Starting phenix.real_space_refine on Fri Dec 15 01:47:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a95_11685/12_2023/7a95_11685.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a95_11685/12_2023/7a95_11685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a95_11685/12_2023/7a95_11685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a95_11685/12_2023/7a95_11685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a95_11685/12_2023/7a95_11685.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a95_11685/12_2023/7a95_11685.pdb" } resolution = 4.3 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= 0.002 sd= 0.029 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 145 5.16 5 C 19081 2.51 5 N 4984 2.21 5 O 5677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 29887 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8364 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 53, 'TRANS': 1015} Chain breaks: 5 Chain: "B" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8350 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 53, 'TRANS': 1013} Chain breaks: 5 Chain: "C" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 5 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Time building chain proxies: 15.17, per 1000 atoms: 0.51 Number of scatterers: 29887 At special positions: 0 Unit cell: (145.53, 161.7, 246.862, 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 145 16.00 O 5677 8.00 N 4984 7.00 C 19081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.84 Conformation dependent library (CDL) restraints added in 5.7 seconds 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 57 sheets defined 26.8% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.541A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.659A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.872A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.699A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.935A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 753 " --> pdb=" O CYS A 749 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 747 through 754' Processing helix chain 'A' and resid 756 through 779 removed outlier: 3.697A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.786A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.600A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.838A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.821A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.506A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 removed outlier: 3.649A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.514A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.916A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.783A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.818A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.046A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 removed outlier: 4.012A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.933A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.007A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 782 removed outlier: 3.862A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.537A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 885 removed outlier: 3.762A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 4.090A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 906 " --> pdb=" O MET B 902 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.799A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.616A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 931 " --> pdb=" O PHE B 927 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.902A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.755A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1032 removed outlier: 4.142A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.818A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.672A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.619A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.677A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 755 removed outlier: 3.512A pdb=" N GLN C 755 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.925A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.720A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.628A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 4.013A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.569A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.532A pdb=" N ILE C 931 " --> pdb=" O PHE C 927 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.631A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.831A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.757A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.767A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.607A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 80 removed outlier: 3.572A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 removed outlier: 3.613A pdb=" N GLN D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.822A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 112 through 129 removed outlier: 3.572A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 121 " --> pdb=" O ASN D 117 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.840A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 removed outlier: 3.858A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU D 162 " --> pdb=" O TYR D 158 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TRP D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.556A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL D 184 " --> pdb=" O TYR D 180 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.674A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 225 through 233 removed outlier: 4.098A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.502A pdb=" N TYR D 243 " --> pdb=" O HIS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.653A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.658A pdb=" N MET D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.659A pdb=" N LYS D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.585A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 385 removed