain '3' and resid 52 through 57 Processing helix chain '3' and resid 102 through 107 Processing helix chain '3' and resid 107 through 115 removed outlier: 3.510A pdb=" N SER 3 112 " --> pdb=" O ARG 3 108 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU 3 115 " --> pdb=" O TRP 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 121 through 136 removed outlier: 3.716A pdb=" N LYS 3 127 " --> pdb=" O PRO 3 123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU 3 129 " --> pdb=" O ALA 3 125 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR 3 130 " --> pdb=" O GLU 3 126 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP 3 131 " --> pdb=" O LYS 3 127 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU 3 132 " --> pdb=" O ALA 3 128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET 3 136 " --> pdb=" O LEU 3 132 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 200 Processing helix chain '4' and resid 204 through 208 removed outlier: 3.812A pdb=" N ILE 4 208 " --> pdb=" O PHE 4 205 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 237 removed outlier: 4.257A pdb=" N LYS 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN 4 229 " --> pdb=" O TYR 4 225 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU 4 230 " --> pdb=" O TYR 4 226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU 4 232 " --> pdb=" O LYS 4 228 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG 4 234 " --> pdb=" O LEU 4 230 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU 4 235 " --> pdb=" O ASN 4 231 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU 4 236 " --> pdb=" O GLU 4 232 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 3.733A pdb=" N LEU 4 262 " --> pdb=" O TYR 4 258 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN 4 263 " --> pdb=" O HIS 4 259 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR 4 264 " --> pdb=" O GLN 4 260 " (cutoff:3.500A) Processing helix chain '4' and resid 266 through 279 removed outlier: 3.770A pdb=" N GLN 4 274 " --> pdb=" O SER 4 270 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR 4 275 " --> pdb=" O ILE 4 271 " (cutoff:3.500A) Processing helix chain '4' and resid 280 through 285 removed outlier: 3.856A pdb=" N ILE 4 284 " --> pdb=" O MET 4 280 " (cutoff:3.500A) Processing helix chain '4' and resid 420 through 424 removed outlier: 3.788A pdb=" N VAL 4 424 " --> pdb=" O ASP 4 421 " (cutoff:3.500A) Processing helix chain '5' and resid 28 through 38 removed outlier: 4.275A pdb=" N PHE 5 34 " --> pdb=" O SER 5 30 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU 5 36 " --> pdb=" O LYS 5 32 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 48 removed outlier: 4.141A pdb=" N ARG 5 47 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) Processing helix chain '5' and resid 51 through 56 removed outlier: 3.640A pdb=" N LEU 5 55 " --> pdb=" O ARG 5 51 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 51 through 56' Processing helix chain '5' and resid 65 through 72 removed outlier: 4.230A pdb=" N ILE 5 69 " --> pdb=" O MET 5 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR 5 71 " --> pdb=" O HIS 5 67 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 82 removed outlier: 4.468A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS 5 78 " --> pdb=" O ASP 5 74 " (cutoff:3.500A) Processing helix chain '5' and resid 86 through 95 removed outlier: 4.272A pdb=" N THR 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR 5 95 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) Processing helix chain '6' and resid 104 through 120 removed outlier: 3.739A pdb=" N GLU 6 120 " --> pdb=" O GLU 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 147 removed outlier: 3.558A pdb=" N GLU 6 141 " --> pdb=" O ARG 6 137 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE 6 142 " --> pdb=" O ALA 6 138 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET 6 143 " --> pdb=" O GLN 6 139 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 160 Processing helix chain '6' and resid 166 through 173 Processing helix chain '6' and resid 177 through 190 removed outlier: 3.623A pdb=" N VAL 6 188 " --> pdb=" O GLY 6 184 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG 6 190 " --> pdb=" O ARG 6 186 " (cutoff:3.500A) Processing helix chain '6' and resid 280 through 284 removed outlier: 4.036A pdb=" N ILE 6 284 " --> pdb=" O SER 6 281 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 368 removed outlier: 3.871A pdb=" N GLU 6 367 " --> pdb=" O ASN 6 364 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE 6 368 " --> pdb=" O ALA 6 365 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 364 through 368' Processing helix chain '7' and resid 15 through 17 No H-bonds generated for 'chain '7' and resid 15 through 17' Processing helix chain '7' and resid 18 through 23 Processing helix chain '7' and resid 61 through 72 removed outlier: 3.910A pdb=" N ALA 7 65 " --> pdb=" O PRO 7 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET 7 66 " --> pdb=" O LYS 7 62 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 92 removed outlier: 3.754A pdb=" N LYS 7 92 " --> pdb=" O TYR 7 88 " (cutoff:3.500A) Processing helix chain '7' and resid 102 through 110 removed outlier: 3.827A pdb=" N GLN 7 108 " --> pdb=" O SER 7 104 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 116 removed outlier: 4.140A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU 7 116 " --> pdb=" O HIS 7 112 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 111 through 116' Processing helix chain '7' and resid 140 through 154 removed outlier: 3.704A pdb=" N ASN 7 144 " --> pdb=" O ASP 7 140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN 7 150 " --> pdb=" O ARG 7 146 " (cutoff:3.500A) Processing helix chain '7' and resid 210 through 215 removed outlier: 3.639A pdb=" N ARG 7 214 " --> pdb=" O ASN 7 210 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 210 through 215' Processing helix chain '7' and resid 231 through 235 removed outlier: 3.914A pdb=" N PHE 7 234 " --> pdb=" O LYS 7 231 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU 7 235 " --> pdb=" O GLY 7 232 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 231 through 235' Processing helix chain 'E' and resid 673 through 680 removed outlier: 3.746A pdb=" N TYR E 677 " --> pdb=" O ASN E 673 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN E 678 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE E 679 " --> pdb=" O ASP E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 732 Processing helix chain 'E' and resid 786 through 790 Processing helix chain 'E' and resid 818 through 844 removed outlier: 5.320A pdb=" N GLU E 824 " --> pdb=" O SER E 820 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU E 825 " --> pdb=" O MET E 821 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU E 826 " --> pdb=" O ALA E 822 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER E 830 " --> pdb=" O GLU E 826 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU E 835 " --> pdb=" O LYS E 831 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 836 " --> pdb=" O VAL E 832 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP E 839 " --> pdb=" O GLU E 835 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR E 840 " --> pdb=" O LEU E 836 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 841 " --> pdb=" O LEU E 837 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU E 842 " --> pdb=" O THR E 838 " (cutoff:3.500A) Processing helix chain 'E' and resid 850 through 876 removed outlier: 3.809A pdb=" N VAL E 854 " --> pdb=" O ASN E 850 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 864 " --> pdb=" O GLY E 860 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 866 " --> pdb=" O TYR E 862 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG E 868 " --> pdb=" O LYS E 864 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU E 869 " --> pdb=" O ALA E 865 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 872 " --> pdb=" O ARG E 868 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP E 876 " --> pdb=" O SER E 872 " (cutoff:3.500A) Processing helix chain 'E' and resid 879 through 885 removed outlier: 3.526A pdb=" N SER E 884 " --> pdb=" O GLU E 880 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU E 885 " --> pdb=" O LYS E 881 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 888 No H-bonds generated for 'chain 'E' and resid 886 through 888' Processing helix chain 'E' and resid 894 through 906 removed outlier: 3.650A pdb=" N VAL E 899 " --> pdb=" O LEU E 895 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS E 900 " --> pdb=" O THR E 896 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 901 " --> pdb=" O ALA E 897 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG E 904 " --> pdb=" O LYS E 900 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA E 905 " --> pdb=" O ILE E 901 " (cutoff:3.500A) Processing helix chain 'E' and resid 907 through 927 removed outlier: 3.601A pdb=" N VAL E 911 " --> pdb=" O LEU E 907 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS E 912 " --> pdb=" O PRO E 908 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS E 913 " --> pdb=" O SER E 909 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 914 " --> pdb=" O LEU E 910 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN E 915 " --> pdb=" O VAL E 911 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 919 " --> pdb=" O ASN E 915 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 920 " --> pdb=" O ASN E 916 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN E 925 " --> pdb=" O ARG E 921 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU E 926 " --> pdb=" O TYR E 922 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS E 927 " --> pdb=" O GLU E 923 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 670 Processing helix chain 'F' and resid 673 through 680 Processing helix chain 'F' and resid 723 through 732 removed outlier: 3.720A pdb=" N GLU F 727 " --> pdb=" O ASP F 723 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP F 729 " --> pdb=" O ASN F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 782 through 788 removed outlier: 3.636A pdb=" N LEU F 786 " --> pdb=" O VAL F 782 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 787 " --> pdb=" O LYS F 783 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU F 788 " --> pdb=" O SER F 784 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 782 through 788' Processing helix chain 'F' and resid 818 through 842 removed outlier: 3.824A pdb=" N ALA F 823 " --> pdb=" O VAL F 819 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU F 824 " --> pdb=" O SER F 820 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU F 825 " --> pdb=" O MET F 821 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU F 833 " --> pdb=" O ARG F 829 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU F 835 " --> pdb=" O LYS F 831 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 837 " --> pdb=" O LEU F 833 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR F 838 " --> pdb=" O SER F 834 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP F 839 " --> pdb=" O GLU F 835 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR F 840 " --> pdb=" O LEU F 836 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 841 " --> pdb=" O LEU F 837 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 876 removed outlier: 3.617A pdb=" N VAL F 854 " --> pdb=" O ASN F 850 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY F 860 " --> pdb=" O ALA F 856 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA F 861 " --> pdb=" O ALA F 857 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU F 867 " --> pdb=" O ASP F 863 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG F 868 " --> pdb=" O LYS F 864 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU F 869 " --> pdb=" O ALA F 865 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE F 870 " --> pdb=" O LEU F 866 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER F 875 " --> pdb=" O ALA F 871 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP F 876 " --> pdb=" O SER F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 887 removed outlier: 3.668A pdb=" N LEU F 885 " --> pdb=" O LYS F 881 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA F 886 " --> pdb=" O ALA F 882 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS F 887 " --> pdb=" O LEU F 883 " (cutoff:3.500A) Processing helix chain 'F' and resid 891 through 903 removed outlier: 3.900A pdb=" N LEU F 895 " --> pdb=" O GLN F 891 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 897 " --> pdb=" O ARG F 893 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 898 " --> pdb=" O ALA F 894 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 899 " --> pdb=" O LEU F 895 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS F 900 " --> pdb=" O THR F 896 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 901 " --> pdb=" O ALA F 897 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER F 902 " --> pdb=" O ALA F 898 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 903 " --> pdb=" O VAL F 899 " (cutoff:3.500A) Processing helix chain 'F' and resid 909 through 926 removed outlier: 4.206A pdb=" N LYS F 913 " --> pdb=" O SER F 909 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 914 " --> pdb=" O LEU F 910 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN F 916 " --> pdb=" O LYS F 912 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 917 " --> pdb=" O LYS F 913 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR F 922 " --> pdb=" O ARG F 918 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU F 923 " --> pdb=" O GLU F 919 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN F 924 " --> pdb=" O ALA F 920 " (cutoff:3.500A) Processing helix chain 'G' and resid 673 through 678 removed outlier: 3.667A pdb=" N TYR G 677 " --> pdb=" O ASN G 673 " (cutoff:3.500A) Processing helix chain 'G' and resid 724 through 733 removed outlier: 3.789A pdb=" N ILE G 728 " --> pdb=" O SER G 724 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP G 729 " --> pdb=" O ASN G 725 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY G 733 " --> pdb=" O TRP G 729 " (cutoff:3.500A) Processing helix chain 'G' and resid 782 through 790 Processing helix chain 'G' and resid 818 through 844 removed outlier: 4.586A pdb=" N GLU G 824 " --> pdb=" O SER G 820 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU G 825 " --> pdb=" O MET G 821 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 828 " --> pdb=" O GLU G 824 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER G 834 " --> pdb=" O SER G 830 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU G 835 " --> pdb=" O LYS G 831 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU G 837 " --> pdb=" O LEU G 833 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR G 838 " --> pdb=" O SER G 834 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP G 839 " --> pdb=" O GLU G 835 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR G 840 " --> pdb=" O LEU G 836 " (cutoff:3.500A) Processing helix chain 'G' and resid 850 through 875 removed outlier: 3.692A pdb=" N VAL G 854 " --> pdb=" O ASN G 850 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA G 856 " --> pdb=" O ASN G 852 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP G 863 " --> pdb=" O ASN G 859 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU G 869 " --> pdb=" O ALA G 865 " (cutoff:3.500A) Processing helix chain 'G' and resid 878 through 882 removed outlier: 3.601A pdb=" N LYS G 881 " --> pdb=" O ASN G 878 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA G 882 " --> pdb=" O VAL G 879 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 878 through 882' Processing helix chain 'G' and resid 884 through 889 Processing helix chain 'G' and resid 891 through 905 removed outlier: 3.884A pdb=" N LEU G 895 " --> pdb=" O GLN G 891 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS G 900 " --> pdb=" O THR G 896 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE G 901 " --> pdb=" O ALA G 897 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER G 902 " --> pdb=" O ALA G 898 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG G 904 " --> pdb=" O LYS G 900 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA G 905 " --> pdb=" O ILE G 901 " (cutoff:3.500A) Processing helix chain 'G' and resid 907 through 922 removed outlier: 3.848A pdb=" N LYS G 912 " --> pdb=" O PRO G 908 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS G 913 " --> pdb=" O SER G 909 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG G 918 " --> pdb=" O ILE G 914 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU G 919 " --> pdb=" O ASN G 915 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.673A pdb=" N GLN A 188 " --> pdb=" O ILE c 58 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU c 27 " --> pdb=" O GLN c 57 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL c 59 " --> pdb=" O LEU c 27 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE c 29 " --> pdb=" O VAL c 59 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE c 61 " --> pdb=" O ILE c 29 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL c 31 " --> pdb=" O ILE c 61 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL c 28 " --> pdb=" O LEU c 82 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL c 84 " --> pdb=" O VAL c 28 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE c 30 " --> pdb=" O VAL c 84 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU c 83 " --> pdb=" O TYR c 121 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ILE c 120 " --> pdb=" O GLN c 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'C' and resid 24 through 25 Processing sheet with id=AA5, first strand: chain 'D' and resid 274 through 278 Processing sheet with id=AA6, first strand: chain 'c' and resid 317 through 323 removed outlier: 3.735A pdb=" N THR c 412 " --> pdb=" O THR c 317 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL c 410 " --> pdb=" O ASN c 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 519 through 520 removed outlier: 4.007A pdb=" N GLU c 631 " --> pdb=" O ARG c 621 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG c 621 " --> pdb=" O GLU c 631 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 241 through 244 removed outlier: 7.337A pdb=" N LEU 2 242 " --> pdb=" O ARG 2 296 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '2' and resid 429 through 431 removed outlier: 3.588A pdb=" N ILE 2 450 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN 2 386 " --> pdb=" O LEU 2 410 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR 2 325 " --> pdb=" O THR 2 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 193 through 198 removed outlier: 3.530A pdb=" N ILE 3 197 " --> pdb=" O THR 3 249 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE 3 321 " --> pdb=" O ASP 3 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 193 through 198 removed outlier: 3.530A pdb=" N ILE 3 197 " --> pdb=" O THR 3 249 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL 3 180 " --> pdb=" O GLY 3 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 201 through 202 Processing sheet with id=AB4, first strand: chain '4' and resid 339 through 342 removed outlier: 9.222A pdb=" N SER 4 414 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N VAL 4 461 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER 4 416 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU 4 456 " --> pdb=" O ILE 4 444 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE 4 444 " --> pdb=" O LEU 4 456 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS 4 458 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR 4 460 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 339 through 342 removed outlier: 7.802A pdb=" N VAL 4 396 " --> pdb=" O SER 4 335 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER 4 335 " --> pdb=" O VAL 4 396 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU 4 434 " --> pdb=" O VAL 4 466 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL 4 466 " --> pdb=" O GLU 4 434 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR 4 436 " --> pdb=" O VAL 4 464 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '4' and resid 344 through 345 removed outlier: 3.550A pdb=" N VAL 4 358 " --> pdb=" O ALA 4 345 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '5' and resid 60 through 64 removed outlier: 6.031A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASN 5 140 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL 5 63 " --> pdb=" O ASN 5 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '5' and resid 273 through 274 removed outlier: 8.647A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '5' and resid 190 through 193 removed outlier: 3.518A pdb=" N ILE 5 181 " --> pdb=" O THR 5 190 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N ALA 5 176 " --> pdb=" O SER 5 248 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N SER 5 248 " --> pdb=" O ALA 5 176 " (cutoff:3.500A) removed outlier: 11.704A pdb=" N TYR 5 178 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N GLU 5 246 " --> pdb=" O TYR 5 178 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '6' and resid 150 through 154 removed outlier: 3.641A pdb=" N ILE 6 151 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER 6 266 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '6' and resid 301 through 303 removed outlier: 3.714A pdb=" N GLY 6 292 " --> pdb=" O CYS 6 395 