outlier: 3.780A pdb=" N LEU D 370 " --> pdb=" O MET D 366 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP D 382 " --> pdb=" O HIS D 378 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.643A pdb=" N VAL D 404 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.655A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.729A pdb=" N LYS D 458 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 463 " --> pdb=" O TRP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.697A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.659A pdb=" N ASN D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.700A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 553 removed outlier: 3.600A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 561 removed outlier: 3.843A pdb=" N LEU D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.647A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.621A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 597 removed outlier: 3.642A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.617A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.888A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.961A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.604A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 160 removed outlier: 3.864A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.883A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 355 removed outlier: 4.276A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.897A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.124A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.627A pdb=" N THR A 719 " --> pdb=" O VAL A1068 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.696A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.528A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.596A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.688A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.688A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 53 through 55 removed outlier: 4.121A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.554A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 152 through 160 removed outlier: 5.480A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 275 through 279 removed outlier: 3.744A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.850A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 597 " --> pdb=" O TYR B 313 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.422A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 540 through 543 Processing sheet with id=AD6, first strand: chain 'B' and resid 551 through 553 removed outlier: 3.787A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.788A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD9, first strand: chain 'B' and resid 713 through 714 removed outlier: 3.673A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 717 through 722 removed outlier: 3.638A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 719 " --> pdb=" O VAL B1068 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.657A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.742A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.690A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE6, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.543A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.884A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.707A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.591A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.015A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.591A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 310 through 314 removed outlier: 3.628A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 354 through 355 removed outlier: 4.731A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 448 through 453 removed outlier: 7.701A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C 495 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.972A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 713 through 715 Processing sheet with id=AF7, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.869A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.986A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C1062 " --> pdb=" O GLU C 725 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.314A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG3, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.180A pdb=" N ALA D 348 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 359 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP D 350 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ARG D 357 " --> pdb=" O ASP D 350 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 352 " --> pdb=" O ASP D 355 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2235 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: 17.83 Time building geometry restraints manager: 11.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8618 1.33 - 1.45: 5533 1.45 - 1.58: 16256 1.58 - 1.70: 0 1.70 - 1.82: 196 Bond restraints: 30603 Sorted by residual: bond pdb=" N GLN B 493 " pdb=" CA GLN B 493 " ideal model delta sigma weight residual 1.452 1.503 -0.051 1.25e-02 6.40e+03 1.64e+01 bond pdb=" N GLN B 498 " pdb=" CA GLN B 498 " ideal model delta sigma weight residual 1.453 1.491 -0.037 9.20e-03 1.18e+04 1.64e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.11e-02 8.12e+03 1.44e+01 bond pdb=" N VAL A1129 " pdb=" CA VAL A1129 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.14e-02 7.69e+03 1.22e+01 bond pdb=" N VAL B1096 " pdb=" CA VAL B1096 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.18e+01 ... (remaining 30598 not shown) Histogram of bond angle deviations from ideal: 100.61 - 107.36: 1034 107.36 - 114.11: 17151 114.11 - 120.86: 13245 120.86 - 127.62: 9946 127.62 - 134.37: 252 Bond angle restraints: 41628 Sorted by residual: angle pdb=" N SER B 494 " pdb=" CA SER B 494 " pdb=" C SER B 494 " ideal model delta sigma weight residual 112.94 121.23 -8.29 1.41e+00 5.03e-01 3.46e+01 angle pdb=" N GLN D 305 " pdb=" CA GLN D 305 " pdb=" C GLN D 305 " ideal model delta sigma weight residual 112.92 106.54 6.38 1.23e+00 6.61e-01 