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS 6 395 " --> pdb=" O GLY 6 292 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '6' and resid 301 through 303 removed outlier: 3.660A pdb=" N GLN 6 357 " --> pdb=" O LEU 6 381 " (cutoff:3.500A) removed outlier: 14.186A pdb=" N THR 6 376 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ILE 6 452 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASP 6 378 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR 6 449 " --> pdb=" O ASP 6 406 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS 6 451 " --> pdb=" O VAL 6 404 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '7' and resid 78 through 79 Processing sheet with id=AC5, first strand: chain '7' and resid 376 through 377 removed outlier: 6.769A pdb=" N ASN 7 332 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE 7 244 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE 7 239 " --> pdb=" O GLY 7 353 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE 7 380 " --> pdb=" O THR 7 352 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '7' and resid 254 through 255 removed outlier: 3.770A pdb=" N SER 7 308 " --> pdb=" O ALA 7 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '7' and resid 259 through 261 removed outlier: 4.830A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 491 through 496 removed outlier: 6.815A pdb=" N VAL E 502 " --> pdb=" O LEU E 494 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N MET E 496 " --> pdb=" O GLY E 500 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY E 500 " --> pdb=" O MET E 496 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR E 511 " --> pdb=" O ASP E 530 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR E 526 " --> pdb=" O VAL E 515 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 536 through 539 removed outlier: 3.905A pdb=" N LEU E 536 " --> pdb=" O GLY E 547 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 553 through 556 removed outlier: 3.782A pdb=" N LYS E 568 " --> pdb=" O ILE E 554 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP E 566 " --> pdb=" O TYR E 556 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 578 through 582 removed outlier: 3.597A pdb=" N SER E 580 " --> pdb=" O GLY E 591 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL E 588 " --> pdb=" O PHE E 600 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 615 through 620 removed outlier: 6.775A pdb=" N VAL E 628 " --> pdb=" O VAL E 616 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU E 618 " --> pdb=" O PHE E 626 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE E 626 " --> pdb=" O LEU E 618 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA E 620 " --> pdb=" O ARG E 624 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG E 624 " --> pdb=" O ALA E 620 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR E 638 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS E 652 " --> pdb=" O LEU E 640 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 686 through 689 removed outlier: 4.061A pdb=" N SER E 686 " --> pdb=" O PHE E 698 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE E 698 " --> pdb=" O SER E 686 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE E 688 " --> pdb=" O CYS E 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 707 through 708 removed outlier: 3.545A pdb=" N LYS E 717 " --> pdb=" O SER E 708 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 744 through 747 removed outlier: 7.263A pdb=" N ASN E 753 " --> pdb=" O LEU E 745 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU E 747 " --> pdb=" O THR E 751 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR E 751 " --> pdb=" O LEU E 747 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 491 through 496 removed outlier: 6.813A pdb=" N VAL F 502 " --> pdb=" O LEU F 494 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE F 528 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR F 526 " --> pdb=" O VAL F 515 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 536 through 539 removed outlier: 3.571A pdb=" N PHE F 546 " --> pdb=" O GLN F 555 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN F 555 " --> pdb=" O PHE F 546 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN F 553 " --> pdb=" O GLN F 548 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS F 568 " --> pdb=" O ILE F 554 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 578 through 583 removed outlier: 3.933A pdb=" N SER F 580 " --> pdb=" O GLY F 591 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY F 591 " --> pdb=" O SER F 580 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE F 589 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR F 592 " --> pdb=" O TYR F 596 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR F 596 " --> pdb=" O THR F 592 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU F 610 " --> pdb=" O PHE F 597 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 615 through 620 removed outlier: 3.617A pdb=" N ALA F 617 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR F 638 " --> pdb=" O ARG F 653 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG F 653 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU F 640 " --> pdb=" O TYR F 651 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 696 through 698 removed outlier: 3.550A pdb=" N ILE F 697 " --> pdb=" O LEU F 705 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 705 " --> pdb=" O ILE F 697 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 744 through 747 removed outlier: 4.463A pdb=" N ALA F 746 " --> pdb=" O AASN F 753 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N AASN F 753 " --> pdb=" O ALA F 746 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'G' and resid 491 through 496 removed outlier: 6.710A pdb=" N VAL G 502 " --> pdb=" O LEU G 494 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET G 496 " --> pdb=" O GLY G 500 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY G 500 " --> pdb=" O MET G 496 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR G 511 " --> pdb=" O ASP G 530 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE G 528 " --> pdb=" O ILE G 513 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 536 through 539 Processing sheet with id=AE6, first strand: chain 'G' and resid 578 through 583 removed outlier: 3.501A pdb=" N SER G 580 " --> pdb=" O GLY G 591 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 615 through 620 removed outlier: 3.925A pdb=" N ALA G 617 " --> pdb=" O VAL G 628 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 615 through 620 removed outlier: 3.925A pdb=" N ALA G 617 " --> pdb=" O VAL G 628 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 686 through 689 removed outlier: 3.773A pdb=" N ILE G 697 " --> pdb=" O LEU G 705 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 686 through 689 removed outlier: 3.773A pdb=" N ILE G 697 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU G 722 " --> pdb=" O LEU G 704 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 740 through 741 Processing sheet with id=AF3, first strand: chain 'G' and resid 744 through 747 removed outlier: 6.822A pdb=" N AASN G 753 " --> pdb=" O LEU G 745 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU G 747 " --> pdb=" O THR G 751 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR G 751 " --> pdb=" O LEU G 747 " (cutoff:3.500A) 821 hydrogen bonds defined for protein. 2278 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: 10.89 Time building geometry restraints manager: 13.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10830 1.34 - 1.46: 7016 1.46 - 1.58: 16970 1.58 - 1.70: 0 1.70 - 1.82: 234 Bond restraints: 35050 Sorted by residual: bond pdb=" CA ASN 6 320 " pdb=" C ASN 6 320 " ideal model delta sigma weight residual 1.519 1.539 -0.020 5.30e-03 3.56e+04 1.46e+01 bond pdb=" C LEU D 76 " pdb=" N LEU D 77 " ideal model delta sigma weight residual 1.330 1.275 0.055 1.47e-02 4.63e+03 1.40e+01 bond pdb=" CA THR 3 325 " pdb=" C THR 3 325 " ideal model delta sigma weight residual 1.525 1.480 0.044 1.35e-02 5.49e+03 1.07e+01 bond pdb=" CA GLU D 221 " pdb=" C GLU D 221 " ideal model delta sigma weight residual 1.532 1.552 -0.020 6.50e-03 2.37e+04 9.34e+00 bond pdb=" N VAL 5 265 " pdb=" CA VAL 5 265 " ideal model delta sigma weight residual 1.468 1.432 0.036 1.22e-02 6.72e+03 8.57e+00 ... (remaining 35045 not shown) Histogram of bond angle deviations from ideal: 90.28 - 99.11: 7 99.11 - 107.95: 1569 107.95 - 116.78: 22822 116.78 - 125.62: 22470 125.62 - 134.45: 561 Bond angle restraints: 47429 Sorted by residual: angle pdb=" N ILE 5 45 " pdb=" CA ILE 5 45 " pdb=" C ILE 5 45 " ideal model delta sigma weight residual 110.62 127.79 -17.17 1.02e+00 9.61e-01 2.83e+02 angle pdb=" N ARG 4 373 " pdb=" CA ARG 4 373 " pdb=" C ARG 4 373 " ideal model delta sigma weight residual 111.02 90.28 20.74 1.25e+00 6.40e-01 2.75e+02 angle pdb=" N GLY 6 399 " pdb=" CA GLY 6 399 " pdb=" C GLY 6 399 " ideal model delta sigma weight residual 112.73 132.16 -19.43 1.20e+00 6.94e-01 2.62e+02 angle pdb=" CA THR 3 325 " pdb=" C THR 3 325 " pdb=" O THR 3 325 " ideal model delta sigma weight residual 119.95 105.72 14.23 1.18e+00 7.18e-01 1.46e+02 angle pdb=" N VAL 5 265 " pdb=" CA VAL 5 265 " pdb=" C VAL 5 265 " ideal model delta sigma weight residual 108.95 120.20 -11.25 9.80e-01 1.04e+00 1.32e+02 ... (remaining 47424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 18825 17.73 - 35.46: 2064 35.46 - 53.19: 348 53.19 - 70.93: 62 70.93 - 88.66: 22 Dihedral angle restraints: 21321 sinusoidal: 8723 harmonic: 12598 Sorted by residual: dihedral pdb=" CA LEU 2 411 " pdb=" C LEU 2 411 " pdb=" N ALA 2 412 " pdb=" CA ALA 2 412 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLN c 286 " pdb=" C GLN c 286 " pdb=" N VAL c 287 " pdb=" CA VAL c 287 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PRO D 254 " pdb=" C PRO D 254 " pdb=" N CYS D 255 " pdb=" CA CYS D 255 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 21318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 5017 0.110 - 0.221: 304 0.221 - 0.331: 17 0.331 - 0.442: 3 0.442 - 0.552: 4 Chirality restraints: 5345 Sorted by residual: chirality pdb=" CA THR 3 187 " pdb=" N THR 3 187 " pdb=" C THR 3 187 " pdb=" CB THR 3 187 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CA PHE 5 44 " pdb=" N PHE 5 44 " pdb=" C PHE 5 44 " pdb=" CB PHE 5 44 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" CA GLU D 221 " pdb=" N GLU D 221 " pdb=" C GLU D 221 " pdb=" CB GLU D 221 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.49e+00 ... (remaining 5342 not shown) Planarity restraints: 6082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG 5 39 " 0.022 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C ARG 5 39 " -0.079 