2.69e+01 angle pdb=" CA ASP C 745 " pdb=" C ASP C 745 " pdb=" O ASP C 745 " ideal model delta sigma weight residual 121.20 116.38 4.82 1.04e+00 9.25e-01 2.15e+01 angle pdb=" CA CYS A 525 " pdb=" C CYS A 525 " pdb=" N GLY A 526 " ideal model delta sigma weight residual 119.56 116.87 2.69 5.80e-01 2.97e+00 2.14e+01 angle pdb=" CA GLN B 493 " pdb=" C GLN B 493 " pdb=" O GLN B 493 " ideal model delta sigma weight residual 121.82 116.40 5.42 1.21e+00 6.83e-01 2.01e+01 ... (remaining 41623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 17833 15.90 - 31.79: 348 31.79 - 47.69: 37 47.69 - 63.58: 5 63.58 - 79.48: 5 Dihedral angle restraints: 18228 sinusoidal: 7169 harmonic: 11059 Sorted by residual: dihedral pdb=" C PHE C1109 " pdb=" N PHE C1109 " pdb=" CA PHE C1109 " pdb=" CB PHE C1109 " ideal model delta harmonic sigma weight residual -122.60 -133.47 10.87 0 2.50e+00 1.60e-01 1.89e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -121.69 35.69 1 1.00e+01 1.00e-02 1.80e+01 dihedral pdb=" C ASN B 481 " pdb=" N ASN B 481 " pdb=" CA ASN B 481 " pdb=" CB ASN B 481 " ideal model delta harmonic sigma weight residual -122.60 -132.40 9.80 0 2.50e+00 1.60e-01 1.54e+01 ... (remaining 18225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4287 0.086 - 0.172: 344 0.172 - 0.258: 14 0.258 - 0.343: 5 0.343 - 0.429: 1 Chirality restraints: 4651 Sorted by residual: chirality pdb=" CA SER B 494 " pdb=" N SER B 494 " pdb=" C SER B 494 " pdb=" CB SER B 494 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA PHE C1109 " pdb=" N PHE C1109 " pdb=" C PHE C1109 " pdb=" CB PHE C1109 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA ASN B 481 " pdb=" N ASN B 481 " pdb=" C ASN B 481 " pdb=" CB ASN B 481 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 4648 not shown) Planarity restraints: 5401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 521 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 528 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C LYS C 528 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS C 528 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS C 529 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 318 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C VAL D 318 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL D 318 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY D 319 " -0.012 2.00e-02 2.50e+03 ... (remaining 5398 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4278 2.76 - 3.30: 26062 3.30 - 3.83: 46005 3.83 - 4.37: 53819 4.37 - 4.90: 94425 Nonbonded interactions: 224589 Sorted by model distance: nonbonded pdb=" O GLN D 305 " pdb=" NE2 GLN D 305 " model vdw 2.226 2.520 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.302 2.440 nonbonded pdb=" OG1 THR D 365 " pdb=" OD1 ASP D 368 " model vdw 2.312 2.440 nonbonded pdb=" OH TYR B 741 " pdb=" O LEU B 962 " model vdw 2.319 2.440 nonbonded pdb=" O PHE D 327 " pdb=" OG SER D 331 " model vdw 2.355 2.440 ... (remaining 224584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 827 or resid 852 through 1146)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 827 or resid 852 through 1146)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.550 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: 27.990 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 83.700 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.160 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:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30603 Z= 0.172 Angle : 0.472 8.295 41628 Z= 0.300 Chirality : 0.043 0.429 4651 Planarity : 0.003 0.052 5401 Dihedral : 5.772 79.479 10977 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 0.90 % Allowed : 2.98 % Favored : 96.12 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.54 % 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: -4.57 (0.10), residues: 3754 helix: -4.11 (0.07), residues: 823 sheet: -2.07 (0.19), residues: 613 loop : -3.02 (0.10), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B1102 HIS 0.001 0.000 HIS D 540 PHE 0.009 0.000 PHE C 329 TYR 0.008 0.000 TYR C1110 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 350 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 8 residues processed: 379 average time/residue: 0.4210 time to fit residues: 254.0951 Evaluate side-chains 143 residues out of total 3323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 3.535 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3036 time to fit residues: 9.1882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.2152 > 50: distance: 16 - 22: 3.193 distance: 59 - 63: 8.517 distance: 63 - 64: 12.986 distance: 64 - 65: 5.454 distance: 64 - 67: 5.564 distance: 65 - 66: 9.541 distance: 65 - 75: 12.383 distance: 67 - 68: 15.392 distance: 68 - 69: 6.412 distance: 68 - 70: 5.465 distance: 70 - 72: 5.083 distance: 71 - 73: 3.813 distance: 72 - 73: 4.238 distance: 75 - 76: 12.616 distance: 76 - 77: 28.388 distance: 76 - 79: 6.599 distance: 77 - 78: 38.026 distance: 77 - 83: 57.215 distance: 79 - 80: 10.006 distance: 79 - 81: 5.690 distance: 80 - 82: 6.137 distance: 83 - 84: 52.636 distance: 84 - 85: 21.897 distance: 84 - 87: 23.884 distance: 85 - 86: 10.962 distance: 85 - 89: 17.024 distance: 87 - 88: 5.607 distance: 89 - 90: 10.164 distance: 89 - 95: 9.146 distance: 90 - 91: 7.879 distance: 90 - 93: 9.161 distance: 91 - 92: 3.239 distance: 91 - 96: 5.332 distance: 93 - 94: 4.427 distance: 94 - 95: 7.114 distance: 96 - 97: 5.686 distance: 97 - 98: 3.836 distance: 97 - 100: 5.024 distance: 100 - 101: 4.617 distance: 100 - 102: 3.606 distance: 104 - 105: 4.727 distance: 105 - 106: 13.056 distance: 106 - 107: 12.287 distance: 106 - 108: 23.702 distance: 108 - 109: 11.888 distance: 109 - 110: 23.329 distance: 109 - 112: 7.832 distance: 110 - 111: 28.486 distance: 110 - 114: 20.961 distance: 112 - 113: 3.040 distance: 114 - 115: 5.901 distance: 115 - 116: 4.409 distance: 115 - 118: 5.247 distance: 116 - 117: 4.122 distance: 116 - 122: 3.094 distance: 118 - 119: 3.201 distance: 122 - 123: 4.821 distance: 123 - 124: 5.429 distance: 123 - 126: 3.922 distance: 124 - 129: 5.598 distance: 130 - 131: 6.937 distance: 130 - 133: 6.240 distance: 131 - 134: 3.642