2.00e-02 2.50e+03 pdb=" O ARG 5 39 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU 5 40 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 7 93 " 0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C PHE 7 93 " -0.071 2.00e-02 2.50e+03 pdb=" O PHE 7 93 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU 7 94 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE 2 331 " 0.065 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO 2 332 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO 2 332 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO 2 332 " 0.053 5.00e-02 4.00e+02 ... (remaining 6079 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 333 2.59 - 3.17: 26408 3.17 - 3.74: 48308 3.74 - 4.32: 64891 4.32 - 4.90: 105962 Nonbonded interactions: 245902 Sorted by model distance: nonbonded pdb=" OD1 ASP 4 294 " pdb=" N GLU 4 295 " model vdw 2.011 2.520 nonbonded pdb=" OE2 GLU B 105 " pdb=" OG SER B 113 " model vdw 2.011 2.440 nonbonded pdb=" C LEU 3 278 " pdb=" OD1 ASP 3 279 " model vdw 2.018 3.270 nonbonded pdb=" O GLU 4 372 " pdb=" O ARG 4 373 " model vdw 2.020 3.040 nonbonded pdb=" O ALA 6 307 " pdb=" O VAL 6 318 " model vdw 2.079 3.040 ... (remaining 245897 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 'E' and (resid 474 through 752 or resid 754 through 923)) selection = (chain 'F' and (resid 474 through 663 or resid 671 through 752 or resid 754 thro \ ugh 923)) selection = (chain 'G' and (resid 474 through 752 or resid 754 through 790 or resid 814 thro \ ugh 923)) } 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=0.35 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.030 Extract box with map and model: 6.590 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 85.820 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.008 0.077 35050 Z= 0.499 Angle : 1.123 20.740 47429 Z= 0.671 Chirality : 0.061 0.552 5345 Planarity : 0.007 0.098 6082 Dihedral : 14.872 88.658 13140 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.63 % Favored : 89.15 % Rotamer: Outliers : 0.39 % Allowed : 10.24 % Favored : 89.37 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.10), residues: 4200 helix: -4.58 (0.06), residues: 1200 sheet: -2.73 (0.19), residues: 673 loop : -3.25 (0.10), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 92 HIS 0.008 0.001 HIS 4 413 PHE 0.024 0.002 PHE A 189 TYR 0.028 0.002 TYR D 201 ARG 0.010 0.001 ARG 3 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 600 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 TYR cc_start: 0.8916 (t80) cc_final: 0.8505 (t80) REVERT: C 5 ASP cc_start: 0.8391 (t0) cc_final: 0.7865 (t0) REVERT: C 8 ASP cc_start: 0.8253 (m-30) cc_final: 0.7759 (m-30) REVERT: C 82 THR cc_start: 0.9065 (m) cc_final: 0.8857 (m) REVERT: C 113 MET cc_start: 0.8042 (mmm) cc_final: 0.7747 (mtt) REVERT: C 117 GLU cc_start: 0.8354 (tt0) cc_final: 0.7973 (tt0) REVERT: C 171 GLU cc_start: 0.8688 (tp30) cc_final: 0.7997 (tp30) REVERT: D 126 LEU cc_start: 0.9180 (mt) cc_final: 0.8959 (tp) REVERT: D 207 GLN cc_start: 0.7007 (mt0) cc_final: 0.6806 (pm20) REVERT: c 127 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7615 (mmm-85) REVERT: c 267 LEU cc_start: 0.9051 (tp) cc_final: 0.8847 (tp) REVERT: 2 224 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7843 (ptp-170) REVERT: 2 276 MET cc_start: 0.8396 (tpt) cc_final: 0.8143 (tpp) REVERT: 2 293 ILE cc_start: 0.8745 (mp) cc_final: 0.8323 (mm) REVERT: 3 30 GLU cc_start: 0.8759 (mp0) cc_final: 0.8517 (mp0) REVERT: 3 205 LYS cc_start: 0.8659 (tmmt) cc_final: 0.8234 (ttpt) REVERT: 3 275 ASP cc_start: 0.8272 (p0) cc_final: 0.8067 (p0) REVERT: 3 320 LEU cc_start: 0.8958 (mt) cc_final: 0.8744 (mp) REVERT: 3 325 THR cc_start: 0.8717 (p) cc_final: 0.8429 (t) REVERT: 4 421 ASP cc_start: 0.8731 (p0) cc_final: 0.8362 (p0) REVERT: 5 287 ILE cc_start: 0.9231 (mt) cc_final: 0.8947 (pt) REVERT: 6 413 PRO cc_start: 0.5647 (Cg_endo) cc_final: 0.5412 (Cg_exo) REVERT: 7 66 MET cc_start: 0.8783 (ttp) cc_final: 0.8517 (ptm) REVERT: 7 360 TYR cc_start: 0.5507 (t80) cc_final: 0.4439 (t80) REVERT: E 661 LEU cc_start: 0.8927 (mt) cc_final: 0.8515 (mt) REVERT: E 704 LEU cc_start: 0.9240 (tp) cc_final: 0.8981 (tt) REVERT: E 726 MET cc_start: 0.8658 (tpt) cc_final: 0.8437 (tpp) REVERT: E 851 GLU cc_start: 0.7555 (mp0) cc_final: 0.6854 (mp0) REVERT: E 852 ASN cc_start: 0.8930 (m-40) cc_final: 0.8687 (p0) REVERT: F 496 MET cc_start: 0.8462 (ttm) cc_final: 0.8169 (mtt) REVERT: F 655 CYS cc_start: 0.8711 (m) cc_final: 0.8360 (m) REVERT: G 679 PHE cc_start: 0.8924 (t80) cc_final: 0.8564 (t80) outliers start: 13 outliers final: 4 residues processed: 610 average time/residue: 0.4912 time to fit residues: 464.2865 Evaluate side-chains 388 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 384 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 7 residue 207 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 357 optimal weight: 9.9990 chunk 320 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 201 optimal weight: 0.0370 chunk 246 optimal weight: 2.9990 chunk 384 optimal weight: 1.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 58 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 183 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 70 HIS ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 133 ASN c 254 GLN c 266 ASN ** c 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 541 ASN 2 245 ASN 2 433 ASN 3 259 GLN 4 240 ASN 4 354 HIS 5 49 GLN 5 254 GLN 5 284 ASN 6 173 GLN 6 274 HIS 6 347 ASN 6 357 GLN 7 90 ASN E 877 GLN E 916 ASN F 507 ASN F 553 GLN F 877 GLN F 915 ASN G 553 GLN G 555 GLN G 680 ASN ** G 753 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35050 Z= 0.192 Angle : 0.668 10.727 47429 Z= 0.350 Chirality : 0.044 0.232 5345 Planarity : 0.005 0.072 6082 Dihedral : 6.170 39.385 4671 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.04 % Favored : 91.92 % Rotamer: Outliers : 2.17 % Allowed : 15.48 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -4.37 (0.11), residues: 4200 helix: -3.38 (0.10), residues: 1251 sheet: -2.02 (0.20), residues: 681 loop : -2.94 (0.11), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 6 356 HIS 0.005 0.001 HIS c 22 PHE 0.020 0.001 PHE F 597 TYR 0.024 0.001 TYR A 89 ARG 0.006 0.000 ARG c 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 443 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8938 (mttt) cc_final: 0.8519 (mtpp) REVERT: B 162 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.6346 (t80) REVERT: C 5 ASP cc_start: 0.8324 (t0) cc_final: 0.7590 (t0) REVERT: C 8 ASP cc_start: 0.8249 (m-30) cc_final: 0.7281 (m-30) REVERT: C 117 GLU cc_start: 0.8274 (tt0) cc_final: 0.7886 (tt0) REVERT: C 171 GLU cc_start: 0.8610 (tp30) cc_final: 0.8217 (tp30) REVERT: c 127 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7502 (mmm-85) REVERT: c 129 TRP cc_start: 0.5365 (OUTLIER) cc_final: 0.4647 (m-90) REVERT: c 465 LYS cc_start: 0.8566 (mttt) cc_final: 0.8007 (tptt) REVERT: c 629 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8713 (mt) REVERT: 2 267 MET cc_start: 0.8872 (tpp) cc_final: 0.8544 (tpp) REVERT: 2 276 MET cc_start: 0.8297 (tpt) cc_final: 0.7947 (tpt) REVERT: 2 293 ILE cc_start: 0.8717 (mp) cc_final: 0.8384 (mm) REVERT: 4 354 HIS cc_start: 0.7471 (t-170) cc_final: 0.7214 (t70) REVERT: 4 356 MET cc_start: 0.6561 (ttm) cc_final: 0.4900 (mtp) REVERT: 4 421 ASP cc_start: 0.8721 (p0) cc_final: 0.8360 (p0) REVERT: 5 82 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7558 (pp20) REVERT: 7 360 TYR cc_start: 0.5188 (t80) cc_final: 0.4117 (t80) REVERT: E 661 LEU cc_start: 0.8911 (mt) cc_final: 0.8662 (mt) REVERT: E 704 LEU cc_start: 0.9225 (tp) cc_final: 0.8997 (tt) REVERT: E 852 ASN cc_start: 0.8869 (m-40) cc_final: 0.8572 (p0) REVERT: F 509 GLU cc_start: 0.6891 (pm20) cc_final: 0.6593 (pm20) REVERT: F 726 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8007 (tpt) REVERT: G 596 TYR cc_start: 0.8955 (m-80) cc_final: 0.8731 (m-80) REVERT: G 618 LEU cc_start: 0.9272 (mt) cc_final: 0.9032 (mt) REVERT: G 679 PHE cc_start: 0.8935 (t80) cc_final: 0.8545 (t80) outliers start: 82 outliers final: 37 residues processed: 497 average time/residue: 0.4130 time to fit residues: 340.6768 Evaluate side-chains 411 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 369 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain c residue 76 ASP Chi-restraints excluded: chain c residue 129 TRP Chi-restraints excluded: chain c residue 142 CYS Chi-restraints excluded: chain c residue 310 VAL Chi-restraints excluded: chain c residue 413 LEU Chi-restraints excluded: chain c residue 555 CYS Chi-restraints excluded: chain c residue 580 LEU Chi-restraints excluded: chain c residue 629 ILE Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 2 residue 444 PHE Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 43 GLN Chi-restraints excluded: chain 5 residue 82 GLU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 173 GLN Chi-restraints excluded: chain 6 residue 273 VAL Chi-restraints excluded: chain 6 residue 355 ASP Chi-restraints excluded: chain 6 residue 395 CYS Chi-restraints excluded: chain 7 residue 83 ASP Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain E residue 686 SER Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain F residue 726 MET Chi-restraints excluded: chain F residue 738 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 213 optimal weight: 4.9990 chunk 119 optimal weight: 0.1980 chunk 319 optimal weight: 4.9990 chunk 261 optimal weight: 40.0000 chunk 105 optimal weight: 0.9990 chunk 384 optimal weight: 0.8980 chunk 415 optimal weight: 20.0000 chunk 342 optimal weight: 6.9990 chunk 381 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 468 ASN 4 231 ASN ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 150 ASN 7 334 HIS ** G 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 702 ASN ** G 753 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35050 Z= 0.202 Angle : 0.627 12.701 47429 Z= 0.322 Chirality : 0.043 0.182 5345 Planarity : 0.004 0.060 6082 Dihedral : 5.647 38.607 4669 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.35 % Favored : 90.63 % Rotamer: Outliers : 2.72 % Allowed : 16.82 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.81 (0.12), residues: 4200 helix: -2.63 (0.12), residues: 1258 sheet: -1.84 (0.19), residues: 703 loop : -2.73 (0.12), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 92 HIS 0.014 0.001 HIS 4 413 PHE 0.017 0.001 PHE 5 44 TYR 0.024 0.001 TYR 6 305 ARG 0.007 0.000 ARG 6 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 386 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 303, in __init__ self.caller(self.optimize_sidechains) 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 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable