Starting phenix.real_space_refine on Thu Mar 14 22:18:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vml_33935/03_2024/7vml_33935.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vml_33935/03_2024/7vml_33935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vml_33935/03_2024/7vml_33935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vml_33935/03_2024/7vml_33935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vml_33935/03_2024/7vml_33935.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vml_33935/03_2024/7vml_33935.pdb" } resolution = 3.3 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 720 5.16 5 C 78204 2.51 5 N 21548 2.21 5 O 23088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A GLU 711": "OE1" <-> "OE2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A GLU 899": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A GLU 1052": "OE1" <-> "OE2" Residue "A GLU 1170": "OE1" <-> "OE2" Residue "A PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1649": "OE1" <-> "OE2" Residue "A ARG 1672": "NH1" <-> "NH2" Residue "A GLU 1732": "OE1" <-> "OE2" Residue "A GLU 1802": "OE1" <-> "OE2" Residue "A GLU 1816": "OE1" <-> "OE2" Residue "A GLU 1922": "OE1" <-> "OE2" Residue "A ARG 1962": "NH1" <-> "NH2" Residue "A GLU 1984": "OE1" <-> "OE2" Residue "A GLU 2000": "OE1" <-> "OE2" Residue "A GLU 2078": "OE1" <-> "OE2" Residue "A GLU 2136": "OE1" <-> "OE2" Residue "A GLU 2137": "OE1" <-> "OE2" Residue "A ARG 2321": "NH1" <-> "NH2" Residue "A GLU 2347": "OE1" <-> "OE2" Residue "A GLU 2354": "OE1" <-> "OE2" Residue "A ARG 2417": "NH1" <-> "NH2" Residue "A PHE 2470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2488": "OE1" <-> "OE2" Residue "A GLU 2714": "OE1" <-> "OE2" Residue "A GLU 2717": "OE1" <-> "OE2" Residue "A GLU 2725": "OE1" <-> "OE2" Residue "A GLU 2744": "OE1" <-> "OE2" Residue "A GLU 2766": "OE1" <-> "OE2" Residue "A GLU 2845": "OE1" <-> "OE2" Residue "A GLU 2880": "OE1" <-> "OE2" Residue "A GLU 2886": "OE1" <-> "OE2" Residue "A ARG 3614": "NH1" <-> "NH2" Residue "A GLU 3631": "OE1" <-> "OE2" Residue "A GLU 3683": "OE1" <-> "OE2" Residue "A GLU 3717": "OE1" <-> "OE2" Residue "A GLU 3814": "OE1" <-> "OE2" Residue "A GLU 3882": "OE1" <-> "OE2" Residue "A GLU 4010": "OE1" <-> "OE2" Residue "A GLU 4081": "OE1" <-> "OE2" Residue "A GLU 4136": "OE1" <-> "OE2" Residue "A GLU 4145": "OE1" <-> "OE2" Residue "A ARG 4146": "NH1" <-> "NH2" Residue "A ARG 4156": "NH1" <-> "NH2" Residue "A GLU 4181": "OE1" <-> "OE2" Residue "A ARG 4495": "NH1" <-> "NH2" Residue "A ARG 4501": "NH1" <-> "NH2" Residue "A GLU 4561": "OE1" <-> "OE2" Residue "A GLU 4602": "OE1" <-> "OE2" Residue "A GLU 4604": "OE1" <-> "OE2" Residue "A GLU 4622": "OE1" <-> "OE2" Residue "A GLU 4658": "OE1" <-> "OE2" Residue "A GLU 4667": "OE1" <-> "OE2" Residue "A GLU 4796": "OE1" <-> "OE2" Residue "A ARG 4821": "NH1" <-> "NH2" Residue "A GLU 4837": "OE1" <-> "OE2" Residue "A GLU 4839": "OE1" <-> "OE2" Residue "A GLU 4877": "OE1" <-> "OE2" Residue "A GLU 4905": "OE1" <-> "OE2" Residue "A GLU 4949": "OE1" <-> "OE2" Residue "G ARG 14": "NH1" <-> "NH2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B GLU 711": "OE1" <-> "OE2" Residue "B GLU 712": "OE1" <-> "OE2" Residue "B GLU 843": "OE1" <-> "OE2" Residue "B GLU 899": "OE1" <-> "OE2" Residue "B GLU 920": "OE1" <-> "OE2" Residue "B GLU 1052": "OE1" <-> "OE2" Residue "B GLU 1170": "OE1" <-> "OE2" Residue "B PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1649": "OE1" <-> "OE2" Residue "B ARG 1672": "NH1" <-> "NH2" Residue "B GLU 1732": "OE1" <-> "OE2" Residue "B GLU 1802": "OE1" <-> "OE2" Residue "B GLU 1816": "OE1" <-> "OE2" Residue "B GLU 1922": "OE1" <-> "OE2" Residue "B ARG 1962": "NH1" <-> "NH2" Residue "B GLU 1984": "OE1" <-> "OE2" Residue "B GLU 2000": "OE1" <-> "OE2" Residue "B GLU 2078": "OE1" <-> "OE2" Residue "B GLU 2136": "OE1" <-> "OE2" Residue "B GLU 2137": "OE1" <-> "OE2" Residue "B ARG 2321": "NH1" <-> "NH2" Residue "B GLU 2347": "OE1" <-> "OE2" Residue "B GLU 2354": "OE1" <-> "OE2" Residue "B ARG 2417": "NH1" <-> "NH2" Residue "B GLU 2488": "OE1" <-> "OE2" Residue "B GLU 2714": "OE1" <-> "OE2" Residue "B GLU 2717": "OE1" <-> "OE2" Residue "B GLU 2725": "OE1" <-> "OE2" Residue "B GLU 2744": "OE1" <-> "OE2" Residue "B GLU 2766": "OE1" <-> "OE2" Residue "B GLU 2845": "OE1" <-> "OE2" Residue "B GLU 2880": "OE1" <-> "OE2" Residue "B GLU 2886": "OE1" <-> "OE2" Residue "B ARG 3614": "NH1" <-> "NH2" Residue "B GLU 3631": "OE1" <-> "OE2" Residue "B GLU 3683": "OE1" <-> "OE2" Residue "B GLU 3717": "OE1" <-> "OE2" Residue "B GLU 3814": "OE1" <-> "OE2" Residue "B GLU 3882": "OE1" <-> "OE2" Residue "B GLU 4010": "OE1" <-> "OE2" Residue "B GLU 4081": "OE1" <-> "OE2" Residue "B GLU 4136": "OE1" <-> "OE2" Residue "B GLU 4145": "OE1" <-> "OE2" Residue "B ARG 4146": "NH1" <-> "NH2" Residue "B ARG 4156": "NH1" <-> "NH2" Residue "B GLU 4181": "OE1" <-> "OE2" Residue "B ARG 4495": "NH1" <-> "NH2" Residue "B ARG 4501": "NH1" <-> "NH2" Residue "B GLU 4561": "OE1" <-> "OE2" Residue "B GLU 4602": "OE1" <-> "OE2" Residue "B GLU 4604": "OE1" <-> "OE2" Residue "B GLU 4622": "OE1" <-> "OE2" Residue "B GLU 4658": "OE1" <-> "OE2" Residue "B GLU 4667": "OE1" <-> "OE2" Residue "B GLU 4796": "OE1" <-> "OE2" Residue "B ARG 4821": "NH1" <-> "NH2" Residue "B GLU 4837": "OE1" <-> "OE2" Residue "B GLU 4839": "OE1" <-> "OE2" Residue "B GLU 4877": "OE1" <-> "OE2" Residue "B GLU 4905": "OE1" <-> "OE2" Residue "B GLU 4949": "OE1" <-> "OE2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C GLU 711": "OE1" <-> "OE2" Residue "C GLU 712": "OE1" <-> "OE2" Residue "C GLU 843": "OE1" <-> "OE2" Residue "C GLU 899": "OE1" <-> "OE2" Residue "C GLU 920": "OE1" <-> "OE2" Residue "C GLU 1052": "OE1" <-> "OE2" Residue "C GLU 1170": "OE1" <-> "OE2" Residue "C PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1649": "OE1" <-> "OE2" Residue "C ARG 1672": "NH1" <-> "NH2" Residue "C GLU 1732": "OE1" <-> "OE2" Residue "C GLU 1802": "OE1" <-> "OE2" Residue "C GLU 1816": "OE1" <-> "OE2" Residue "C GLU 1922": "OE1" <-> "OE2" Residue "C ARG 1962": "NH1" <-> "NH2" Residue "C GLU 1984": "OE1" <-> "OE2" Residue "C GLU 2000": "OE1" <-> "OE2" Residue "C GLU 2078": "OE1" <-> "OE2" Residue "C GLU 2136": "OE1" <-> "OE2" Residue "C GLU 2137": "OE1" <-> "OE2" Residue "C ARG 2321": "NH1" <-> "NH2" Residue "C GLU 2347": "OE1" <-> "OE2" Residue "C GLU 2354": "OE1" <-> "OE2" Residue "C ARG 2417": "NH1" <-> "NH2" Residue "C PHE 2470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2488": "OE1" <-> "OE2" Residue "C GLU 2714": "OE1" <-> "OE2" Residue "C GLU 2717": "OE1" <-> "OE2" Residue "C GLU 2725": "OE1" <-> "OE2" Residue "C GLU 2744": "OE1" <-> "OE2" Residue "C GLU 2766": "OE1" <-> "OE2" Residue "C GLU 2845": "OE1" <-> "OE2" Residue "C GLU 2880": "OE1" <-> "OE2" Residue "C GLU 2886": "OE1" <-> "OE2" Residue "C ARG 3614": "NH1" <-> "NH2" Residue "C GLU 3631": "OE1" <-> "OE2" Residue "C GLU 3683": "OE1" <-> "OE2" Residue "C GLU 3717": "OE1" <-> "OE2" Residue "C GLU 3814": "OE1" <-> "OE2" Residue "C GLU 3882": "OE1" <-> "OE2" Residue "C GLU 4010": "OE1" <-> "OE2" Residue "C GLU 4081": "OE1" <-> "OE2" Residue "C GLU 4136": "OE1" <-> "OE2" Residue "C GLU 4145": "OE1" <-> "OE2" Residue "C ARG 4146": "NH1" <-> "NH2" Residue "C ARG 4156": "NH1" <-> "NH2" Residue "C GLU 4181": "OE1" <-> "OE2" Residue "C ARG 4495": "NH1" <-> "NH2" Residue "C ARG 4501": "NH1" <-> "NH2" Residue "C GLU 4561": "OE1" <-> "OE2" Residue "C GLU 4602": "OE1" <-> "OE2" Residue "C GLU 4604": "OE1" <-> "OE2" Residue "C GLU 4622": "OE1" <-> "OE2" Residue "C GLU 4658": "OE1" <-> "OE2" Residue "C GLU 4667": "OE1" <-> "OE2" Residue "C GLU 4796": "OE1" <-> "OE2" Residue "C ARG 4821": "NH1" <-> "NH2" Residue "C GLU 4837": "OE1" <-> "OE2" Residue "C GLU 4839": "OE1" <-> "OE2" Residue "C GLU 4877": "OE1" <-> "OE2" Residue "C GLU 4905": "OE1" <-> "OE2" Residue "C GLU 4949": "OE1" <-> "OE2" Residue "I ARG 14": "NH1" <-> "NH2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D GLU 535": "OE1" <-> "OE2" Residue "D GLU 566": "OE1" <-> "OE2" Residue "D GLU 711": "OE1" <-> "OE2" Residue "D GLU 712": "OE1" <-> "OE2" Residue "D GLU 843": "OE1" <-> "OE2" Residue "D GLU 899": "OE1" <-> "OE2" Residue "D GLU 920": "OE1" <-> "OE2" Residue "D GLU 1052": "OE1" <-> "OE2" Residue "D GLU 1170": "OE1" <-> "OE2" Residue "D PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1649": "OE1" <-> "OE2" Residue "D ARG 1672": "NH1" <-> "NH2" Residue "D GLU 1732": "OE1" <-> "OE2" Residue "D GLU 1802": "OE1" <-> "OE2" Residue "D GLU 1816": "OE1" <-> "OE2" Residue "D GLU 1922": "OE1" <-> "OE2" Residue "D ARG 1962": "NH1" <-> "NH2" Residue "D GLU 1984": "OE1" <-> "OE2" Residue "D GLU 2000": "OE1" <-> "OE2" Residue "D GLU 2078": "OE1" <-> "OE2" Residue "D GLU 2136": "OE1" <-> "OE2" Residue "D GLU 2137": "OE1" <-> "OE2" Residue "D ARG 2321": "NH1" <-> "NH2" Residue "D GLU 2347": "OE1" <-> "OE2" Residue "D GLU 2354": "OE1" <-> "OE2" Residue "D ARG 2417": "NH1" <-> "NH2" Residue "D GLU 2488": "OE1" <-> "OE2" Residue "D GLU 2714": "OE1" <-> "OE2" Residue "D GLU 2717": "OE1" <-> "OE2" Residue "D GLU 2725": "OE1" <-> "OE2" Residue "D GLU 2744": "OE1" <-> "OE2" Residue "D GLU 2766": "OE1" <-> "OE2" Residue "D GLU 2845": "OE1" <-> "OE2" Residue "D GLU 2880": "OE1" <-> "OE2" Residue "D GLU 2886": "OE1" <-> "OE2" Residue "D ARG 3614": "NH1" <-> "NH2" Residue "D GLU 3631": "OE1" <-> "OE2" Residue "D GLU 3683": "OE1" <-> "OE2" Residue "D GLU 3717": "OE1" <-> "OE2" Residue "D GLU 3814": "OE1" <-> "OE2" Residue "D GLU 3882": "OE1" <-> "OE2" Residue "D GLU 4010": "OE1" <-> "OE2" Residue "D GLU 4081": "OE1" <-> "OE2" Residue "D GLU 4136": "OE1" <-> "OE2" Residue "D GLU 4145": "OE1" <-> "OE2" Residue "D ARG 4146": "NH1" <-> "NH2" Residue "D ARG 4156": "NH1" <-> "NH2" Residue "D GLU 4181": "OE1" <-> "OE2" Residue "D ARG 4495": "NH1" <-> "NH2" Residue "D ARG 4501": "NH1" <-> "NH2" Residue "D GLU 4561": "OE1" <-> "OE2" Residue "D GLU 4602": "OE1" <-> "OE2" Residue "D GLU 4604": "OE1" <-> "OE2" Residue "D GLU 4622": "OE1" <-> "OE2" Residue "D GLU 4658": "OE1" <-> "OE2" Residue "D GLU 4667": "OE1" <-> "OE2" Residue "D GLU 4796": "OE1" <-> "OE2" Residue "D ARG 4821": "NH1" <-> "NH2" Residue "D GLU 4837": "OE1" <-> "OE2" Residue "D GLU 4839": "OE1" <-> "OE2" Residue "D GLU 4877": "OE1" <-> "OE2" Residue "D GLU 4905": "OE1" <-> "OE2" Residue "D GLU 4949": "OE1" <-> "OE2" Residue "J ARG 14": "NH1" <-> "NH2" Time to flip residues: 0.35s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 123564 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 30071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30071 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 30071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30071 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "H" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 30071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30071 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "I" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 30071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30071 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "J" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29425 SG CYS A4887 192.851 199.793 119.919 1.00 47.26 S ATOM 29450 SG CYS A4890 190.763 199.331 116.858 1.00 17.83 S ATOM 60315 SG CYS B4887 167.430 192.815 119.907 1.00 64.65 S ATOM 60340 SG CYS B4890 167.889 190.725 116.846 1.00 11.74 S ATOM 91205 SG CYS C4887 174.414 167.432 119.912 1.00 47.26 S ATOM 91230 SG CYS C4890 176.503 167.892 116.851 1.00 16.46 S ATOM A0H1R SG CYS D4887 199.768 174.405 119.921 1.00 56.97 S ATOM A0H2G SG CYS D4890 199.309 176.495 116.860 1.00 11.54 S Time building chain proxies: 45.46, per 1000 atoms: 0.37 Number of scatterers: 123564 At special positions: 0 Unit cell: (368.508, 367.224, 208.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 720 16.00 O 23088 8.00 N 21548 7.00 C 78204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.15 Conformation dependent library (CDL) restraints added in 13.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4907 " pdb="ZN ZN A6000 " - pdb=" ND1 HIS A4912 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4890 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4887 " pdb=" ZN B6000 " pdb="ZN ZN B6000 " - pdb=" NE2 HIS B4907 " pdb="ZN ZN B6000 " - pdb=" ND1 HIS B4912 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4890 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4887 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4907 " pdb="ZN ZN C6000 " - pdb=" ND1 HIS C4912 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4890 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4887 " pdb=" ZN D6000 " pdb="ZN ZN D6000 " - pdb=" NE2 HIS D4907 " pdb="ZN ZN D6000 " - pdb=" ND1 HIS D4912 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4890 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4887 " Number of angles added : 4 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31448 Finding SS restraints... Secondary structure from input PDB file: 648 helices and 104 sheets defined 68.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.27 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 264 through 273 removed outlier: 4.153A pdb=" N VAL A 267 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA A 271 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ARG A 272 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 273 " --> pdb=" O HIS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.913A pdb=" N LYS A 321 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.751A pdb=" N ARG A 383 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 438 removed outlier: 3.755A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.579A pdb=" N GLY A 461 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 491 Processing helix chain 'A' and resid 493 through 506 removed outlier: 3.579A pdb=" N LEU A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 519 removed outlier: 3.726A pdb=" N ASP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL A 517 " --> pdb=" O HIS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 541 removed outlier: 4.772A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 4.165A pdb=" N CYS A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 removed outlier: 3.699A pdb=" N SER A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.508A pdb=" N ILE A 589 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.998A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A 612 " --> pdb=" O HIS A 608 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.922A pdb=" N LEU A 637 " --> pdb=" O CYS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 878 through 901 removed outlier: 4.021A pdb=" N LYS A 897 " --> pdb=" O TRP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 4.062A pdb=" N ASN A 930 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASN A 932 " --> pdb=" O GLU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1012 Processing helix chain 'A' and resid 1029 through 1033 removed outlier: 4.121A pdb=" N VAL A1033 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1060 removed outlier: 3.915A pdb=" N ASN A1046 " --> pdb=" O THR A1042 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1050 " --> pdb=" O ASN A1046 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A1052 " --> pdb=" O ASP A1048 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA A1053 " --> pdb=" O SER A1049 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A1054 " --> pdb=" O LEU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1095 Processing helix chain 'A' and resid 1643 through 1647 removed outlier: 3.557A pdb=" N GLU A1647 " --> pdb=" O GLU A1644 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1665 Processing helix chain 'A' and resid 1671 through 1682 removed outlier: 3.717A pdb=" N ALA A1676 " --> pdb=" O ARG A1672 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A1679 " --> pdb=" O HIS A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1692 removed outlier: 4.340A pdb=" N LEU A1687 " --> pdb=" O GLU A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1711 removed outlier: 3.720A pdb=" N HIS A1711 " --> pdb=" O LEU A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1722 removed outlier: 4.493A pdb=" N TYR A1715 " --> pdb=" O HIS A1711 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET A1722 " --> pdb=" O ALA A1718 " (cutoff:3.500A) Processing helix chain 'A' and resid 1784 through 1806 removed outlier: 3.790A pdb=" N LEU A1788 " --> pdb=" O PRO A1784 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A1805 " --> pdb=" O LYS A1801 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS A1806 " --> pdb=" O GLU A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1832 removed outlier: 3.600A pdb=" N LEU A1818 " --> pdb=" O THR A1814 " (cutoff:3.500A) Proline residue: A1821 - end of helix Processing helix chain 'A' and resid 1836 through 1846 Processing helix chain 'A' and resid 1898 through 1949 removed outlier: 3.619A pdb=" N GLN A1904 " --> pdb=" O PRO A1900 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A1907 " --> pdb=" O LEU A1903 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A1916 " --> pdb=" O LEU A1912 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A1930 " --> pdb=" O ALA A1926 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP A1937 " --> pdb=" O ALA A1933 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A1938 " --> pdb=" O LYS A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1965 removed outlier: 4.711A pdb=" N ARG A1962 " --> pdb=" O ALA A1958 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU A1963 " --> pdb=" O ARG A1959 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A1964 " --> pdb=" O LYS A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1976 Processing helix chain 'A' and resid 1989 through 2006 removed outlier: 3.891A pdb=" N ASP A1993 " --> pdb=" O GLU A1989 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A1994 " --> pdb=" O GLU A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2072 removed outlier: 3.510A pdb=" N VAL A2066 " --> pdb=" O SER A2062 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A2069 " --> pdb=" O MET A2065 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2093 removed outlier: 3.866A pdb=" N VAL A2080 " --> pdb=" O ASP A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2101 removed outlier: 4.164A pdb=" N LEU A2097 " --> pdb=" O GLY A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2112 through 2130 Processing helix chain 'A' and resid 2134 through 2151 Processing helix chain 'A' and resid 2152 through 2157 Processing helix chain 'A' and resid 2157 through 2165 removed outlier: 3.896A pdb=" N MET A2161 " --> pdb=" O HIS A2157 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A2162 " --> pdb=" O PRO A2158 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2179 removed outlier: 3.839A pdb=" N ASN A2176 " --> pdb=" O GLU A2172 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A2177 " --> pdb=" O VAL A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2188 through 2205 removed outlier: 3.873A pdb=" N CYS A2195 " --> pdb=" O MET A2191 " (cutoff:3.500A) Processing helix chain 'A' and resid 2207 through 2221 removed outlier: 3.991A pdb=" N LYS A2211 " --> pdb=" O ARG A2207 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A2215 " --> pdb=" O LYS A2211 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS A2216 " --> pdb=" O ALA A2212 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER A2218 " --> pdb=" O PHE A2214 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR A2219 " --> pdb=" O ASP A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2237 through 2247 Processing helix chain 'A' and resid 2249 through 2256 Processing helix chain 'A' and resid 2260 through 2274 Processing helix chain 'A' and resid 2276 through 2283 Processing helix chain 'A' and resid 2292 through 2305 Processing helix chain 'A' and resid 2312 through 2326 Processing helix chain 'A' and resid 2327 through 2330 Processing helix chain 'A' and resid 2341 through 2355 Processing helix chain 'A' and resid 2356 through 2359 removed outlier: 3.645A pdb=" N ASP A2359 " --> pdb=" O PRO A2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2356 through 2359' Processing helix chain 'A' and resid 2382 through 2402 Processing helix chain 'A' and resid 2413 through 2426 Processing helix chain 'A' and resid 2427 through 2436 Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.827A pdb=" N ALA A2465 " --> pdb=" O PRO A2461 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A2466 " --> pdb=" O ASP A2462 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET A2467 " --> pdb=" O HIS A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2479 through 2491 Processing helix chain 'A' and resid 2491 through 2500 Processing helix chain 'A' and resid 2507 through 2524 removed outlier: 4.156A pdb=" N UNK A2511 " --> pdb=" O SER A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2533 through 2547 Processing helix chain 'A' and resid 2553 through 2571 Processing helix chain 'A' and resid 2575 through 2589 Processing helix chain 'A' and resid 2594 through 2612 Processing helix chain 'A' and resid 2617 through 2635 removed outlier: 3.651A pdb=" N UNK A2621 " --> pdb=" O UNK A2617 " (cutoff:3.500A) Processing helix chain 'A' and resid 2641 through 2649 removed outlier: 4.072A pdb=" N UNK A2645 " --> pdb=" O UNK A2641 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNK A2646 " --> pdb=" O UNK A2642 " (cutoff:3.500A) Processing helix chain 'A' and resid 2650 through 2657 Processing helix chain 'A' and resid 2713 through 2739 removed outlier: 4.037A pdb=" N ASN A2721 " --> pdb=" O GLU A2717 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A2722 " --> pdb=" O TYR A2718 " (cutoff:3.500A) Processing helix chain 'A' and resid 2763 through 2770 removed outlier: 3.833A pdb=" N GLU A2768 " --> pdb=" O GLU A2764 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR A2770 " --> pdb=" O GLU A2766 " (cutoff:3.500A) Processing helix chain 'A' and resid 2772 through 2784 removed outlier: 4.236A pdb=" N GLU A2776 " --> pdb=" O TRP A2772 " (cutoff:3.500A) Processing helix chain 'A' and resid 2836 through 2863 removed outlier: 3.684A pdb=" N TRP A2851 " --> pdb=" O TYR A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2877 through 2898 removed outlier: 3.855A pdb=" N ASP A2884 " --> pdb=" O GLU A2880 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A2887 " --> pdb=" O LYS A2883 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A2894 " --> pdb=" O ASP A2890 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A2895 " --> pdb=" O ILE A2891 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2942 Processing helix chain 'A' and resid 2962 through 2982 removed outlier: 4.253A pdb=" N UNK A2975 " --> pdb=" O UNK A2971 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N UNK A2976 " --> pdb=" O UNK A2972 " (cutoff:3.500A) Processing helix chain 'A' and resid 2992 through 3007 Processing helix chain 'A' and resid 3015 through 3029 Processing helix chain 'A' and resid 3105 through 3129 removed outlier: 3.587A pdb=" N UNK A3116 " --> pdb=" O UNK A3112 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N UNK A3120 " --> pdb=" O UNK A3116 " (cutoff:3.500A) Processing helix chain 'A' and resid 3137 through 3157 removed outlier: 4.158A pdb=" N UNK A3156 " --> pdb=" O UNK A3152 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N UNK A3157 " --> pdb=" O UNK A3153 " (cutoff:3.500A) Processing helix chain 'A' and resid 3163 through 3182 Processing helix chain 'A' and resid 3183 through 3200 removed outlier: 3.652A pdb=" N UNK A3187 " --> pdb=" O UNK A3183 " (cutoff:3.500A) Processing helix chain 'A' and resid 3208 through 3220 removed outlier: 3.701A pdb=" N UNK A3219 " --> pdb=" O UNK A3215 " (cutoff:3.500A) Processing helix chain 'A' and resid 3232 through 3251 Processing helix chain 'A' and resid 3255 through 3270 Processing helix chain 'A' and resid 3271 through 3277 Processing helix chain 'A' and resid 3281 through 3296 removed outlier: 4.013A pdb=" N UNK A3285 " --> pdb=" O UNK A3281 " (cutoff:3.500A) Processing helix chain 'A' and resid 3301 through 3315 Processing helix chain 'A' and resid 3323 through 3356 Processing helix chain 'A' and resid 3362 through 3392 removed outlier: 4.233A pdb=" N UNK A3383 " --> pdb=" O UNK A3379 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N UNK A3389 " --> pdb=" O UNK A3385 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N UNK A3390 " --> pdb=" O UNK A3386 " (cutoff:3.500A) Processing helix chain 'A' and resid 3400 through 3420 removed outlier: 3.995A pdb=" N UNK A3404 " --> pdb=" O UNK A3400 " (cutoff:3.500A) Processing helix chain 'A' and resid 3421 through 3434 removed outlier: 4.637A pdb=" N UNK A3428 " --> pdb=" O UNK A3424 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N UNK A3429 " --> pdb=" O UNK A3425 " (cutoff:3.500A) Processing helix chain 'A' and resid 3478 through 3495 removed outlier: 4.166A pdb=" N UNK A3495 " --> pdb=" O UNK A3491 " (cutoff:3.500A) Processing helix chain 'A' and resid 3503 through 3514 Processing helix chain 'A' and resid 3516 through 3527 removed outlier: 3.922A pdb=" N UNK A3527 " --> pdb=" O UNK A3523 " (cutoff:3.500A) Processing helix chain 'A' and resid 3541 through 3548 removed outlier: 4.394A pdb=" N UNK A3545 " --> pdb=" O UNK A3541 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3579 Processing helix chain 'A' and resid 3612 through 3627 removed outlier: 4.141A pdb=" N VAL A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A3617 " --> pdb=" O HIS A3613 " (cutoff:3.500A) Processing helix chain 'A' and resid 3637 through 3643 Processing helix chain 'A' and resid 3661 through 3676 Processing helix chain 'A' and resid 3684 through 3697 removed outlier: 4.169A pdb=" N ASP A3692 " --> pdb=" O MET A3688 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A3693 " --> pdb=" O ALA A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3732 removed outlier: 4.179A pdb=" N GLU A3719 " --> pdb=" O GLU A3715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A3720 " --> pdb=" O LYS A3716 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A3724 " --> pdb=" O LYS A3720 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A3730 " --> pdb=" O GLN A3726 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP A3732 " --> pdb=" O ALA A3728 " (cutoff:3.500A) Processing helix chain 'A' and resid 3734 through 3745 removed outlier: 3.750A pdb=" N LEU A3740 " --> pdb=" O ALA A3736 " (cutoff:3.500A) Processing helix chain 'A' and resid 3753 through 3765 removed outlier: 4.153A pdb=" N LYS A3759 " --> pdb=" O ALA A3755 " (cutoff:3.500A) Processing helix chain 'A' and resid 3769 through 3783 Processing helix chain 'A' and resid 3788 through 3797 Processing helix chain 'A' and resid 3803 through 3817 removed outlier: 3.524A pdb=" N PHE A3807 " --> pdb=" O ASP A3803 " (cutoff:3.500A) Processing helix chain 'A' and resid 3824 through 3828 Processing helix chain 'A' and resid 3831 through 3845 Processing helix chain 'A' and resid 3850 through 3857 Processing helix chain 'A' and resid 3868 through 3891 removed outlier: 3.578A pdb=" N SER A3872 " --> pdb=" O ASN A3868 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A3891 " --> pdb=" O PHE A3887 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3923 removed outlier: 3.841A pdb=" N PHE A3905 " --> pdb=" O GLY A3901 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A3908 " --> pdb=" O ASN A3904 " (cutoff:3.500A) Processing helix chain 'A' and resid 3927 through 3936 Processing helix chain 'A' and resid 3938 through 3959 removed outlier: 3.744A pdb=" N ALA A3942 " --> pdb=" O ARG A3938 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS A3952 " --> pdb=" O HIS A3948 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET A3955 " --> pdb=" O ALA A3951 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A3958 " --> pdb=" O GLN A3954 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A3959 " --> pdb=" O MET A3955 " (cutoff:3.500A) Processing helix chain 'A' and resid 3963 through 3983 Processing helix chain 'A' and resid 3984 through 3986 No H-bonds generated for 'chain 'A' and resid 3984 through 3986' Processing helix chain 'A' and resid 3992 through 4004 removed outlier: 3.611A pdb=" N LYS A3996 " --> pdb=" O GLY A3992 " (cutoff:3.500A) Processing helix chain 'A' and resid 4005 through 4021 Processing helix chain 'A' and resid 4022 through 4027 removed outlier: 4.055A pdb=" N SER A4027 " --> pdb=" O LYS A4023 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4035 removed outlier: 4.396A pdb=" N ASP A4035 " --> pdb=" O PHE A4031 " (cutoff:3.500A) Processing helix chain 'A' and resid 4045 through 4053 removed outlier: 3.527A pdb=" N LYS A4049 " --> pdb=" O ARG A4045 " (cutoff:3.500A) Processing helix chain 'A' and resid 4058 through 4068 Processing helix chain 'A' and resid 4078 through 4087 Processing helix chain 'A' and resid 4087 through 4108 removed outlier: 3.580A pdb=" N ASP A4092 " --> pdb=" O GLU A4088 " (cutoff:3.500A) Processing helix chain 'A' and resid 4111 through 4126 removed outlier: 4.072A pdb=" N PHE A4117 " --> pdb=" O ARG A4113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A4120 " --> pdb=" O THR A4116 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER A4123 " --> pdb=" O GLU A4119 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL A4124 " --> pdb=" O LEU A4120 " (cutoff:3.500A) Processing helix chain 'A' and resid 4128 through 4130 No H-bonds generated for 'chain 'A' and resid 4128 through 4130' Processing helix chain 'A' and resid 4152 through 4158 Processing helix chain 'A' and resid 4161 through 4179 removed outlier: 3.763A pdb=" N GLU A4178 " --> pdb=" O ASP A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4183 through 4204 removed outlier: 3.537A pdb=" N ASN A4190 " --> pdb=" O GLU A4186 " (cutoff:3.500A) Processing helix chain 'A' and resid 4276 through 4284 removed outlier: 3.947A pdb=" N LEU A4280 " --> pdb=" O LYS A4276 " (cutoff:3.500A) Processing helix chain 'A' and resid 4286 through 4302 removed outlier: 3.838A pdb=" N THR A4292 " --> pdb=" O SER A4288 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A4300 " --> pdb=" O PHE A4296 " (cutoff:3.500A) Processing helix chain 'A' and resid 4304 through 4309 removed outlier: 3.545A pdb=" N SER A4309 " --> pdb=" O PHE A4305 " (cutoff:3.500A) Processing helix chain 'A' and resid 4479 through 4496 removed outlier: 3.701A pdb=" N TYR A4485 " --> pdb=" O LYS A4481 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A4488 " --> pdb=" O ALA A4484 " (cutoff:3.500A) Processing helix chain 'A' and resid 4496 through 4515 Processing helix chain 'A' and resid 4567 through 4593 removed outlier: 3.574A pdb=" N LEU A4571 " --> pdb=" O MET A4567 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A4572 " --> pdb=" O GLU A4568 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR A4590 " --> pdb=" O ILE A4586 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS A4591 " --> pdb=" O ILE A4587 " (cutoff:3.500A) Processing helix chain 'A' and resid 4593 through 4613 Processing helix chain 'A' and resid 4613 through 4618 Processing helix chain 'A' and resid 4625 through 4630 Processing helix chain 'A' and resid 4648 through 4656 Processing helix chain 'A' and resid 4661 through 4667 removed outlier: 3.857A pdb=" N SER A4666 " --> pdb=" O ARG A4662 " (cutoff:3.500A) Processing helix chain 'A' and resid 4671 through 4682 Processing helix chain 'A' and resid 4701 through 4713 Processing helix chain 'A' and resid 4715 through 4734 removed outlier: 3.684A pdb=" N LEU A4721 " --> pdb=" O SER A4717 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS A4732 " --> pdb=" O SER A4728 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR A4733 " --> pdb=" O VAL A4729 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4742 removed outlier: 3.616A pdb=" N HIS A4741 " --> pdb=" O PHE A4738 " (cutoff:3.500A) Processing helix chain 'A' and resid 4743 through 4748 Processing helix chain 'A' and resid 4752 through 4761 removed outlier: 4.340A pdb=" N SER A4758 " --> pdb=" O THR A4754 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A4759 " --> pdb=" O ILE A4755 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4807 through 4819 Processing helix chain 'A' and resid 4840 through 4854 Processing helix chain 'A' and resid 4857 through 4886 removed outlier: 3.885A pdb=" N ILE A4861 " --> pdb=" O LEU A4857 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A4865 " --> pdb=" O ILE A4861 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A4868 " --> pdb=" O LEU A4864 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A4869 " --> pdb=" O ILE A4865 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A4870 " --> pdb=" O ILE A4866 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A4886 " --> pdb=" O ASP A4882 " (cutoff:3.500A) Processing helix chain 'A' and resid 4893 through 4898 removed outlier: 3.924A pdb=" N PHE A4897 " --> pdb=" O GLY A4893 " (cutoff:3.500A) Processing helix chain 'A' and resid 4902 through 4910 removed outlier: 3.825A pdb=" N THR A4906 " --> pdb=" O HIS A4902 " (cutoff:3.500A) Processing helix chain 'A' and resid 4913 through 4928 removed outlier: 4.556A pdb=" N ASP A4928 " --> pdb=" O LEU A4924 " (cutoff:3.500A) Processing helix chain 'A' and resid 4933 through 4946 Processing helix chain 'A' and resid 4956 through 4961 removed outlier: 3.658A pdb=" N TYR A4961 " --> pdb=" O PHE A4957 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 65 removed outlier: 4.049A pdb=" N GLY G 63 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 264 through 273 removed outlier: 4.154A pdb=" N VAL B 267 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA B 271 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG B 272 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 273 " --> pdb=" O HIS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.913A pdb=" N LYS B 321 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 379 through 383 removed outlier: 3.752A pdb=" N ARG B 383 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 438 removed outlier: 3.755A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 463 removed outlier: 3.579A pdb=" N GLY B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 491 Processing helix chain 'B' and resid 493 through 506 removed outlier: 3.579A pdb=" N LEU B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 519 removed outlier: 3.726A pdb=" N ASP B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL B 517 " --> pdb=" O HIS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 541 removed outlier: 4.773A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 removed outlier: 4.165A pdb=" N CYS B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 562 removed outlier: 3.698A pdb=" N SER B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 580 Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.508A pdb=" N ILE B 589 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 604 Processing helix chain 'B' and resid 607 through 619 removed outlier: 3.998A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 612 " --> pdb=" O HIS B 608 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 619 " --> pdb=" O CYS B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.922A pdb=" N LEU B 637 " --> pdb=" O CYS B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 875 through 877 No H-bonds generated for 'chain 'B' and resid 875 through 877' Processing helix chain 'B' and resid 878 through 901 removed outlier: 4.021A pdb=" N LYS B 897 " --> pdb=" O TRP B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 4.061A pdb=" N ASN B 930 " --> pdb=" O GLU B 926 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR B 931 " --> pdb=" O GLN B 927 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASN B 932 " --> pdb=" O GLU B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1012 Processing helix chain 'B' and resid 1029 through 1033 removed outlier: 4.121A pdb=" N VAL B1033 " --> pdb=" O PRO B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1060 removed outlier: 3.914A pdb=" N ASN B1046 " --> pdb=" O THR B1042 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B1050 " --> pdb=" O ASN B1046 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B1052 " --> pdb=" O ASP B1048 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA B1053 " --> pdb=" O SER B1049 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B1054 " --> pdb=" O LEU B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1095 Processing helix chain 'B' and resid 1643 through 1647 removed outlier: 3.556A pdb=" N GLU B1647 " --> pdb=" O GLU B1644 " (cutoff:3.500A) Processing helix chain 'B' and resid 1648 through 1665 Processing helix chain 'B' and resid 1671 through 1682 removed outlier: 3.717A pdb=" N ALA B1676 " --> pdb=" O ARG B1672 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER B1679 " --> pdb=" O HIS B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1683 through 1692 removed outlier: 4.341A pdb=" N LEU B1687 " --> pdb=" O GLU B1683 " (cutoff:3.500A) Processing helix chain 'B' and resid 1697 through 1711 removed outlier: 3.720A pdb=" N HIS B1711 " --> pdb=" O LEU B1707 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1722 removed outlier: 4.493A pdb=" N TYR B1715 " --> pdb=" O HIS B1711 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET B1722 " --> pdb=" O ALA B1718 " (cutoff:3.500A) Processing helix chain 'B' and resid 1784 through 1806 removed outlier: 3.790A pdb=" N LEU B1788 " --> pdb=" O PRO B1784 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B1805 " --> pdb=" O LYS B1801 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B1806 " --> pdb=" O GLU B1802 " (cutoff:3.500A) Processing helix chain 'B' and resid 1814 through 1832 removed outlier: 3.599A pdb=" N LEU B1818 " --> pdb=" O THR B1814 " (cutoff:3.500A) Proline residue: B1821 - end of helix Processing helix chain 'B' and resid 1836 through 1846 Processing helix chain 'B' and resid 1898 through 1949 removed outlier: 3.620A pdb=" N GLN B1904 " --> pdb=" O PRO B1900 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B1907 " --> pdb=" O LEU B1903 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B1916 " --> pdb=" O LEU B1912 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B1930 " --> pdb=" O ALA B1926 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP B1937 " --> pdb=" O ALA B1933 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN B1938 " --> pdb=" O LYS B1934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1955 through 1965 removed outlier: 4.712A pdb=" N ARG B1962 " --> pdb=" O ALA B1958 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU B1963 " --> pdb=" O ARG B1959 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE B1964 " --> pdb=" O LYS B1960 " (cutoff:3.500A) Processing helix chain 'B' and resid 1967 through 1976 Processing helix chain 'B' and resid 1989 through 2006 removed outlier: 3.891A pdb=" N ASP B1993 " --> pdb=" O GLU B1989 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2072 removed outlier: 3.509A pdb=" N VAL B2066 " --> pdb=" O SER B2062 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B2069 " --> pdb=" O MET B2065 " (cutoff:3.500A) Processing helix chain 'B' and resid 2076 through 2093 removed outlier: 3.867A pdb=" N VAL B2080 " --> pdb=" O ASP B2076 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2101 removed outlier: 4.163A pdb=" N LEU B2097 " --> pdb=" O GLY B2093 " (cutoff:3.500A) Processing helix chain 'B' and resid 2112 through 2130 Processing helix chain 'B' and resid 2134 through 2151 Processing helix chain 'B' and resid 2152 through 2157 Processing helix chain 'B' and resid 2157 through 2165 removed outlier: 3.896A pdb=" N MET B2161 " --> pdb=" O HIS B2157 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B2162 " --> pdb=" O PRO B2158 " (cutoff:3.500A) Processing helix chain 'B' and resid 2165 through 2179 removed outlier: 3.839A pdb=" N ASN B2176 " --> pdb=" O GLU B2172 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B2177 " --> pdb=" O VAL B2173 " (cutoff:3.500A) Processing helix chain 'B' and resid 2188 through 2205 removed outlier: 3.873A pdb=" N CYS B2195 " --> pdb=" O MET B2191 " (cutoff:3.500A) Processing helix chain 'B' and resid 2207 through 2221 removed outlier: 3.991A pdb=" N LYS B2211 " --> pdb=" O ARG B2207 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B2215 " --> pdb=" O LYS B2211 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS B2216 " --> pdb=" O ALA B2212 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B2218 " --> pdb=" O PHE B2214 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR B2219 " --> pdb=" O ASP B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2237 through 2247 Processing helix chain 'B' and resid 2249 through 2256 Processing helix chain 'B' and resid 2260 through 2274 Processing helix chain 'B' and resid 2276 through 2283 Processing helix chain 'B' and resid 2292 through 2305 Processing helix chain 'B' and resid 2312 through 2326 Processing helix chain 'B' and resid 2327 through 2330 Processing helix chain 'B' and resid 2341 through 2355 Processing helix chain 'B' and resid 2356 through 2359 removed outlier: 3.644A pdb=" N ASP B2359 " --> pdb=" O PRO B2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2356 through 2359' Processing helix chain 'B' and resid 2382 through 2402 Processing helix chain 'B' and resid 2413 through 2426 Processing helix chain 'B' and resid 2427 through 2436 Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.827A pdb=" N ALA B2465 " --> pdb=" O PRO B2461 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B2466 " --> pdb=" O ASP B2462 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET B2467 " --> pdb=" O HIS B2463 " (cutoff:3.500A) Processing helix chain 'B' and resid 2479 through 2491 Processing helix chain 'B' and resid 2491 through 2500 Processing helix chain 'B' and resid 2507 through 2524 removed outlier: 4.157A pdb=" N UNK B2511 " --> pdb=" O SER B2507 " (cutoff:3.500A) Processing helix chain 'B' and resid 2533 through 2547 Processing helix chain 'B' and resid 2553 through 2571 Processing helix chain 'B' and resid 2575 through 2589 Processing helix chain 'B' and resid 2594 through 2612 Processing helix chain 'B' and resid 2617 through 2635 removed outlier: 3.651A pdb=" N UNK B2621 " --> pdb=" O UNK B2617 " (cutoff:3.500A) Processing helix chain 'B' and resid 2641 through 2649 removed outlier: 4.072A pdb=" N UNK B2645 " --> pdb=" O UNK B2641 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNK B2646 " --> pdb=" O UNK B2642 " (cutoff:3.500A) Processing helix chain 'B' and resid 2650 through 2657 Processing helix chain 'B' and resid 2713 through 2739 removed outlier: 4.037A pdb=" N ASN B2721 " --> pdb=" O GLU B2717 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B2722 " --> pdb=" O TYR B2718 " (cutoff:3.500A) Processing helix chain 'B' and resid 2763 through 2770 removed outlier: 3.833A pdb=" N GLU B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR B2770 " --> pdb=" O GLU B2766 " (cutoff:3.500A) Processing helix chain 'B' and resid 2772 through 2784 removed outlier: 4.236A pdb=" N GLU B2776 " --> pdb=" O TRP B2772 " (cutoff:3.500A) Processing helix chain 'B' and resid 2836 through 2863 removed outlier: 3.684A pdb=" N TRP B2851 " --> pdb=" O TYR B2847 " (cutoff:3.500A) Processing helix chain 'B' and resid 2877 through 2898 removed outlier: 3.854A pdb=" N ASP B2884 " --> pdb=" O GLU B2880 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B2887 " --> pdb=" O LYS B2883 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE B2894 " --> pdb=" O ASP B2890 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B2895 " --> pdb=" O ILE B2891 " (cutoff:3.500A) Processing helix chain 'B' and resid 2917 through 2942 Processing helix chain 'B' and resid 2962 through 2982 removed outlier: 4.252A pdb=" N UNK B2975 " --> pdb=" O UNK B2971 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N UNK B2976 " --> pdb=" O UNK B2972 " (cutoff:3.500A) Processing helix chain 'B' and resid 2992 through 3007 Processing helix chain 'B' and resid 3015 through 3029 Processing helix chain 'B' and resid 3105 through 3129 removed outlier: 3.587A pdb=" N UNK B3116 " --> pdb=" O UNK B3112 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N UNK B3120 " --> pdb=" O UNK B3116 " (cutoff:3.500A) Processing helix chain 'B' and resid 3137 through 3157 removed outlier: 4.159A pdb=" N UNK B3156 " --> pdb=" O UNK B3152 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N UNK B3157 " --> pdb=" O UNK B3153 " (cutoff:3.500A) Processing helix chain 'B' and resid 3163 through 3182 Processing helix chain 'B' and resid 3183 through 3200 removed outlier: 3.652A pdb=" N UNK B3187 " --> pdb=" O UNK B3183 " (cutoff:3.500A) Processing helix chain 'B' and resid 3208 through 3220 removed outlier: 3.701A pdb=" N UNK B3219 " --> pdb=" O UNK B3215 " (cutoff:3.500A) Processing helix chain 'B' and resid 3232 through 3251 Processing helix chain 'B' and resid 3255 through 3270 Processing helix chain 'B' and resid 3271 through 3277 Processing helix chain 'B' and resid 3281 through 3296 removed outlier: 4.013A pdb=" N UNK B3285 " --> pdb=" O UNK B3281 " (cutoff:3.500A) Processing helix chain 'B' and resid 3301 through 3315 Processing helix chain 'B' and resid 3323 through 3356 Processing helix chain 'B' and resid 3362 through 3392 removed outlier: 4.233A pdb=" N UNK B3383 " --> pdb=" O UNK B3379 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N UNK B3389 " --> pdb=" O UNK B3385 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N UNK B3390 " --> pdb=" O UNK B3386 " (cutoff:3.500A) Processing helix chain 'B' and resid 3400 through 3420 removed outlier: 3.995A pdb=" N UNK B3404 " --> pdb=" O UNK B3400 " (cutoff:3.500A) Processing helix chain 'B' and resid 3421 through 3434 removed outlier: 4.637A pdb=" N UNK B3428 " --> pdb=" O UNK B3424 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N UNK B3429 " --> pdb=" O UNK B3425 " (cutoff:3.500A) Processing helix chain 'B' and resid 3478 through 3495 removed outlier: 4.166A pdb=" N UNK B3495 " --> pdb=" O UNK B3491 " (cutoff:3.500A) Processing helix chain 'B' and resid 3503 through 3514 Processing helix chain 'B' and resid 3516 through 3527 removed outlier: 3.921A pdb=" N UNK B3527 " --> pdb=" O UNK B3523 " (cutoff:3.500A) Processing helix chain 'B' and resid 3541 through 3548 removed outlier: 4.394A pdb=" N UNK B3545 " --> pdb=" O UNK B3541 " (cutoff:3.500A) Processing helix chain 'B' and resid 3555 through 3579 Processing helix chain 'B' and resid 3612 through 3627 removed outlier: 4.142A pdb=" N VAL B3616 " --> pdb=" O ARG B3612 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN B3617 " --> pdb=" O HIS B3613 " (cutoff:3.500A) Processing helix chain 'B' and resid 3637 through 3643 Processing helix chain 'B' and resid 3661 through 3676 Processing helix chain 'B' and resid 3684 through 3697 removed outlier: 4.169A pdb=" N ASP B3692 " --> pdb=" O MET B3688 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B3693 " --> pdb=" O ALA B3689 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3732 removed outlier: 4.179A pdb=" N GLU B3719 " --> pdb=" O GLU B3715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B3720 " --> pdb=" O LYS B3716 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B3724 " --> pdb=" O LYS B3720 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU B3730 " --> pdb=" O GLN B3726 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP B3732 " --> pdb=" O ALA B3728 " (cutoff:3.500A) Processing helix chain 'B' and resid 3734 through 3745 removed outlier: 3.751A pdb=" N LEU B3740 " --> pdb=" O ALA B3736 " (cutoff:3.500A) Processing helix chain 'B' and resid 3753 through 3765 removed outlier: 4.152A pdb=" N LYS B3759 " --> pdb=" O ALA B3755 " (cutoff:3.500A) Processing helix chain 'B' and resid 3769 through 3783 Processing helix chain 'B' and resid 3788 through 3797 Processing helix chain 'B' and resid 3803 through 3817 removed outlier: 3.523A pdb=" N PHE B3807 " --> pdb=" O ASP B3803 " (cutoff:3.500A) Processing helix chain 'B' and resid 3824 through 3828 Processing helix chain 'B' and resid 3831 through 3845 Processing helix chain 'B' and resid 3850 through 3857 Processing helix chain 'B' and resid 3868 through 3891 removed outlier: 3.578A pdb=" N SER B3872 " --> pdb=" O ASN B3868 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B3891 " --> pdb=" O PHE B3887 " (cutoff:3.500A) Processing helix chain 'B' and resid 3898 through 3923 removed outlier: 3.842A pdb=" N PHE B3905 " --> pdb=" O GLY B3901 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B3908 " --> pdb=" O ASN B3904 " (cutoff:3.500A) Processing helix chain 'B' and resid 3927 through 3936 Processing helix chain 'B' and resid 3938 through 3959 removed outlier: 3.743A pdb=" N ALA B3942 " --> pdb=" O ARG B3938 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS B3952 " --> pdb=" O HIS B3948 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET B3955 " --> pdb=" O ALA B3951 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B3958 " --> pdb=" O GLN B3954 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B3959 " --> pdb=" O MET B3955 " (cutoff:3.500A) Processing helix chain 'B' and resid 3963 through 3983 Processing helix chain 'B' and resid 3984 through 3986 No H-bonds generated for 'chain 'B' and resid 3984 through 3986' Processing helix chain 'B' and resid 3992 through 4004 removed outlier: 3.611A pdb=" N LYS B3996 " --> pdb=" O GLY B3992 " (cutoff:3.500A) Processing helix chain 'B' and resid 4005 through 4021 Processing helix chain 'B' and resid 4022 through 4027 removed outlier: 4.055A pdb=" N SER B4027 " --> pdb=" O LYS B4023 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4035 removed outlier: 4.396A pdb=" N ASP B4035 " --> pdb=" O PHE B4031 " (cutoff:3.500A) Processing helix chain 'B' and resid 4045 through 4053 removed outlier: 3.526A pdb=" N LYS B4049 " --> pdb=" O ARG B4045 " (cutoff:3.500A) Processing helix chain 'B' and resid 4058 through 4068 Processing helix chain 'B' and resid 4078 through 4087 Processing helix chain 'B' and resid 4087 through 4107 removed outlier: 3.580A pdb=" N ASP B4092 " --> pdb=" O GLU B4088 " (cutoff:3.500A) Processing helix chain 'B' and resid 4111 through 4126 removed outlier: 4.072A pdb=" N PHE B4117 " --> pdb=" O ARG B4113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B4120 " --> pdb=" O THR B4116 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER B4123 " --> pdb=" O GLU B4119 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL B4124 " --> pdb=" O LEU B4120 " (cutoff:3.500A) Processing helix chain 'B' and resid 4128 through 4130 No H-bonds generated for 'chain 'B' and resid 4128 through 4130' Processing helix chain 'B' and resid 4152 through 4158 Processing helix chain 'B' and resid 4161 through 4179 removed outlier: 3.763A pdb=" N GLU B4178 " --> pdb=" O ASP B4174 " (cutoff:3.500A) Processing helix chain 'B' and resid 4183 through 4204 removed outlier: 3.538A pdb=" N ASN B4190 " --> pdb=" O GLU B4186 " (cutoff:3.500A) Processing helix chain 'B' and resid 4276 through 4284 removed outlier: 3.946A pdb=" N LEU B4280 " --> pdb=" O LYS B4276 " (cutoff:3.500A) Processing helix chain 'B' and resid 4286 through 4302 removed outlier: 3.838A pdb=" N THR B4292 " --> pdb=" O SER B4288 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B4300 " --> pdb=" O PHE B4296 " (cutoff:3.500A) Processing helix chain 'B' and resid 4304 through 4309 removed outlier: 3.544A pdb=" N SER B4309 " --> pdb=" O PHE B4305 " (cutoff:3.500A) Processing helix chain 'B' and resid 4479 through 4496 removed outlier: 3.702A pdb=" N TYR B4485 " --> pdb=" O LYS B4481 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B4488 " --> pdb=" O ALA B4484 " (cutoff:3.500A) Processing helix chain 'B' and resid 4496 through 4515 Processing helix chain 'B' and resid 4567 through 4593 removed outlier: 3.574A pdb=" N LEU B4571 " --> pdb=" O MET B4567 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B4572 " --> pdb=" O GLU B4568 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR B4590 " --> pdb=" O ILE B4586 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS B4591 " --> pdb=" O ILE B4587 " (cutoff:3.500A) Processing helix chain 'B' and resid 4593 through 4613 Processing helix chain 'B' and resid 4613 through 4618 Processing helix chain 'B' and resid 4625 through 4630 Processing helix chain 'B' and resid 4648 through 4656 Processing helix chain 'B' and resid 4661 through 4667 removed outlier: 3.856A pdb=" N SER B4666 " --> pdb=" O ARG B4662 " (cutoff:3.500A) Processing helix chain 'B' and resid 4671 through 4682 Processing helix chain 'B' and resid 4701 through 4713 Processing helix chain 'B' and resid 4715 through 4734 removed outlier: 3.683A pdb=" N LEU B4721 " --> pdb=" O SER B4717 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS B4732 " --> pdb=" O SER B4728 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR B4733 " --> pdb=" O VAL B4729 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4742 removed outlier: 3.616A pdb=" N HIS B4741 " --> pdb=" O PHE B4738 " (cutoff:3.500A) Processing helix chain 'B' and resid 4743 through 4748 Processing helix chain 'B' and resid 4752 through 4761 removed outlier: 4.340A pdb=" N SER B4758 " --> pdb=" O THR B4754 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B4759 " --> pdb=" O ILE B4755 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4807 through 4819 Processing helix chain 'B' and resid 4840 through 4854 Processing helix chain 'B' and resid 4857 through 4886 removed outlier: 3.886A pdb=" N ILE B4861 " --> pdb=" O LEU B4857 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B4865 " --> pdb=" O ILE B4861 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B4868 " --> pdb=" O LEU B4864 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B4869 " --> pdb=" O ILE B4865 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B4870 " --> pdb=" O ILE B4866 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B4886 " --> pdb=" O ASP B4882 " (cutoff:3.500A) Processing helix chain 'B' and resid 4893 through 4898 removed outlier: 3.925A pdb=" N PHE B4897 " --> pdb=" O GLY B4893 " (cutoff:3.500A) Processing helix chain 'B' and resid 4902 through 4910 removed outlier: 3.826A pdb=" N THR B4906 " --> pdb=" O HIS B4902 " (cutoff:3.500A) Processing helix chain 'B' and resid 4913 through 4928 removed outlier: 4.555A pdb=" N ASP B4928 " --> pdb=" O LEU B4924 " (cutoff:3.500A) Processing helix chain 'B' and resid 4933 through 4946 Processing helix chain 'B' and resid 4956 through 4961 removed outlier: 3.658A pdb=" N TYR B4961 " --> pdb=" O PHE B4957 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 65 removed outlier: 4.049A pdb=" N GLY H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 264 through 273 removed outlier: 4.154A pdb=" N VAL C 267 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA C 271 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG C 272 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 273 " --> pdb=" O HIS C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.913A pdb=" N LYS C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 379 through 383 removed outlier: 3.751A pdb=" N ARG C 383 " --> pdb=" O LYS C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 438 removed outlier: 3.754A pdb=" N LEU C 436 " --> pdb=" O GLY C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 463 removed outlier: 3.579A pdb=" N GLY C 461 " --> pdb=" O GLN C 457 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 491 Processing helix chain 'C' and resid 493 through 506 removed outlier: 3.580A pdb=" N LEU C 497 " --> pdb=" O GLY C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 519 removed outlier: 3.726A pdb=" N ASP C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL C 517 " --> pdb=" O HIS C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 541 removed outlier: 4.773A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 removed outlier: 4.165A pdb=" N CYS C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 549 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 562 removed outlier: 3.698A pdb=" N SER C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 580 Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.508A pdb=" N ILE C 589 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 604 Processing helix chain 'C' and resid 607 through 619 removed outlier: 3.998A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 612 " --> pdb=" O HIS C 608 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.922A pdb=" N LEU C 637 " --> pdb=" O CYS C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 826 Processing helix chain 'C' and resid 875 through 877 No H-bonds generated for 'chain 'C' and resid 875 through 877' Processing helix chain 'C' and resid 878 through 901 removed outlier: 4.020A pdb=" N LYS C 897 " --> pdb=" O TRP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 4.061A pdb=" N ASN C 930 " --> pdb=" O GLU C 926 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR C 931 " --> pdb=" O GLN C 927 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASN C 932 " --> pdb=" O GLU C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1012 Processing helix chain 'C' and resid 1029 through 1033 removed outlier: 4.121A pdb=" N VAL C1033 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1060 removed outlier: 3.914A pdb=" N ASN C1046 " --> pdb=" O THR C1042 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C1050 " --> pdb=" O ASN C1046 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU C1052 " --> pdb=" O ASP C1048 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA C1053 " --> pdb=" O SER C1049 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C1054 " --> pdb=" O LEU C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1095 Processing helix chain 'C' and resid 1643 through 1647 removed outlier: 3.556A pdb=" N GLU C1647 " --> pdb=" O GLU C1644 " (cutoff:3.500A) Processing helix chain 'C' and resid 1648 through 1665 Processing helix chain 'C' and resid 1671 through 1682 removed outlier: 3.718A pdb=" N ALA C1676 " --> pdb=" O ARG C1672 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C1679 " --> pdb=" O HIS C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1683 through 1692 removed outlier: 4.340A pdb=" N LEU C1687 " --> pdb=" O GLU C1683 " (cutoff:3.500A) Processing helix chain 'C' and resid 1697 through 1711 removed outlier: 3.720A pdb=" N HIS C1711 " --> pdb=" O LEU C1707 " (cutoff:3.500A) Processing helix chain 'C' and resid 1711 through 1722 removed outlier: 4.493A pdb=" N TYR C1715 " --> pdb=" O HIS C1711 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET C1722 " --> pdb=" O ALA C1718 " (cutoff:3.500A) Processing helix chain 'C' and resid 1784 through 1806 removed outlier: 3.790A pdb=" N LEU C1788 " --> pdb=" O PRO C1784 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C1805 " --> pdb=" O LYS C1801 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS C1806 " --> pdb=" O GLU C1802 " (cutoff:3.500A) Processing helix chain 'C' and resid 1814 through 1832 removed outlier: 3.600A pdb=" N LEU C1818 " --> pdb=" O THR C1814 " (cutoff:3.500A) Proline residue: C1821 - end of helix Processing helix chain 'C' and resid 1836 through 1846 Processing helix chain 'C' and resid 1898 through 1949 removed outlier: 3.619A pdb=" N GLN C1904 " --> pdb=" O PRO C1900 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C1907 " --> pdb=" O LEU C1903 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN C1916 " --> pdb=" O LEU C1912 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP C1930 " --> pdb=" O ALA C1926 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C1937 " --> pdb=" O ALA C1933 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN C1938 " --> pdb=" O LYS C1934 " (cutoff:3.500A) Processing helix chain 'C' and resid 1955 through 1965 removed outlier: 4.711A pdb=" N ARG C1962 " --> pdb=" O ALA C1958 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU C1963 " --> pdb=" O ARG C1959 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE C1964 " --> pdb=" O LYS C1960 " (cutoff:3.500A) Processing helix chain 'C' and resid 1967 through 1976 Processing helix chain 'C' and resid 1989 through 2006 removed outlier: 3.890A pdb=" N ASP C1993 " --> pdb=" O GLU C1989 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN C1994 " --> pdb=" O GLU C1990 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2072 removed outlier: 3.509A pdb=" N VAL C2066 " --> pdb=" O SER C2062 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C2069 " --> pdb=" O MET C2065 " (cutoff:3.500A) Processing helix chain 'C' and resid 2076 through 2093 removed outlier: 3.867A pdb=" N VAL C2080 " --> pdb=" O ASP C2076 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2101 removed outlier: 4.164A pdb=" N LEU C2097 " --> pdb=" O GLY C2093 " (cutoff:3.500A) Processing helix chain 'C' and resid 2112 through 2130 Processing helix chain 'C' and resid 2134 through 2151 Processing helix chain 'C' and resid 2152 through 2157 Processing helix chain 'C' and resid 2157 through 2165 removed outlier: 3.895A pdb=" N MET C2161 " --> pdb=" O HIS C2157 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C2162 " --> pdb=" O PRO C2158 " (cutoff:3.500A) Processing helix chain 'C' and resid 2165 through 2179 removed outlier: 3.839A pdb=" N ASN C2176 " --> pdb=" O GLU C2172 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C2177 " --> pdb=" O VAL C2173 " (cutoff:3.500A) Processing helix chain 'C' and resid 2188 through 2205 removed outlier: 3.873A pdb=" N CYS C2195 " --> pdb=" O MET C2191 " (cutoff:3.500A) Processing helix chain 'C' and resid 2207 through 2221 removed outlier: 3.990A pdb=" N LYS C2211 " --> pdb=" O ARG C2207 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C2215 " --> pdb=" O LYS C2211 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS C2216 " --> pdb=" O ALA C2212 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER C2218 " --> pdb=" O PHE C2214 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR C2219 " --> pdb=" O ASP C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2237 through 2247 Processing helix chain 'C' and resid 2249 through 2256 Processing helix chain 'C' and resid 2260 through 2274 Processing helix chain 'C' and resid 2276 through 2283 Processing helix chain 'C' and resid 2292 through 2305 Processing helix chain 'C' and resid 2312 through 2326 Processing helix chain 'C' and resid 2327 through 2330 Processing helix chain 'C' and resid 2341 through 2355 Processing helix chain 'C' and resid 2356 through 2359 removed outlier: 3.645A pdb=" N ASP C2359 " --> pdb=" O PRO C2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2356 through 2359' Processing helix chain 'C' and resid 2382 through 2402 Processing helix chain 'C' and resid 2413 through 2426 Processing helix chain 'C' and resid 2427 through 2436 Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.827A pdb=" N ALA C2465 " --> pdb=" O PRO C2461 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C2466 " --> pdb=" O ASP C2462 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET C2467 " --> pdb=" O HIS C2463 " (cutoff:3.500A) Processing helix chain 'C' and resid 2479 through 2491 Processing helix chain 'C' and resid 2491 through 2500 Processing helix chain 'C' and resid 2507 through 2524 removed outlier: 4.156A pdb=" N UNK C2511 " --> pdb=" O SER C2507 " (cutoff:3.500A) Processing helix chain 'C' and resid 2533 through 2547 Processing helix chain 'C' and resid 2553 through 2571 Processing helix chain 'C' and resid 2575 through 2589 Processing helix chain 'C' and resid 2594 through 2612 Processing helix chain 'C' and resid 2617 through 2635 removed outlier: 3.651A pdb=" N UNK C2621 " --> pdb=" O UNK C2617 " (cutoff:3.500A) Processing helix chain 'C' and resid 2641 through 2649 removed outlier: 4.072A pdb=" N UNK C2645 " --> pdb=" O UNK C2641 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N UNK C2646 " --> pdb=" O UNK C2642 " (cutoff:3.500A) Processing helix chain 'C' and resid 2650 through 2657 Processing helix chain 'C' and resid 2713 through 2739 removed outlier: 4.037A pdb=" N ASN C2721 " --> pdb=" O GLU C2717 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS C2722 " --> pdb=" O TYR C2718 " (cutoff:3.500A) Processing helix chain 'C' and resid 2763 through 2770 removed outlier: 3.835A pdb=" N GLU C2768 " --> pdb=" O GLU C2764 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR C2770 " --> pdb=" O GLU C2766 " (cutoff:3.500A) Processing helix chain 'C' and resid 2772 through 2784 removed outlier: 4.236A pdb=" N GLU C2776 " --> pdb=" O TRP C2772 " (cutoff:3.500A) Processing helix chain 'C' and resid 2836 through 2863 removed outlier: 3.684A pdb=" N TRP C2851 " --> pdb=" O TYR C2847 " (cutoff:3.500A) Processing helix chain 'C' and resid 2877 through 2898 removed outlier: 3.855A pdb=" N ASP C2884 " --> pdb=" O GLU C2880 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS C2887 " --> pdb=" O LYS C2883 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE C2894 " --> pdb=" O ASP C2890 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C2895 " --> pdb=" O ILE C2891 " (cutoff:3.500A) Processing helix chain 'C' and resid 2917 through 2942 Processing helix chain 'C' and resid 2962 through 2982 removed outlier: 4.252A pdb=" N UNK C2975 " --> pdb=" O UNK C2971 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N UNK C2976 " --> pdb=" O UNK C2972 " (cutoff:3.500A) Processing helix chain 'C' and resid 2992 through 3007 Processing helix chain 'C' and resid 3015 through 3029 Processing helix chain 'C' and resid 3105 through 3129 removed outlier: 3.588A pdb=" N UNK C3116 " --> pdb=" O UNK C3112 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N UNK C3120 " --> pdb=" O UNK C3116 " (cutoff:3.500A) Processing helix chain 'C' and resid 3137 through 3157 removed outlier: 4.158A pdb=" N UNK C3156 " --> pdb=" O UNK C3152 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N UNK C3157 " --> pdb=" O UNK C3153 " (cutoff:3.500A) Processing helix chain 'C' and resid 3163 through 3182 Processing helix chain 'C' and resid 3183 through 3200 removed outlier: 3.652A pdb=" N UNK C3187 " --> pdb=" O UNK C3183 " (cutoff:3.500A) Processing helix chain 'C' and resid 3208 through 3220 removed outlier: 3.701A pdb=" N UNK C3219 " --> pdb=" O UNK C3215 " (cutoff:3.500A) Processing helix chain 'C' and resid 3232 through 3251 Processing helix chain 'C' and resid 3255 through 3270 Processing helix chain 'C' and resid 3271 through 3277 Processing helix chain 'C' and resid 3281 through 3296 removed outlier: 4.013A pdb=" N UNK C3285 " --> pdb=" O UNK C3281 " (cutoff:3.500A) Processing helix chain 'C' and resid 3301 through 3315 Processing helix chain 'C' and resid 3323 through 3356 Processing helix chain 'C' and resid 3362 through 3392 removed outlier: 4.232A pdb=" N UNK C3383 " --> pdb=" O UNK C3379 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N UNK C3389 " --> pdb=" O UNK C3385 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N UNK C3390 " --> pdb=" O UNK C3386 " (cutoff:3.500A) Processing helix chain 'C' and resid 3400 through 3420 removed outlier: 3.995A pdb=" N UNK C3404 " --> pdb=" O UNK C3400 " (cutoff:3.500A) Processing helix chain 'C' and resid 3421 through 3434 removed outlier: 4.637A pdb=" N UNK C3428 " --> pdb=" O UNK C3424 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N UNK C3429 " --> pdb=" O UNK C3425 " (cutoff:3.500A) Processing helix chain 'C' and resid 3478 through 3495 removed outlier: 4.165A pdb=" N UNK C3495 " --> pdb=" O UNK C3491 " (cutoff:3.500A) Processing helix chain 'C' and resid 3503 through 3514 Processing helix chain 'C' and resid 3516 through 3527 removed outlier: 3.921A pdb=" N UNK C3527 " --> pdb=" O UNK C3523 " (cutoff:3.500A) Processing helix chain 'C' and resid 3541 through 3548 removed outlier: 4.395A pdb=" N UNK C3545 " --> pdb=" O UNK C3541 " (cutoff:3.500A) Processing helix chain 'C' and resid 3555 through 3579 Processing helix chain 'C' and resid 3612 through 3627 removed outlier: 4.142A pdb=" N VAL C3616 " --> pdb=" O ARG C3612 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C3617 " --> pdb=" O HIS C3613 " (cutoff:3.500A) Processing helix chain 'C' and resid 3637 through 3643 Processing helix chain 'C' and resid 3661 through 3676 Processing helix chain 'C' and resid 3684 through 3697 removed outlier: 4.168A pdb=" N ASP C3692 " --> pdb=" O MET C3688 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C3693 " --> pdb=" O ALA C3689 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3732 removed outlier: 4.179A pdb=" N GLU C3719 " --> pdb=" O GLU C3715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS C3720 " --> pdb=" O LYS C3716 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C3724 " --> pdb=" O LYS C3720 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C3730 " --> pdb=" O GLN C3726 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP C3732 " --> pdb=" O ALA C3728 " (cutoff:3.500A) Processing helix chain 'C' and resid 3734 through 3745 removed outlier: 3.751A pdb=" N LEU C3740 " --> pdb=" O ALA C3736 " (cutoff:3.500A) Processing helix chain 'C' and resid 3753 through 3765 removed outlier: 4.153A pdb=" N LYS C3759 " --> pdb=" O ALA C3755 " (cutoff:3.500A) Processing helix chain 'C' and resid 3769 through 3783 Processing helix chain 'C' and resid 3788 through 3797 Processing helix chain 'C' and resid 3803 through 3817 removed outlier: 3.523A pdb=" N PHE C3807 " --> pdb=" O ASP C3803 " (cutoff:3.500A) Processing helix chain 'C' and resid 3824 through 3828 Processing helix chain 'C' and resid 3831 through 3845 Processing helix chain 'C' and resid 3850 through 3857 Processing helix chain 'C' and resid 3868 through 3891 removed outlier: 3.578A pdb=" N SER C3872 " --> pdb=" O ASN C3868 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C3891 " --> pdb=" O PHE C3887 " (cutoff:3.500A) Processing helix chain 'C' and resid 3898 through 3923 removed outlier: 3.842A pdb=" N PHE C3905 " --> pdb=" O GLY C3901 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C3908 " --> pdb=" O ASN C3904 " (cutoff:3.500A) Processing helix chain 'C' and resid 3927 through 3936 Processing helix chain 'C' and resid 3938 through 3959 removed outlier: 3.743A pdb=" N ALA C3942 " --> pdb=" O ARG C3938 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS C3952 " --> pdb=" O HIS C3948 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET C3955 " --> pdb=" O ALA C3951 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C3958 " --> pdb=" O GLN C3954 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN C3959 " --> pdb=" O MET C3955 " (cutoff:3.500A) Processing helix chain 'C' and resid 3963 through 3983 Processing helix chain 'C' and resid 3984 through 3986 No H-bonds generated for 'chain 'C' and resid 3984 through 3986' Processing helix chain 'C' and resid 3992 through 4004 removed outlier: 3.611A pdb=" N LYS C3996 " --> pdb=" O GLY C3992 " (cutoff:3.500A) Processing helix chain 'C' and resid 4005 through 4021 Processing helix chain 'C' and resid 4022 through 4027 removed outlier: 4.055A pdb=" N SER C4027 " --> pdb=" O LYS C4023 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4035 removed outlier: 4.396A pdb=" N ASP C4035 " --> pdb=" O PHE C4031 " (cutoff:3.500A) Processing helix chain 'C' and resid 4045 through 4053 removed outlier: 3.527A pdb=" N LYS C4049 " --> pdb=" O ARG C4045 " (cutoff:3.500A) Processing helix chain 'C' and resid 4058 through 4068 Processing helix chain 'C' and resid 4078 through 4087 Processing helix chain 'C' and resid 4087 through 4107 removed outlier: 3.580A pdb=" N ASP C4092 " --> pdb=" O GLU C4088 " (cutoff:3.500A) Processing helix chain 'C' and resid 4111 through 4126 removed outlier: 4.072A pdb=" N PHE C4117 " --> pdb=" O ARG C4113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C4120 " --> pdb=" O THR C4116 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER C4123 " --> pdb=" O GLU C4119 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL C4124 " --> pdb=" O LEU C4120 " (cutoff:3.500A) Processing helix chain 'C' and resid 4128 through 4130 No H-bonds generated for 'chain 'C' and resid 4128 through 4130' Processing helix chain 'C' and resid 4152 through 4158 Processing helix chain 'C' and resid 4161 through 4179 removed outlier: 3.763A pdb=" N GLU C4178 " --> pdb=" O ASP C4174 " (cutoff:3.500A) Processing helix chain 'C' and resid 4183 through 4204 removed outlier: 3.538A pdb=" N ASN C4190 " --> pdb=" O GLU C4186 " (cutoff:3.500A) Processing helix chain 'C' and resid 4276 through 4284 removed outlier: 3.946A pdb=" N LEU C4280 " --> pdb=" O LYS C4276 " (cutoff:3.500A) Processing helix chain 'C' and resid 4286 through 4302 removed outlier: 3.838A pdb=" N THR C4292 " --> pdb=" O SER C4288 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C4300 " --> pdb=" O PHE C4296 " (cutoff:3.500A) Processing helix chain 'C' and resid 4304 through 4309 removed outlier: 3.545A pdb=" N SER C4309 " --> pdb=" O PHE C4305 " (cutoff:3.500A) Processing helix chain 'C' and resid 4479 through 4496 removed outlier: 3.702A pdb=" N TYR C4485 " --> pdb=" O LYS C4481 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C4488 " --> pdb=" O ALA C4484 " (cutoff:3.500A) Processing helix chain 'C' and resid 4496 through 4515 Processing helix chain 'C' and resid 4567 through 4593 removed outlier: 3.574A pdb=" N LEU C4571 " --> pdb=" O MET C4567 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C4572 " --> pdb=" O GLU C4568 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR C4590 " --> pdb=" O ILE C4586 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS C4591 " --> pdb=" O ILE C4587 " (cutoff:3.500A) Processing helix chain 'C' and resid 4593 through 4613 Processing helix chain 'C' and resid 4613 through 4618 Processing helix chain 'C' and resid 4625 through 4630 Processing helix chain 'C' and resid 4648 through 4656 Processing helix chain 'C' and resid 4661 through 4667 removed outlier: 3.857A pdb=" N SER C4666 " --> pdb=" O ARG C4662 " (cutoff:3.500A) Processing helix chain 'C' and resid 4671 through 4682 Processing helix chain 'C' and resid 4701 through 4713 Processing helix chain 'C' and resid 4715 through 4734 removed outlier: 3.684A pdb=" N LEU C4721 " --> pdb=" O SER C4717 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS C4732 " --> pdb=" O SER C4728 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR C4733 " --> pdb=" O VAL C4729 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4742 removed outlier: 3.617A pdb=" N HIS C4741 " --> pdb=" O PHE C4738 " (cutoff:3.500A) Processing helix chain 'C' and resid 4743 through 4748 Processing helix chain 'C' and resid 4752 through 4761 removed outlier: 4.340A pdb=" N SER C4758 " --> pdb=" O THR C4754 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL C4759 " --> pdb=" O ILE C4755 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4807 through 4819 Processing helix chain 'C' and resid 4840 through 4854 Processing helix chain 'C' and resid 4857 through 4886 removed outlier: 3.886A pdb=" N ILE C4861 " --> pdb=" O LEU C4857 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C4865 " --> pdb=" O ILE C4861 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C4868 " --> pdb=" O LEU C4864 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C4869 " --> pdb=" O ILE C4865 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C4870 " --> pdb=" O ILE C4866 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C4886 " --> pdb=" O ASP C4882 " (cutoff:3.500A) Processing helix chain 'C' and resid 4893 through 4898 removed outlier: 3.924A pdb=" N PHE C4897 " --> pdb=" O GLY C4893 " (cutoff:3.500A) Processing helix chain 'C' and resid 4902 through 4910 removed outlier: 3.825A pdb=" N THR C4906 " --> pdb=" O HIS C4902 " (cutoff:3.500A) Processing helix chain 'C' and resid 4913 through 4928 removed outlier: 4.555A pdb=" N ASP C4928 " --> pdb=" O LEU C4924 " (cutoff:3.500A) Processing helix chain 'C' and resid 4933 through 4946 removed outlier: 3.500A pdb=" N GLU C4945 " --> pdb=" O LYS C4941 " (cutoff:3.500A) Processing helix chain 'C' and resid 4956 through 4961 removed outlier: 3.658A pdb=" N TYR C4961 " --> pdb=" O PHE C4957 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 65 removed outlier: 4.050A pdb=" N GLY I 63 " --> pdb=" O GLY I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 83 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 264 through 273 removed outlier: 4.153A pdb=" N VAL D 267 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA D 271 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG D 272 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER D 273 " --> pdb=" O HIS D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.913A pdb=" N LYS D 321 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 379 through 383 removed outlier: 3.752A pdb=" N ARG D 383 " --> pdb=" O LYS D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 438 removed outlier: 3.754A pdb=" N LEU D 436 " --> pdb=" O GLY D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 463 removed outlier: 3.579A pdb=" N GLY D 461 " --> pdb=" O GLN D 457 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 463 " --> pdb=" O LEU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 491 Processing helix chain 'D' and resid 493 through 506 removed outlier: 3.579A pdb=" N LEU D 497 " --> pdb=" O GLY D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 519 removed outlier: 3.726A pdb=" N ASP D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL D 517 " --> pdb=" O HIS D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 541 removed outlier: 4.773A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 552 removed outlier: 4.164A pdb=" N CYS D 548 " --> pdb=" O ASN D 544 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 549 " --> pdb=" O ARG D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 562 removed outlier: 3.698A pdb=" N SER D 560 " --> pdb=" O ASP D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 580 Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.508A pdb=" N ILE D 589 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 604 Processing helix chain 'D' and resid 607 through 619 removed outlier: 3.997A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D 612 " --> pdb=" O HIS D 608 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 619 " --> pdb=" O CYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.922A pdb=" N LEU D 637 " --> pdb=" O CYS D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 826 Processing helix chain 'D' and resid 875 through 877 No H-bonds generated for 'chain 'D' and resid 875 through 877' Processing helix chain 'D' and resid 878 through 901 removed outlier: 4.021A pdb=" N LYS D 897 " --> pdb=" O TRP D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 4.060A pdb=" N ASN D 930 " --> pdb=" O GLU D 926 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR D 931 " --> pdb=" O GLN D 927 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASN D 932 " --> pdb=" O GLU D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1012 Processing helix chain 'D' and resid 1029 through 1033 removed outlier: 4.121A pdb=" N VAL D1033 " --> pdb=" O PRO D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1060 removed outlier: 3.915A pdb=" N ASN D1046 " --> pdb=" O THR D1042 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D1050 " --> pdb=" O ASN D1046 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU D1052 " --> pdb=" O ASP D1048 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA D1053 " --> pdb=" O SER D1049 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL D1054 " --> pdb=" O LEU D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1091 through 1095 Processing helix chain 'D' and resid 1643 through 1647 removed outlier: 3.556A pdb=" N GLU D1647 " --> pdb=" O GLU D1644 " (cutoff:3.500A) Processing helix chain 'D' and resid 1648 through 1665 Processing helix chain 'D' and resid 1671 through 1682 removed outlier: 3.718A pdb=" N ALA D1676 " --> pdb=" O ARG D1672 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER D1679 " --> pdb=" O HIS D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1683 through 1692 removed outlier: 4.340A pdb=" N LEU D1687 " --> pdb=" O GLU D1683 " (cutoff:3.500A) Processing helix chain 'D' and resid 1697 through 1711 removed outlier: 3.719A pdb=" N HIS D1711 " --> pdb=" O LEU D1707 " (cutoff:3.500A) Processing helix chain 'D' and resid 1711 through 1722 removed outlier: 4.493A pdb=" N TYR D1715 " --> pdb=" O HIS D1711 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET D1722 " --> pdb=" O ALA D1718 " (cutoff:3.500A) Processing helix chain 'D' and resid 1784 through 1806 removed outlier: 3.790A pdb=" N LEU D1788 " --> pdb=" O PRO D1784 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU D1805 " --> pdb=" O LYS D1801 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS D1806 " --> pdb=" O GLU D1802 " (cutoff:3.500A) Processing helix chain 'D' and resid 1814 through 1832 removed outlier: 3.599A pdb=" N LEU D1818 " --> pdb=" O THR D1814 " (cutoff:3.500A) Proline residue: D1821 - end of helix Processing helix chain 'D' and resid 1836 through 1846 Processing helix chain 'D' and resid 1898 through 1949 removed outlier: 3.619A pdb=" N GLN D1904 " --> pdb=" O PRO D1900 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D1907 " --> pdb=" O LEU D1903 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN D1916 " --> pdb=" O LEU D1912 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP D1930 " --> pdb=" O ALA D1926 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP D1937 " --> pdb=" O ALA D1933 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN D1938 " --> pdb=" O LYS D1934 " (cutoff:3.500A) Processing helix chain 'D' and resid 1955 through 1965 removed outlier: 4.711A pdb=" N ARG D1962 " --> pdb=" O ALA D1958 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU D1963 " --> pdb=" O ARG D1959 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE D1964 " --> pdb=" O LYS D1960 " (cutoff:3.500A) Processing helix chain 'D' and resid 1967 through 1976 Processing helix chain 'D' and resid 1989 through 2006 removed outlier: 3.891A pdb=" N ASP D1993 " --> pdb=" O GLU D1989 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN D1994 " --> pdb=" O GLU D1990 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2072 removed outlier: 3.510A pdb=" N VAL D2066 " --> pdb=" O SER D2062 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA D2069 " --> pdb=" O MET D2065 " (cutoff:3.500A) Processing helix chain 'D' and resid 2076 through 2093 removed outlier: 3.867A pdb=" N VAL D2080 " --> pdb=" O ASP D2076 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2101 removed outlier: 4.164A pdb=" N LEU D2097 " --> pdb=" O GLY D2093 " (cutoff:3.500A) Processing helix chain 'D' and resid 2112 through 2130 Processing helix chain 'D' and resid 2134 through 2151 Processing helix chain 'D' and resid 2152 through 2157 Processing helix chain 'D' and resid 2157 through 2165 removed outlier: 3.895A pdb=" N MET D2161 " --> pdb=" O HIS D2157 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D2162 " --> pdb=" O PRO D2158 " (cutoff:3.500A) Processing helix chain 'D' and resid 2165 through 2179 removed outlier: 3.840A pdb=" N ASN D2176 " --> pdb=" O GLU D2172 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D2177 " --> pdb=" O VAL D2173 " (cutoff:3.500A) Processing helix chain 'D' and resid 2188 through 2205 removed outlier: 3.873A pdb=" N CYS D2195 " --> pdb=" O MET D2191 " (cutoff:3.500A) Processing helix chain 'D' and resid 2207 through 2221 removed outlier: 3.990A pdb=" N LYS D2211 " --> pdb=" O ARG D2207 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D2215 " --> pdb=" O LYS D2211 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS D2216 " --> pdb=" O ALA D2212 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER D2218 " --> pdb=" O PHE D2214 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR D2219 " --> pdb=" O ASP D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2237 through 2247 Processing helix chain 'D' and resid 2249 through 2256 Processing helix chain 'D' and resid 2260 through 2274 Processing helix chain 'D' and resid 2276 through 2283 Processing helix chain 'D' and resid 2292 through 2305 Processing helix chain 'D' and resid 2312 through 2326 Processing helix chain 'D' and resid 2327 through 2330 Processing helix chain 'D' and resid 2341 through 2355 Processing helix chain 'D' and resid 2356 through 2359 removed outlier: 3.645A pdb=" N ASP D2359 " --> pdb=" O PRO D2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2356 through 2359' Processing helix chain 'D' and resid 2382 through 2402 Processing helix chain 'D' and resid 2413 through 2426 Processing helix chain 'D' and resid 2427 through 2436 Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.827A pdb=" N ALA D2465 " --> pdb=" O PRO D2461 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D2466 " --> pdb=" O ASP D2462 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET D2467 " --> pdb=" O HIS D2463 " (cutoff:3.500A) Processing helix chain 'D' and resid 2479 through 2491 Processing helix chain 'D' and resid 2491 through 2500 Processing helix chain 'D' and resid 2507 through 2524 removed outlier: 4.156A pdb=" N UNK D2511 " --> pdb=" O SER D2507 " (cutoff:3.500A) Processing helix chain 'D' and resid 2533 through 2547 Processing helix chain 'D' and resid 2553 through 2571 Processing helix chain 'D' and resid 2575 through 2589 Processing helix chain 'D' and resid 2594 through 2612 Processing helix chain 'D' and resid 2617 through 2635 removed outlier: 3.650A pdb=" N UNK D2621 " --> pdb=" O UNK D2617 " (cutoff:3.500A) Processing helix chain 'D' and resid 2641 through 2649 removed outlier: 4.073A pdb=" N UNK D2645 " --> pdb=" O UNK D2641 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNK D2646 " --> pdb=" O UNK D2642 " (cutoff:3.500A) Processing helix chain 'D' and resid 2650 through 2657 Processing helix chain 'D' and resid 2713 through 2739 removed outlier: 4.037A pdb=" N ASN D2721 " --> pdb=" O GLU D2717 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D2722 " --> pdb=" O TYR D2718 " (cutoff:3.500A) Processing helix chain 'D' and resid 2763 through 2770 removed outlier: 3.834A pdb=" N GLU D2768 " --> pdb=" O GLU D2764 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR D2770 " --> pdb=" O GLU D2766 " (cutoff:3.500A) Processing helix chain 'D' and resid 2772 through 2784 removed outlier: 4.236A pdb=" N GLU D2776 " --> pdb=" O TRP D2772 " (cutoff:3.500A) Processing helix chain 'D' and resid 2836 through 2863 removed outlier: 3.684A pdb=" N TRP D2851 " --> pdb=" O TYR D2847 " (cutoff:3.500A) Processing helix chain 'D' and resid 2877 through 2898 removed outlier: 3.855A pdb=" N ASP D2884 " --> pdb=" O GLU D2880 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS D2887 " --> pdb=" O LYS D2883 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE D2894 " --> pdb=" O ASP D2890 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D2895 " --> pdb=" O ILE D2891 " (cutoff:3.500A) Processing helix chain 'D' and resid 2917 through 2942 Processing helix chain 'D' and resid 2962 through 2982 removed outlier: 4.252A pdb=" N UNK D2975 " --> pdb=" O UNK D2971 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N UNK D2976 " --> pdb=" O UNK D2972 " (cutoff:3.500A) Processing helix chain 'D' and resid 2992 through 3007 Processing helix chain 'D' and resid 3015 through 3029 Processing helix chain 'D' and resid 3105 through 3129 removed outlier: 3.587A pdb=" N UNK D3116 " --> pdb=" O UNK D3112 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N UNK D3120 " --> pdb=" O UNK D3116 " (cutoff:3.500A) Processing helix chain 'D' and resid 3137 through 3157 removed outlier: 4.158A pdb=" N UNK D3156 " --> pdb=" O UNK D3152 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N UNK D3157 " --> pdb=" O UNK D3153 " (cutoff:3.500A) Processing helix chain 'D' and resid 3163 through 3182 Processing helix chain 'D' and resid 3183 through 3200 removed outlier: 3.653A pdb=" N UNK D3187 " --> pdb=" O UNK D3183 " (cutoff:3.500A) Processing helix chain 'D' and resid 3208 through 3220 removed outlier: 3.701A pdb=" N UNK D3219 " --> pdb=" O UNK D3215 " (cutoff:3.500A) Processing helix chain 'D' and resid 3232 through 3251 Processing helix chain 'D' and resid 3255 through 3270 Processing helix chain 'D' and resid 3271 through 3277 Processing helix chain 'D' and resid 3281 through 3296 removed outlier: 4.013A pdb=" N UNK D3285 " --> pdb=" O UNK D3281 " (cutoff:3.500A) Processing helix chain 'D' and resid 3301 through 3315 Processing helix chain 'D' and resid 3323 through 3356 Processing helix chain 'D' and resid 3362 through 3392 removed outlier: 4.233A pdb=" N UNK D3383 " --> pdb=" O UNK D3379 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N UNK D3389 " --> pdb=" O UNK D3385 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N UNK D3390 " --> pdb=" O UNK D3386 " (cutoff:3.500A) Processing helix chain 'D' and resid 3400 through 3420 removed outlier: 3.995A pdb=" N UNK D3404 " --> pdb=" O UNK D3400 " (cutoff:3.500A) Processing helix chain 'D' and resid 3421 through 3434 removed outlier: 4.638A pdb=" N UNK D3428 " --> pdb=" O UNK D3424 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N UNK D3429 " --> pdb=" O UNK D3425 " (cutoff:3.500A) Processing helix chain 'D' and resid 3478 through 3495 removed outlier: 4.165A pdb=" N UNK D3495 " --> pdb=" O UNK D3491 " (cutoff:3.500A) Processing helix chain 'D' and resid 3503 through 3514 Processing helix chain 'D' and resid 3516 through 3527 removed outlier: 3.921A pdb=" N UNK D3527 " --> pdb=" O UNK D3523 " (cutoff:3.500A) Processing helix chain 'D' and resid 3541 through 3548 removed outlier: 4.395A pdb=" N UNK D3545 " --> pdb=" O UNK D3541 " (cutoff:3.500A) Processing helix chain 'D' and resid 3555 through 3579 Processing helix chain 'D' and resid 3612 through 3627 removed outlier: 4.142A pdb=" N VAL D3616 " --> pdb=" O ARG D3612 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN D3617 " --> pdb=" O HIS D3613 " (cutoff:3.500A) Processing helix chain 'D' and resid 3637 through 3643 Processing helix chain 'D' and resid 3661 through 3676 Processing helix chain 'D' and resid 3684 through 3697 removed outlier: 4.168A pdb=" N ASP D3692 " --> pdb=" O MET D3688 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE D3693 " --> pdb=" O ALA D3689 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3732 removed outlier: 4.179A pdb=" N GLU D3719 " --> pdb=" O GLU D3715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS D3720 " --> pdb=" O LYS D3716 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D3724 " --> pdb=" O LYS D3720 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D3730 " --> pdb=" O GLN D3726 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP D3732 " --> pdb=" O ALA D3728 " (cutoff:3.500A) Processing helix chain 'D' and resid 3734 through 3745 removed outlier: 3.750A pdb=" N LEU D3740 " --> pdb=" O ALA D3736 " (cutoff:3.500A) Processing helix chain 'D' and resid 3753 through 3765 removed outlier: 4.153A pdb=" N LYS D3759 " --> pdb=" O ALA D3755 " (cutoff:3.500A) Processing helix chain 'D' and resid 3769 through 3783 Processing helix chain 'D' and resid 3788 through 3797 Processing helix chain 'D' and resid 3803 through 3817 removed outlier: 3.523A pdb=" N PHE D3807 " --> pdb=" O ASP D3803 " (cutoff:3.500A) Processing helix chain 'D' and resid 3824 through 3828 Processing helix chain 'D' and resid 3831 through 3845 Processing helix chain 'D' and resid 3850 through 3857 Processing helix chain 'D' and resid 3868 through 3891 removed outlier: 3.578A pdb=" N SER D3872 " --> pdb=" O ASN D3868 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR D3891 " --> pdb=" O PHE D3887 " (cutoff:3.500A) Processing helix chain 'D' and resid 3898 through 3923 removed outlier: 3.842A pdb=" N PHE D3905 " --> pdb=" O GLY D3901 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D3908 " --> pdb=" O ASN D3904 " (cutoff:3.500A) Processing helix chain 'D' and resid 3927 through 3936 Processing helix chain 'D' and resid 3938 through 3959 removed outlier: 3.743A pdb=" N ALA D3942 " --> pdb=" O ARG D3938 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS D3952 " --> pdb=" O HIS D3948 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET D3955 " --> pdb=" O ALA D3951 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER D3958 " --> pdb=" O GLN D3954 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN D3959 " --> pdb=" O MET D3955 " (cutoff:3.500A) Processing helix chain 'D' and resid 3963 through 3983 Processing helix chain 'D' and resid 3984 through 3986 No H-bonds generated for 'chain 'D' and resid 3984 through 3986' Processing helix chain 'D' and resid 3992 through 4004 removed outlier: 3.611A pdb=" N LYS D3996 " --> pdb=" O GLY D3992 " (cutoff:3.500A) Processing helix chain 'D' and resid 4005 through 4021 Processing helix chain 'D' and resid 4022 through 4027 removed outlier: 4.055A pdb=" N SER D4027 " --> pdb=" O LYS D4023 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4035 removed outlier: 4.396A pdb=" N ASP D4035 " --> pdb=" O PHE D4031 " (cutoff:3.500A) Processing helix chain 'D' and resid 4045 through 4053 removed outlier: 3.527A pdb=" N LYS D4049 " --> pdb=" O ARG D4045 " (cutoff:3.500A) Processing helix chain 'D' and resid 4058 through 4068 Processing helix chain 'D' and resid 4078 through 4087 Processing helix chain 'D' and resid 4087 through 4108 removed outlier: 3.580A pdb=" N ASP D4092 " --> pdb=" O GLU D4088 " (cutoff:3.500A) Processing helix chain 'D' and resid 4111 through 4126 removed outlier: 4.072A pdb=" N PHE D4117 " --> pdb=" O ARG D4113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D4120 " --> pdb=" O THR D4116 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER D4123 " --> pdb=" O GLU D4119 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL D4124 " --> pdb=" O LEU D4120 " (cutoff:3.500A) Processing helix chain 'D' and resid 4128 through 4130 No H-bonds generated for 'chain 'D' and resid 4128 through 4130' Processing helix chain 'D' and resid 4152 through 4158 Processing helix chain 'D' and resid 4161 through 4179 removed outlier: 3.763A pdb=" N GLU D4178 " --> pdb=" O ASP D4174 " (cutoff:3.500A) Processing helix chain 'D' and resid 4183 through 4204 removed outlier: 3.537A pdb=" N ASN D4190 " --> pdb=" O GLU D4186 " (cutoff:3.500A) Processing helix chain 'D' and resid 4276 through 4284 removed outlier: 3.946A pdb=" N LEU D4280 " --> pdb=" O LYS D4276 " (cutoff:3.500A) Processing helix chain 'D' and resid 4286 through 4302 removed outlier: 3.838A pdb=" N THR D4292 " --> pdb=" O SER D4288 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL D4300 " --> pdb=" O PHE D4296 " (cutoff:3.500A) Processing helix chain 'D' and resid 4304 through 4309 removed outlier: 3.544A pdb=" N SER D4309 " --> pdb=" O PHE D4305 " (cutoff:3.500A) Processing helix chain 'D' and resid 4479 through 4496 removed outlier: 3.701A pdb=" N TYR D4485 " --> pdb=" O LYS D4481 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS D4488 " --> pdb=" O ALA D4484 " (cutoff:3.500A) Processing helix chain 'D' and resid 4496 through 4515 Processing helix chain 'D' and resid 4567 through 4593 removed outlier: 3.574A pdb=" N LEU D4571 " --> pdb=" O MET D4567 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG D4572 " --> pdb=" O GLU D4568 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR D4590 " --> pdb=" O ILE D4586 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS D4591 " --> pdb=" O ILE D4587 " (cutoff:3.500A) Processing helix chain 'D' and resid 4593 through 4613 Processing helix chain 'D' and resid 4613 through 4618 Processing helix chain 'D' and resid 4625 through 4630 Processing helix chain 'D' and resid 4648 through 4656 Processing helix chain 'D' and resid 4661 through 4667 removed outlier: 3.856A pdb=" N SER D4666 " --> pdb=" O ARG D4662 " (cutoff:3.500A) Processing helix chain 'D' and resid 4671 through 4682 Processing helix chain 'D' and resid 4701 through 4713 Processing helix chain 'D' and resid 4715 through 4734 removed outlier: 3.684A pdb=" N LEU D4721 " --> pdb=" O SER D4717 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS D4732 " --> pdb=" O SER D4728 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR D4733 " --> pdb=" O VAL D4729 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4742 removed outlier: 3.617A pdb=" N HIS D4741 " --> pdb=" O PHE D4738 " (cutoff:3.500A) Processing helix chain 'D' and resid 4743 through 4748 Processing helix chain 'D' and resid 4752 through 4761 removed outlier: 4.340A pdb=" N SER D4758 " --> pdb=" O THR D4754 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL D4759 " --> pdb=" O ILE D4755 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4807 through 4819 Processing helix chain 'D' and resid 4840 through 4854 Processing helix chain 'D' and resid 4857 through 4886 removed outlier: 3.886A pdb=" N ILE D4861 " --> pdb=" O LEU D4857 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D4865 " --> pdb=" O ILE D4861 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D4868 " --> pdb=" O LEU D4864 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE D4869 " --> pdb=" O ILE D4865 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D4870 " --> pdb=" O ILE D4866 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D4886 " --> pdb=" O ASP D4882 " (cutoff:3.500A) Processing helix chain 'D' and resid 4893 through 4898 removed outlier: 3.924A pdb=" N PHE D4897 " --> pdb=" O GLY D4893 " (cutoff:3.500A) Processing helix chain 'D' and resid 4902 through 4910 removed outlier: 3.825A pdb=" N THR D4906 " --> pdb=" O HIS D4902 " (cutoff:3.500A) Processing helix chain 'D' and resid 4913 through 4928 removed outlier: 4.555A pdb=" N ASP D4928 " --> pdb=" O LEU D4924 " (cutoff:3.500A) Processing helix chain 'D' and resid 4933 through 4946 Processing helix chain 'D' and resid 4956 through 4961 removed outlier: 3.658A pdb=" N TYR D4961 " --> pdb=" O PHE D4957 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 65 removed outlier: 4.049A pdb=" N GLY J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 5.359A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU A 69 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG A 122 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN A 71 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 5.359A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU A 19 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132 removed outlier: 4.215A pdb=" N VAL A 147 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 203 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 362 through 365 Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 246 removed outlier: 3.684A pdb=" N ARG A 389 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AA7, first strand: chain 'A' and resid 645 through 650 Processing sheet with id=AA8, first strand: chain 'A' and resid 738 through 740 Processing sheet with id=AA9, first strand: chain 'A' and resid 773 through 774 removed outlier: 6.873A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB2, first strand: chain 'A' and resid 850 through 851 removed outlier: 3.783A pdb=" N PHE A1192 " --> pdb=" O MET A1173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1180 through 1181 Processing sheet with id=AB4, first strand: chain 'A' and resid 1086 through 1089 Processing sheet with id=AB5, first strand: chain 'A' and resid 1250 through 1252 Processing sheet with id=AB6, first strand: chain 'A' and resid 1258 through 1260 Processing sheet with id=AB7, first strand: chain 'A' and resid 1269 through 1270 Processing sheet with id=AB8, first strand: chain 'A' and resid 1302 through 1303 Processing sheet with id=AB9, first strand: chain 'A' and resid 1302 through 1303 Processing sheet with id=AC1, first strand: chain 'A' and resid 1317 through 1320 Processing sheet with id=AC2, first strand: chain 'A' and resid 1353 through 1358 removed outlier: 3.724A pdb=" N LYS A1363 " --> pdb=" O ASP A1357 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1726 through 1727 removed outlier: 6.368A pdb=" N PHE A1726 " --> pdb=" O TYR A2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 2306 through 2307 Processing sheet with id=AC5, first strand: chain 'A' and resid 2741 through 2742 removed outlier: 5.707A pdb=" N ILE A2741 " --> pdb=" O GLN A2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 4132 through 4138 removed outlier: 3.768A pdb=" N PHE A4149 " --> pdb=" O GLY A4133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 4519 through 4520 Processing sheet with id=AC8, first strand: chain 'G' and resid 4 through 9 removed outlier: 6.510A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE G 100 " --> pdb=" O MET G 30 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N MET G 30 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL G 102 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR G 28 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU G 104 " --> pdb=" O HIS G 26 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS G 26 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.360A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU B 69 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 122 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN B 71 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.360A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU B 19 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 129 through 132 removed outlier: 4.215A pdb=" N VAL B 147 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 203 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 362 through 365 Processing sheet with id=AD4, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.684A pdb=" N ARG B 389 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 305 through 308 Processing sheet with id=AD6, first strand: chain 'B' and resid 645 through 650 Processing sheet with id=AD7, first strand: chain 'B' and resid 738 through 740 Processing sheet with id=AD8, first strand: chain 'B' and resid 773 through 774 removed outlier: 6.872A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AE1, first strand: chain 'B' and resid 850 through 851 removed outlier: 3.783A pdb=" N PHE B1192 " --> pdb=" O MET B1173 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1180 through 1181 Processing sheet with id=AE3, first strand: chain 'B' and resid 1086 through 1089 Processing sheet with id=AE4, first strand: chain 'B' and resid 1250 through 1252 Processing sheet with id=AE5, first strand: chain 'B' and resid 1258 through 1260 Processing sheet with id=AE6, first strand: chain 'B' and resid 1269 through 1270 Processing sheet with id=AE7, first strand: chain 'B' and resid 1302 through 1303 Processing sheet with id=AE8, first strand: chain 'B' and resid 1302 through 1303 Processing sheet with id=AE9, first strand: chain 'B' and resid 1317 through 1320 Processing sheet with id=AF1, first strand: chain 'B' and resid 1353 through 1358 removed outlier: 3.723A pdb=" N LYS B1363 " --> pdb=" O ASP B1357 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 1726 through 1727 removed outlier: 6.368A pdb=" N PHE B1726 " --> pdb=" O TYR B2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'B' and resid 2306 through 2307 Processing sheet with id=AF4, first strand: chain 'B' and resid 2741 through 2742 removed outlier: 5.706A pdb=" N ILE B2741 " --> pdb=" O GLN B2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 4132 through 4138 removed outlier: 3.767A pdb=" N PHE B4149 " --> pdb=" O GLY B4133 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 4519 through 4520 Processing sheet with id=AF7, first strand: chain 'H' and resid 4 through 9 removed outlier: 6.510A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE H 100 " --> pdb=" O MET H 30 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N MET H 30 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL H 102 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR H 28 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU H 104 " --> pdb=" O HIS H 26 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS H 26 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 48 through 51 removed outlier: 5.360A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU C 69 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG C 122 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN C 71 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 48 through 51 removed outlier: 5.360A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU C 19 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 129 through 132 removed outlier: 4.215A pdb=" N VAL C 147 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 203 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 362 through 365 Processing sheet with id=AG3, first strand: chain 'C' and resid 244 through 246 removed outlier: 3.684A pdb=" N ARG C 389 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AG5, first strand: chain 'C' and resid 645 through 650 Processing sheet with id=AG6, first strand: chain 'C' and resid 738 through 740 Processing sheet with id=AG7, first strand: chain 'C' and resid 773 through 774 removed outlier: 6.873A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AG9, first strand: chain 'C' and resid 850 through 851 removed outlier: 3.782A pdb=" N PHE C1192 " --> pdb=" O MET C1173 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 1180 through 1181 Processing sheet with id=AH2, first strand: chain 'C' and resid 1086 through 1089 Processing sheet with id=AH3, first strand: chain 'C' and resid 1250 through 1252 Processing sheet with id=AH4, first strand: chain 'C' and resid 1258 through 1260 Processing sheet with id=AH5, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AH6, first strand: chain 'C' and resid 1302 through 1303 Processing sheet with id=AH7, first strand: chain 'C' and resid 1302 through 1303 Processing sheet with id=AH8, first strand: chain 'C' and resid 1317 through 1320 Processing sheet with id=AH9, first strand: chain 'C' and resid 1353 through 1358 removed outlier: 3.723A pdb=" N LYS C1363 " --> pdb=" O ASP C1357 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 1726 through 1727 removed outlier: 6.368A pdb=" N PHE C1726 " --> pdb=" O TYR C2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'C' and resid 2306 through 2307 Processing sheet with id=AI3, first strand: chain 'C' and resid 2741 through 2742 removed outlier: 5.706A pdb=" N ILE C2741 " --> pdb=" O GLN C2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'C' and resid 4132 through 4138 removed outlier: 3.767A pdb=" N PHE C4149 " --> pdb=" O GLY C4133 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 4519 through 4520 Processing sheet with id=AI6, first strand: chain 'I' and resid 4 through 9 removed outlier: 6.510A pdb=" N ARG I 72 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE I 100 " --> pdb=" O MET I 30 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N MET I 30 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL I 102 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR I 28 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU I 104 " --> pdb=" O HIS I 26 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS I 26 " --> pdb=" O LEU I 104 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 48 through 51 removed outlier: 5.359A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU D 69 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG D 122 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN D 71 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 48 through 51 removed outlier: 5.359A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU D 19 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 129 through 132 removed outlier: 4.215A pdb=" N VAL D 147 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL D 203 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'D' and resid 362 through 365 Processing sheet with id=AJ2, first strand: chain 'D' and resid 244 through 246 removed outlier: 3.684A pdb=" N ARG D 389 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'D' and resid 305 through 308 Processing sheet with id=AJ4, first strand: chain 'D' and resid 645 through 650 Processing sheet with id=AJ5, first strand: chain 'D' and resid 738 through 740 Processing sheet with id=AJ6, first strand: chain 'D' and resid 773 through 774 removed outlier: 6.872A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 779 through 780 Processing sheet with id=AJ8, first strand: chain 'D' and resid 850 through 851 removed outlier: 3.782A pdb=" N PHE D1192 " --> pdb=" O MET D1173 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 1180 through 1181 Processing sheet with id=AK1, first strand: chain 'D' and resid 1086 through 1089 Processing sheet with id=AK2, first strand: chain 'D' and resid 1250 through 1252 Processing sheet with id=AK3, first strand: chain 'D' and resid 1258 through 1260 Processing sheet with id=AK4, first strand: chain 'D' and resid 1269 through 1270 Processing sheet with id=AK5, first strand: chain 'D' and resid 1302 through 1303 Processing sheet with id=AK6, first strand: chain 'D' and resid 1302 through 1303 Processing sheet with id=AK7, first strand: chain 'D' and resid 1317 through 1320 Processing sheet with id=AK8, first strand: chain 'D' and resid 1353 through 1358 removed outlier: 3.723A pdb=" N LYS D1363 " --> pdb=" O ASP D1357 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'D' and resid 1726 through 1727 removed outlier: 6.368A pdb=" N PHE D1726 " --> pdb=" O TYR D2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK9 Processing sheet with id=AL1, first strand: chain 'D' and resid 2306 through 2307 Processing sheet with id=AL2, first strand: chain 'D' and resid 2741 through 2742 removed outlier: 5.707A pdb=" N ILE D2741 " --> pdb=" O GLN D2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'D' and resid 4132 through 4138 removed outlier: 3.768A pdb=" N PHE D4149 " --> pdb=" O GLY D4133 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'D' and resid 4519 through 4520 Processing sheet with id=AL5, first strand: chain 'J' and resid 4 through 9 removed outlier: 6.510A pdb=" N ARG J 72 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE J 100 " --> pdb=" O MET J 30 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N MET J 30 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL J 102 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR J 28 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU J 104 " --> pdb=" O HIS J 26 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS J 26 " --> pdb=" O LEU J 104 " (cutoff:3.500A) 7077 hydrogen bonds defined for protein. 20403 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: 89.12 Time building geometry restraints manager: 37.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 41070 1.34 - 1.46: 15668 1.46 - 1.57: 67970 1.57 - 1.69: 0 1.69 - 1.81: 1168 Bond restraints: 125876 Sorted by residual: bond pdb=" C GLU A1848 " pdb=" N PRO A1849 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.24e+00 bond pdb=" C GLU C1848 " pdb=" N PRO C1849 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.18e+00 bond pdb=" C GLU B1848 " pdb=" N PRO B1849 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.18e+00 bond pdb=" C GLU D1848 " pdb=" N PRO D1849 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.10e+00 bond pdb=" C GLY A2283 " pdb=" N TYR A2284 " ideal model delta sigma weight residual 1.329 1.297 0.032 1.86e-02 2.89e+03 3.00e+00 ... (remaining 125871 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.02: 1817 105.02 - 112.27: 63824 112.27 - 119.52: 39256 119.52 - 126.77: 64269 126.77 - 134.02: 1498 Bond angle restraints: 170664 Sorted by residual: angle pdb=" C ARG C2204 " pdb=" N ILE C2205 " pdb=" CA ILE C2205 " ideal model delta sigma weight residual 121.65 117.42 4.23 9.40e-01 1.13e+00 2.03e+01 angle pdb=" C ARG A2204 " pdb=" N ILE A2205 " pdb=" CA ILE A2205 " ideal model delta sigma weight residual 121.65 117.44 4.21 9.40e-01 1.13e+00 2.00e+01 angle pdb=" C ARG D2204 " pdb=" N ILE D2205 " pdb=" CA ILE D2205 " ideal model delta sigma weight residual 121.65 117.45 4.20 9.40e-01 1.13e+00 2.00e+01 angle pdb=" C ARG B2204 " pdb=" N ILE B2205 " pdb=" CA ILE B2205 " ideal model delta sigma weight residual 121.65 117.46 4.19 9.40e-01 1.13e+00 1.99e+01 angle pdb=" N ILE C2205 " pdb=" CA ILE C2205 " pdb=" C ILE C2205 " ideal model delta sigma weight residual 106.21 110.32 -4.11 1.07e+00 8.73e-01 1.48e+01 ... (remaining 170659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 68617 17.76 - 35.53: 5466 35.53 - 53.29: 1093 53.29 - 71.05: 192 71.05 - 88.82: 112 Dihedral angle restraints: 75480 sinusoidal: 27076 harmonic: 48404 Sorted by residual: dihedral pdb=" CA GLU D2258 " pdb=" C GLU D2258 " pdb=" N PRO D2259 " pdb=" CA PRO D2259 " ideal model delta harmonic sigma weight residual 180.00 155.16 24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLU B2258 " pdb=" C GLU B2258 " pdb=" N PRO B2259 " pdb=" CA PRO B2259 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLU A2258 " pdb=" C GLU A2258 " pdb=" N PRO A2259 " pdb=" CA PRO A2259 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 75477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 15179 0.039 - 0.079: 3292 0.079 - 0.118: 831 0.118 - 0.158: 98 0.158 - 0.197: 4 Chirality restraints: 19404 Sorted by residual: chirality pdb=" CB ILE B2769 " pdb=" CA ILE B2769 " pdb=" CG1 ILE B2769 " pdb=" CG2 ILE B2769 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CB ILE C2769 " pdb=" CA ILE C2769 " pdb=" CG1 ILE C2769 " pdb=" CG2 ILE C2769 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CB ILE A2769 " pdb=" CA ILE A2769 " pdb=" CG1 ILE A2769 " pdb=" CG2 ILE A2769 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.70e-01 ... (remaining 19401 not shown) Planarity restraints: 22256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B1987 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B1988 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B1988 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B1988 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D4073 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C GLU D4073 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU D4073 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN D4074 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A4073 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C GLU A4073 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU A4073 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A4074 " -0.009 2.00e-02 2.50e+03 ... (remaining 22253 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 3265 2.71 - 3.25: 126244 3.25 - 3.80: 198328 3.80 - 4.35: 241969 4.35 - 4.90: 404676 Nonbonded interactions: 974482 Sorted by model distance: nonbonded pdb=" OG SER B2275 " pdb=" O ILE B2287 " model vdw 2.158 2.440 nonbonded pdb=" OG SER A2275 " pdb=" O ILE A2287 " model vdw 2.158 2.440 nonbonded pdb=" OG SER D2275 " pdb=" O ILE D2287 " model vdw 2.159 2.440 nonbonded pdb=" OG SER C2275 " pdb=" O ILE C2287 " model vdw 2.159 2.440 nonbonded pdb=" OG1 THR A 973 " pdb=" O TYR A 976 " model vdw 2.179 2.440 ... (remaining 974477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 17.840 Check model and map are aligned: 1.330 Set scattering table: 0.800 Process input model: 291.820 Find NCS groups from input model: 5.560 Set up NCS constraints: 0.640 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:1.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 322.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 : 0.002 0.042 125876 Z= 0.145 Angle : 0.514 8.177 170664 Z= 0.294 Chirality : 0.035 0.197 19404 Planarity : 0.003 0.040 22256 Dihedral : 13.791 88.817 44032 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.39 % Allowed : 9.05 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.64 (0.06), residues: 13424 helix: -0.50 (0.06), residues: 6384 sheet: -2.60 (0.12), residues: 1500 loop : -3.01 (0.07), residues: 5540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C4644 HIS 0.006 0.001 HIS B1711 PHE 0.019 0.001 PHE B1740 TYR 0.010 0.001 TYR B2723 ARG 0.004 0.000 ARG A4143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2170 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 2006 time to evaluate : 9.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8110 (m-80) cc_final: 0.7440 (m-80) REVERT: A 637 LEU cc_start: 0.8186 (pt) cc_final: 0.7873 (pt) REVERT: A 730 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8276 (mm) REVERT: A 935 MET cc_start: 0.5380 (mtt) cc_final: 0.4837 (tpt) REVERT: A 1302 TYR cc_start: 0.7975 (m-80) cc_final: 0.7772 (m-80) REVERT: A 1606 LYS cc_start: 0.8013 (tmtt) cc_final: 0.7773 (tptp) REVERT: A 2258 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6168 (tm-30) REVERT: A 2267 TYR cc_start: 0.8269 (m-10) cc_final: 0.7926 (m-10) REVERT: A 3753 MET cc_start: 0.8747 (mmm) cc_final: 0.8532 (mmm) REVERT: A 3827 LYS cc_start: 0.6107 (ttpt) cc_final: 0.5733 (tptp) REVERT: A 3886 ASP cc_start: 0.7740 (m-30) cc_final: 0.7495 (m-30) REVERT: A 4187 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7912 (mt) REVERT: A 4727 MET cc_start: 0.8185 (mmt) cc_final: 0.7896 (mmt) REVERT: A 4808 MET cc_start: 0.8505 (mmm) cc_final: 0.8020 (tpp) REVERT: A 4922 MET cc_start: 0.8835 (ttt) cc_final: 0.8447 (ttt) REVERT: B 191 TYR cc_start: 0.8103 (m-80) cc_final: 0.7656 (m-80) REVERT: B 454 LEU cc_start: 0.8841 (tp) cc_final: 0.8266 (tp) REVERT: B 458 ASP cc_start: 0.7645 (m-30) cc_final: 0.7187 (m-30) REVERT: B 637 LEU cc_start: 0.8153 (pt) cc_final: 0.7843 (pt) REVERT: B 678 MET cc_start: 0.6395 (ptm) cc_final: 0.4950 (ptm) REVERT: B 730 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8307 (mm) REVERT: B 1606 LYS cc_start: 0.8155 (tmtt) cc_final: 0.7892 (tptp) REVERT: B 2222 GLU cc_start: 0.6814 (tp30) cc_final: 0.6603 (tp30) REVERT: B 2258 GLU cc_start: 0.6737 (tm-30) cc_final: 0.6163 (tm-30) REVERT: B 2267 TYR cc_start: 0.8169 (m-10) cc_final: 0.7817 (m-10) REVERT: B 2455 MET cc_start: 0.5925 (tpp) cc_final: 0.5652 (tpt) REVERT: B 3827 LYS cc_start: 0.5941 (ttpt) cc_final: 0.5681 (tptp) REVERT: B 4187 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7843 (mt) REVERT: B 4727 MET cc_start: 0.8154 (mmt) cc_final: 0.7874 (mmt) REVERT: B 4808 MET cc_start: 0.8477 (mmm) cc_final: 0.8002 (tpp) REVERT: B 4922 MET cc_start: 0.8821 (ttt) cc_final: 0.8412 (ttt) REVERT: B 4942 MET cc_start: 0.8564 (mmm) cc_final: 0.8005 (mtp) REVERT: B 4949 GLU cc_start: 0.7308 (mp0) cc_final: 0.6995 (mp0) REVERT: C 191 TYR cc_start: 0.8085 (m-80) cc_final: 0.7642 (m-80) REVERT: C 454 LEU cc_start: 0.8849 (tp) cc_final: 0.8280 (tp) REVERT: C 458 ASP cc_start: 0.7640 (m-30) cc_final: 0.7179 (m-30) REVERT: C 637 LEU cc_start: 0.8139 (pt) cc_final: 0.7812 (pt) REVERT: C 730 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8293 (mm) REVERT: C 1606 LYS cc_start: 0.8110 (tmtt) cc_final: 0.7855 (tptp) REVERT: C 2133 MET cc_start: 0.8181 (tpp) cc_final: 0.7980 (mmm) REVERT: C 2258 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6265 (tm-30) REVERT: C 2267 TYR cc_start: 0.8192 (m-10) cc_final: 0.7838 (m-10) REVERT: C 2400 ARG cc_start: 0.7731 (mtt-85) cc_final: 0.7337 (mtp85) REVERT: C 2455 MET cc_start: 0.5920 (tpp) cc_final: 0.5664 (tpt) REVERT: C 3827 LYS cc_start: 0.5999 (ttpt) cc_final: 0.5731 (tptp) REVERT: C 4187 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7930 (mt) REVERT: C 4727 MET cc_start: 0.8157 (mmt) cc_final: 0.7880 (mmt) REVERT: C 4808 MET cc_start: 0.8490 (mmm) cc_final: 0.8033 (tpp) REVERT: C 4922 MET cc_start: 0.8783 (ttt) cc_final: 0.8376 (ttt) REVERT: C 4942 MET cc_start: 0.8568 (mmm) cc_final: 0.7997 (mtp) REVERT: C 4949 GLU cc_start: 0.7319 (mp0) cc_final: 0.7007 (mp0) REVERT: D 191 TYR cc_start: 0.8089 (m-80) cc_final: 0.7528 (m-80) REVERT: D 637 LEU cc_start: 0.8180 (pt) cc_final: 0.7852 (pt) REVERT: D 678 MET cc_start: 0.6378 (ptm) cc_final: 0.4992 (ptm) REVERT: D 730 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8295 (mm) REVERT: D 1606 LYS cc_start: 0.8095 (tmtt) cc_final: 0.7839 (tptp) REVERT: D 2133 MET cc_start: 0.8215 (tpp) cc_final: 0.7898 (mmm) REVERT: D 2258 GLU cc_start: 0.6913 (tm-30) cc_final: 0.6096 (tm-30) REVERT: D 2267 TYR cc_start: 0.8230 (m-10) cc_final: 0.7897 (m-10) REVERT: D 2455 MET cc_start: 0.5934 (tpp) cc_final: 0.5404 (tpt) REVERT: D 2843 MET cc_start: 0.0971 (tpp) cc_final: 0.0585 (tpt) REVERT: D 3827 LYS cc_start: 0.5910 (ttpt) cc_final: 0.5622 (tptp) REVERT: D 4054 HIS cc_start: 0.5083 (m90) cc_final: 0.4745 (m170) REVERT: D 4187 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7970 (mt) REVERT: D 4727 MET cc_start: 0.8098 (mmt) cc_final: 0.7811 (mmt) REVERT: D 4808 MET cc_start: 0.8409 (mmm) cc_final: 0.7950 (tpp) REVERT: D 4922 MET cc_start: 0.8815 (ttt) cc_final: 0.8477 (ttt) outliers start: 164 outliers final: 73 residues processed: 2109 average time/residue: 1.0593 time to fit residues: 3858.4846 Evaluate side-chains 1343 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1262 time to evaluate : 8.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1348 LYS Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 2215 ASP Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2897 ILE Chi-restraints excluded: chain A residue 2901 VAL Chi-restraints excluded: chain A residue 2903 SER Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4803 MET Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1261 VAL Chi-restraints excluded: chain B residue 1348 LYS Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 2215 ASP Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2897 ILE Chi-restraints excluded: chain B residue 2901 VAL Chi-restraints excluded: chain B residue 2903 SER Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4803 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain C residue 1348 LYS Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 2215 ASP Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2897 ILE Chi-restraints excluded: chain C residue 2901 VAL Chi-restraints excluded: chain C residue 2903 SER Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 4187 LEU Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4803 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain D residue 270 HIS Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1261 VAL Chi-restraints excluded: chain D residue 1348 LYS Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 2215 ASP Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2897 ILE Chi-restraints excluded: chain D residue 2901 VAL Chi-restraints excluded: chain D residue 2903 SER Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 4187 LEU Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4803 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 26 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1398 optimal weight: 0.0870 chunk 1255 optimal weight: 8.9990 chunk 696 optimal weight: 20.0000 chunk 428 optimal weight: 10.0000 chunk 846 optimal weight: 10.0000 chunk 670 optimal weight: 40.0000 chunk 1297 optimal weight: 9.9990 chunk 502 optimal weight: 5.9990 chunk 789 optimal weight: 0.8980 chunk 966 optimal weight: 7.9990 chunk 1503 optimal weight: 30.0000 overall best weight: 4.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 HIS A 150 GLN A 238 HIS A 288 HIS A 293 GLN A 299 HIS ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 531 ASN A 550 GLN A 593 HIS ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A 731 HIS A 808 HIS A 888 ASN A 915 HIS A 934 GLN A 992 GLN ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 ASN A1233 GLN ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1616 GLN ** A1632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1675 HIS ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1919 HIS A1973 ASN A2088 HIS ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2150 ASN A2151 ASN ** A2274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2277 GLN A2317 ASN A2382 HIS A2385 ASN A2726 HIS A2866 ASN A3613 HIS ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3952 HIS ** A3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3959 GLN ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4110 ASN ** A4487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4491 ASN A4496 ASN A4619 GLN A4741 HIS A4761 HIS A4762 ASN A4786 ASN G 26 HIS G 32 GLN G 88 HIS B 44 ASN B 117 HIS B 123 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS B 288 HIS B 293 GLN B 299 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 531 ASN B 550 GLN B 593 HIS ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN B 808 HIS B 888 ASN B 915 HIS B 934 GLN B 992 GLN ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1178 ASN B1233 GLN ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1616 GLN B1675 HIS ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1919 HIS B1973 ASN B2088 HIS ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2150 ASN B2151 ASN ** B2274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2277 GLN B2317 ASN B2382 HIS B2385 ASN B2726 HIS B2848 HIS B2866 ASN B3613 HIS ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3952 HIS ** B3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3959 GLN ** B3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4110 ASN B4487 GLN B4491 ASN B4496 ASN B4619 GLN B4741 HIS B4761 HIS B4762 ASN B4786 ASN H 26 HIS H 32 GLN H 88 HIS C 44 ASN C 117 HIS C 123 HIS C 150 GLN C 238 HIS C 288 HIS C 293 GLN C 299 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 531 ASN C 550 GLN C 593 HIS ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN C 808 HIS C 888 ASN C 915 HIS C 934 GLN C 992 GLN ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1233 GLN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1616 GLN C1675 HIS ** C1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1919 HIS C1973 ASN C2088 HIS C2090 GLN C2150 ASN C2151 ASN ** C2274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2277 GLN C2317 ASN C2382 HIS C2385 ASN C2726 HIS C2848 HIS C2866 ASN C3613 HIS ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3932 GLN C3952 HIS ** C3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3959 GLN ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4110 ASN C4487 GLN C4491 ASN C4496 ASN C4619 GLN C4741 HIS C4761 HIS C4762 ASN C4786 ASN I 26 HIS I 32 GLN I 88 HIS D 44 ASN D 117 HIS D 123 HIS D 150 GLN D 238 HIS D 288 HIS D 293 GLN D 299 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 ASN D 531 ASN D 550 GLN D 593 HIS ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN D 808 HIS D 888 ASN D 915 HIS D 934 GLN D 992 GLN ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1178 ASN D1233 GLN ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1616 GLN D1675 HIS ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1973 ASN D2088 HIS D2090 GLN D2150 ASN D2151 ASN ** D2274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2277 GLN D2317 ASN D2382 HIS D2385 ASN D2726 HIS D2848 HIS D2866 ASN D3613 HIS ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3952 HIS ** D3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3959 GLN ** D3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4110 ASN ** D4487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4491 ASN D4496 ASN D4619 GLN D4741 HIS D4761 HIS D4762 ASN D4786 ASN J 26 HIS J 32 GLN J 88 HIS Total number of N/Q/H flips: 193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 125876 Z= 0.469 Angle : 0.724 9.367 170664 Z= 0.372 Chirality : 0.044 0.202 19404 Planarity : 0.005 0.106 22256 Dihedral : 5.157 53.476 17790 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.35 % Allowed : 16.64 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.08 (0.07), residues: 13424 helix: -0.10 (0.06), residues: 6444 sheet: -2.15 (0.13), residues: 1364 loop : -2.74 (0.07), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 697 HIS 0.011 0.002 HIS C2406 PHE 0.037 0.003 PHE C1740 TYR 0.027 0.003 TYR A4938 ARG 0.009 0.001 ARG C 801 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1641 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 395 poor density : 1246 time to evaluate : 8.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8173 (m-80) cc_final: 0.7558 (m-80) REVERT: A 730 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8417 (mm) REVERT: A 1232 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8140 (tt) REVERT: A 1364 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5800 (pt0) REVERT: A 1606 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7611 (tptm) REVERT: A 2258 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7326 (tm-30) REVERT: A 2335 ARG cc_start: 0.6558 (ttp80) cc_final: 0.6356 (tmt-80) REVERT: A 2340 ASN cc_start: 0.6702 (OUTLIER) cc_final: 0.6490 (p0) REVERT: A 2405 MET cc_start: 0.7440 (ppp) cc_final: 0.6671 (ppp) REVERT: A 2455 MET cc_start: 0.5828 (tpp) cc_final: 0.5388 (tpt) REVERT: A 2491 PHE cc_start: 0.7101 (m-10) cc_final: 0.6885 (m-10) REVERT: A 2781 MET cc_start: -0.0138 (ttp) cc_final: -0.0407 (ptm) REVERT: A 4187 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8593 (pp) REVERT: A 4645 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.6627 (p0) REVERT: A 4922 MET cc_start: 0.8866 (ttt) cc_final: 0.8663 (ttt) REVERT: A 4942 MET cc_start: 0.8523 (mmm) cc_final: 0.7957 (mtt) REVERT: B 191 TYR cc_start: 0.8171 (m-80) cc_final: 0.7624 (m-80) REVERT: B 730 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8414 (mm) REVERT: B 1306 MET cc_start: 0.8994 (mtm) cc_final: 0.8727 (mtm) REVERT: B 1364 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5784 (pt0) REVERT: B 1606 LYS cc_start: 0.8086 (tmtt) cc_final: 0.7668 (tptm) REVERT: B 2258 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7262 (tm-30) REVERT: B 2455 MET cc_start: 0.5836 (tpp) cc_final: 0.5375 (tpt) REVERT: B 2491 PHE cc_start: 0.7108 (m-10) cc_final: 0.6872 (m-10) REVERT: B 4187 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8610 (pp) REVERT: B 4645 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.6768 (p0) REVERT: B 4922 MET cc_start: 0.8893 (ttt) cc_final: 0.8672 (ttt) REVERT: B 4942 MET cc_start: 0.8451 (mmm) cc_final: 0.8125 (mtt) REVERT: B 4949 GLU cc_start: 0.7417 (mp0) cc_final: 0.7163 (mp0) REVERT: H 33 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8678 (p0) REVERT: H 75 LEU cc_start: 0.8421 (mp) cc_final: 0.8168 (mp) REVERT: C 191 TYR cc_start: 0.8157 (m-80) cc_final: 0.7608 (m-80) REVERT: C 678 MET cc_start: 0.7568 (ptm) cc_final: 0.7356 (ptm) REVERT: C 730 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8405 (mm) REVERT: C 1232 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8087 (tt) REVERT: C 1306 MET cc_start: 0.8994 (mtm) cc_final: 0.8727 (mtm) REVERT: C 1364 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5796 (pt0) REVERT: C 1606 LYS cc_start: 0.8035 (tmtt) cc_final: 0.7611 (tptm) REVERT: C 2258 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7257 (tm-30) REVERT: C 2340 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6642 (p0) REVERT: C 2455 MET cc_start: 0.5833 (tpp) cc_final: 0.5377 (tpt) REVERT: C 2491 PHE cc_start: 0.7135 (m-10) cc_final: 0.6879 (m-10) REVERT: C 4187 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8597 (pp) REVERT: C 4645 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.6820 (p0) REVERT: C 4922 MET cc_start: 0.8860 (ttt) cc_final: 0.8627 (ttt) REVERT: C 4942 MET cc_start: 0.8520 (mmm) cc_final: 0.8194 (mtt) REVERT: C 4949 GLU cc_start: 0.7416 (mp0) cc_final: 0.7184 (mp0) REVERT: I 33 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8659 (p0) REVERT: D 191 TYR cc_start: 0.8151 (m-80) cc_final: 0.7619 (m-80) REVERT: D 564 ARG cc_start: 0.6457 (mmt-90) cc_final: 0.6218 (tpt170) REVERT: D 730 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8416 (mm) REVERT: D 1364 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5806 (pt0) REVERT: D 1606 LYS cc_start: 0.8026 (tmtt) cc_final: 0.7607 (tptm) REVERT: D 2340 ASN cc_start: 0.6785 (OUTLIER) cc_final: 0.6582 (p0) REVERT: D 2455 MET cc_start: 0.5845 (tpp) cc_final: 0.5384 (tpt) REVERT: D 2491 PHE cc_start: 0.7119 (m-10) cc_final: 0.6867 (m-10) REVERT: D 4187 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8608 (pp) REVERT: D 4645 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.6707 (p0) REVERT: D 4922 MET cc_start: 0.8832 (ttt) cc_final: 0.8631 (ttt) REVERT: D 4942 MET cc_start: 0.8513 (mmm) cc_final: 0.7940 (mtt) REVERT: J 33 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8659 (p0) outliers start: 395 outliers final: 208 residues processed: 1562 average time/residue: 0.9663 time to fit residues: 2666.1717 Evaluate side-chains 1338 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1106 time to evaluate : 9.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1668 LEU Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1737 ILE Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2094 ILE Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2215 ASP Chi-restraints excluded: chain A residue 2236 SER Chi-restraints excluded: chain A residue 2276 CYS Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2340 ASN Chi-restraints excluded: chain A residue 2761 LEU Chi-restraints excluded: chain A residue 2877 THR Chi-restraints excluded: chain A residue 2901 VAL Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4645 ASP Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4714 THR Chi-restraints excluded: chain A residue 4781 THR Chi-restraints excluded: chain A residue 4799 ASP Chi-restraints excluded: chain A residue 4803 MET Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1161 VAL Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1737 ILE Chi-restraints excluded: chain B residue 1921 ILE Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2094 ILE Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2215 ASP Chi-restraints excluded: chain B residue 2236 SER Chi-restraints excluded: chain B residue 2276 CYS Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2761 LEU Chi-restraints excluded: chain B residue 2877 THR Chi-restraints excluded: chain B residue 2901 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4714 THR Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4799 ASP Chi-restraints excluded: chain B residue 4803 MET Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1300 MET Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1364 GLU Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1737 ILE Chi-restraints excluded: chain C residue 1921 ILE Chi-restraints excluded: chain C residue 2079 LEU Chi-restraints excluded: chain C residue 2094 ILE Chi-restraints excluded: chain C residue 2110 VAL Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2215 ASP Chi-restraints excluded: chain C residue 2236 SER Chi-restraints excluded: chain C residue 2276 CYS Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2340 ASN Chi-restraints excluded: chain C residue 2761 LEU Chi-restraints excluded: chain C residue 2877 THR Chi-restraints excluded: chain C residue 2901 VAL Chi-restraints excluded: chain C residue 3676 THR Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 4012 ILE Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4187 LEU Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4714 THR Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4799 ASP Chi-restraints excluded: chain C residue 4803 MET Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 784 ILE Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1161 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1212 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1364 GLU Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1668 LEU Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 1737 ILE Chi-restraints excluded: chain D residue 1921 ILE Chi-restraints excluded: chain D residue 2079 LEU Chi-restraints excluded: chain D residue 2110 VAL Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2215 ASP Chi-restraints excluded: chain D residue 2236 SER Chi-restraints excluded: chain D residue 2276 CYS Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2340 ASN Chi-restraints excluded: chain D residue 2761 LEU Chi-restraints excluded: chain D residue 2877 THR Chi-restraints excluded: chain D residue 2901 VAL Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4187 LEU Chi-restraints excluded: chain D residue 4509 PHE Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4714 THR Chi-restraints excluded: chain D residue 4781 THR Chi-restraints excluded: chain D residue 4799 ASP Chi-restraints excluded: chain D residue 4803 MET Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 95 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 835 optimal weight: 4.9990 chunk 466 optimal weight: 1.9990 chunk 1251 optimal weight: 7.9990 chunk 1024 optimal weight: 0.9980 chunk 414 optimal weight: 10.0000 chunk 1506 optimal weight: 20.0000 chunk 1627 optimal weight: 0.8980 chunk 1341 optimal weight: 10.0000 chunk 1493 optimal weight: 30.0000 chunk 513 optimal weight: 9.9990 chunk 1208 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 117 HIS ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1632 HIS ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2194 ASN A2274 GLN A2480 GLN A2848 HIS ** A3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4054 HIS A4487 GLN B 150 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** B1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2194 ASN B2274 GLN ** B3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1178 ASN ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1973 ASN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2194 ASN C2274 GLN ** C3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4054 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2274 GLN D2480 GLN ** D3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4487 GLN J 32 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 125876 Z= 0.222 Angle : 0.556 7.816 170664 Z= 0.285 Chirality : 0.038 0.168 19404 Planarity : 0.004 0.047 22256 Dihedral : 4.745 58.635 17744 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.04 % Allowed : 18.26 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.07), residues: 13424 helix: 0.43 (0.07), residues: 6408 sheet: -1.96 (0.13), residues: 1408 loop : -2.59 (0.07), residues: 5608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D4644 HIS 0.009 0.001 HIS C1004 PHE 0.024 0.001 PHE A1740 TYR 0.013 0.001 TYR B4938 ARG 0.009 0.000 ARG B2326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1543 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 1184 time to evaluate : 9.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8157 (m-80) cc_final: 0.7425 (m-80) REVERT: A 319 LYS cc_start: 0.6229 (mtpp) cc_final: 0.5783 (pttt) REVERT: A 551 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.5374 (p90) REVERT: A 730 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8287 (mm) REVERT: A 1232 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8141 (tt) REVERT: A 1364 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5994 (pt0) REVERT: A 1976 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8307 (pp) REVERT: A 2191 MET cc_start: 0.8427 (tpp) cc_final: 0.8037 (tpt) REVERT: A 2455 MET cc_start: 0.5824 (tpp) cc_final: 0.5365 (tpt) REVERT: A 2491 PHE cc_start: 0.7159 (m-10) cc_final: 0.6934 (m-10) REVERT: A 2781 MET cc_start: -0.0311 (ttp) cc_final: -0.0514 (ptm) REVERT: A 4187 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8672 (pp) REVERT: A 4645 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6536 (p0) REVERT: A 4922 MET cc_start: 0.8641 (ttt) cc_final: 0.8354 (ttt) REVERT: A 4942 MET cc_start: 0.8593 (mmm) cc_final: 0.8210 (mtt) REVERT: B 191 TYR cc_start: 0.8141 (m-80) cc_final: 0.7570 (m-80) REVERT: B 551 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.5996 (p90) REVERT: B 730 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8281 (mm) REVERT: B 1007 TRP cc_start: 0.6652 (t60) cc_final: 0.6340 (t60) REVERT: B 1364 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5991 (pt0) REVERT: B 1606 LYS cc_start: 0.8053 (tmtt) cc_final: 0.7644 (tptm) REVERT: B 1976 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8272 (pp) REVERT: B 2191 MET cc_start: 0.8420 (tpp) cc_final: 0.8023 (tpt) REVERT: B 2455 MET cc_start: 0.5833 (tpp) cc_final: 0.5362 (tpt) REVERT: B 4187 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8643 (pp) REVERT: B 4645 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6532 (p0) REVERT: B 4922 MET cc_start: 0.8723 (ttt) cc_final: 0.8449 (ttt) REVERT: H 33 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8642 (p0) REVERT: C 191 TYR cc_start: 0.8124 (m-80) cc_final: 0.7547 (m-80) REVERT: C 319 LYS cc_start: 0.6040 (mtpp) cc_final: 0.5734 (pttt) REVERT: C 551 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.6003 (p90) REVERT: C 730 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8276 (mm) REVERT: C 1007 TRP cc_start: 0.6631 (t60) cc_final: 0.6323 (t60) REVERT: C 1232 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8065 (tt) REVERT: C 1364 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.6007 (pt0) REVERT: C 1606 LYS cc_start: 0.8043 (tmtt) cc_final: 0.7738 (tptp) REVERT: C 2191 MET cc_start: 0.8447 (tpp) cc_final: 0.8054 (tpt) REVERT: C 2425 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7621 (mp) REVERT: C 2455 MET cc_start: 0.5834 (tpp) cc_final: 0.5369 (tpt) REVERT: C 2491 PHE cc_start: 0.7147 (m-10) cc_final: 0.6904 (m-10) REVERT: C 4187 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8692 (pp) REVERT: C 4645 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6709 (p0) REVERT: C 4922 MET cc_start: 0.8696 (ttt) cc_final: 0.8413 (ttt) REVERT: C 4942 MET cc_start: 0.8457 (mmm) cc_final: 0.8157 (mtt) REVERT: I 33 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8628 (p0) REVERT: D 191 TYR cc_start: 0.8138 (m-80) cc_final: 0.7480 (m-80) REVERT: D 319 LYS cc_start: 0.6079 (mtpp) cc_final: 0.5778 (pttt) REVERT: D 551 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.5463 (p90) REVERT: D 730 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8278 (mm) REVERT: D 1364 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.6047 (pt0) REVERT: D 1606 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7606 (tptm) REVERT: D 2491 PHE cc_start: 0.7137 (m-10) cc_final: 0.6900 (m-10) REVERT: D 4187 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8662 (pp) REVERT: D 4645 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6478 (p0) REVERT: D 4659 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: D 4922 MET cc_start: 0.8625 (ttt) cc_final: 0.8331 (ttt) REVERT: D 4942 MET cc_start: 0.8601 (mmm) cc_final: 0.8205 (mtt) outliers start: 359 outliers final: 207 residues processed: 1466 average time/residue: 1.0824 time to fit residues: 2814.3465 Evaluate side-chains 1343 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1108 time to evaluate : 9.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1309 GLU Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1646 THR Chi-restraints excluded: chain A residue 1668 LEU Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1737 ILE Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2215 ASP Chi-restraints excluded: chain A residue 2236 SER Chi-restraints excluded: chain A residue 2320 VAL Chi-restraints excluded: chain A residue 2334 LEU Chi-restraints excluded: chain A residue 2480 GLN Chi-restraints excluded: chain A residue 2891 ILE Chi-restraints excluded: chain A residue 2901 VAL Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3771 THR Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3867 VAL Chi-restraints excluded: chain A residue 4034 TYR Chi-restraints excluded: chain A residue 4117 PHE Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4509 PHE Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4645 ASP Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4714 THR Chi-restraints excluded: chain A residue 4781 THR Chi-restraints excluded: chain A residue 4799 ASP Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 713 TRP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1212 VAL Chi-restraints excluded: chain B residue 1261 VAL Chi-restraints excluded: chain B residue 1309 GLU Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1572 PHE Chi-restraints excluded: chain B residue 1646 THR Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1737 ILE Chi-restraints excluded: chain B residue 1976 LEU Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2215 ASP Chi-restraints excluded: chain B residue 2236 SER Chi-restraints excluded: chain B residue 2320 VAL Chi-restraints excluded: chain B residue 2891 ILE Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3771 THR Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3867 VAL Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4509 PHE Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4714 THR Chi-restraints excluded: chain B residue 4799 ASP Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain C residue 1300 MET Chi-restraints excluded: chain C residue 1309 GLU Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1364 GLU Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1646 THR Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1737 ILE Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2106 THR Chi-restraints excluded: chain C residue 2110 VAL Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2215 ASP Chi-restraints excluded: chain C residue 2236 SER Chi-restraints excluded: chain C residue 2320 VAL Chi-restraints excluded: chain C residue 2425 LEU Chi-restraints excluded: chain C residue 2891 ILE Chi-restraints excluded: chain C residue 3676 THR Chi-restraints excluded: chain C residue 3771 THR Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3867 VAL Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 4187 LEU Chi-restraints excluded: chain C residue 4509 PHE Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4714 THR Chi-restraints excluded: chain C residue 4799 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1261 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1364 GLU Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1646 THR Chi-restraints excluded: chain D residue 1668 LEU Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 1737 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2106 THR Chi-restraints excluded: chain D residue 2110 VAL Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2206 SER Chi-restraints excluded: chain D residue 2215 ASP Chi-restraints excluded: chain D residue 2236 SER Chi-restraints excluded: chain D residue 2320 VAL Chi-restraints excluded: chain D residue 2480 GLN Chi-restraints excluded: chain D residue 2901 VAL Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3771 THR Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3867 VAL Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 4187 LEU Chi-restraints excluded: chain D residue 4509 PHE Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4714 THR Chi-restraints excluded: chain D residue 4799 ASP Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 95 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1488 optimal weight: 20.0000 chunk 1132 optimal weight: 0.8980 chunk 781 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 718 optimal weight: 0.7980 chunk 1011 optimal weight: 5.9990 chunk 1511 optimal weight: 40.0000 chunk 1600 optimal weight: 30.0000 chunk 789 optimal weight: 1.9990 chunk 1432 optimal weight: 1.9990 chunk 431 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 GLN ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2480 GLN ** A3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4054 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 HIS ** B1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 971 GLN ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1973 ASN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4054 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 971 GLN ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1973 ASN ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2480 GLN ** D3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 125876 Z= 0.224 Angle : 0.544 7.863 170664 Z= 0.279 Chirality : 0.037 0.211 19404 Planarity : 0.004 0.046 22256 Dihedral : 4.656 56.027 17726 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.02 % Allowed : 18.18 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.07), residues: 13424 helix: 0.63 (0.07), residues: 6420 sheet: -1.81 (0.13), residues: 1404 loop : -2.48 (0.08), residues: 5600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D4644 HIS 0.008 0.001 HIS B3731 PHE 0.020 0.001 PHE D1740 TYR 0.019 0.001 TYR B4938 ARG 0.010 0.000 ARG C2326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1635 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 474 poor density : 1161 time to evaluate : 8.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8170 (m-80) cc_final: 0.7438 (m-80) REVERT: A 272 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6363 (ptt-90) REVERT: A 551 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.5775 (p90) REVERT: A 730 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8593 (mm) REVERT: A 1232 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8184 (tt) REVERT: A 1364 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.6009 (pt0) REVERT: A 2191 MET cc_start: 0.8406 (tpp) cc_final: 0.8134 (tpt) REVERT: A 2455 MET cc_start: 0.5775 (tpp) cc_final: 0.5334 (tpt) REVERT: A 2491 PHE cc_start: 0.7163 (m-10) cc_final: 0.6901 (m-10) REVERT: A 2776 GLU cc_start: 0.1135 (OUTLIER) cc_final: 0.0678 (tp30) REVERT: A 4187 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8637 (pp) REVERT: A 4574 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 4645 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6488 (p0) REVERT: A 4898 ASP cc_start: 0.8242 (m-30) cc_final: 0.7978 (m-30) REVERT: A 4922 MET cc_start: 0.8723 (ttt) cc_final: 0.8413 (ttt) REVERT: A 4942 MET cc_start: 0.8574 (mmm) cc_final: 0.8143 (mtt) REVERT: B 191 TYR cc_start: 0.8157 (m-80) cc_final: 0.7573 (m-80) REVERT: B 272 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6436 (ptt-90) REVERT: B 551 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.5781 (p90) REVERT: B 730 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8553 (mm) REVERT: B 1007 TRP cc_start: 0.6639 (t60) cc_final: 0.6313 (t60) REVERT: B 1224 LEU cc_start: 0.5643 (OUTLIER) cc_final: 0.5210 (mp) REVERT: B 1364 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5987 (pt0) REVERT: B 1606 LYS cc_start: 0.8048 (tmtt) cc_final: 0.7644 (tptm) REVERT: B 2191 MET cc_start: 0.8394 (tpp) cc_final: 0.8121 (tpt) REVERT: B 2455 MET cc_start: 0.5787 (tpp) cc_final: 0.5330 (tpt) REVERT: B 2776 GLU cc_start: 0.1121 (OUTLIER) cc_final: 0.0643 (tp30) REVERT: B 3694 MET cc_start: 0.8768 (mtp) cc_final: 0.8566 (mtm) REVERT: B 4187 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8578 (pp) REVERT: B 4574 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8348 (mp) REVERT: B 4645 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6477 (p0) REVERT: B 4922 MET cc_start: 0.8720 (ttt) cc_final: 0.8437 (ttt) REVERT: H 33 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8623 (p0) REVERT: C 191 TYR cc_start: 0.8142 (m-80) cc_final: 0.7557 (m-80) REVERT: C 272 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6412 (ptt-90) REVERT: C 319 LYS cc_start: 0.6023 (mtpp) cc_final: 0.5776 (mmmt) REVERT: C 551 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.5784 (p90) REVERT: C 730 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8546 (mm) REVERT: C 1224 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5266 (mp) REVERT: C 1232 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8138 (tt) REVERT: C 1364 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5988 (pt0) REVERT: C 2191 MET cc_start: 0.8425 (tpp) cc_final: 0.8163 (tpt) REVERT: C 2425 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7860 (mp) REVERT: C 2455 MET cc_start: 0.5673 (tpp) cc_final: 0.5192 (tpt) REVERT: C 2491 PHE cc_start: 0.7159 (m-10) cc_final: 0.6882 (m-10) REVERT: C 2776 GLU cc_start: 0.1095 (OUTLIER) cc_final: 0.0646 (tp30) REVERT: C 3694 MET cc_start: 0.8793 (mtp) cc_final: 0.8582 (mtm) REVERT: C 4187 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8625 (pp) REVERT: C 4574 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8352 (mp) REVERT: C 4645 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6536 (p0) REVERT: C 4922 MET cc_start: 0.8691 (ttt) cc_final: 0.8405 (ttt) REVERT: C 4942 MET cc_start: 0.8592 (mmm) cc_final: 0.8155 (mtt) REVERT: I 33 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8602 (p0) REVERT: D 191 TYR cc_start: 0.8161 (m-80) cc_final: 0.7463 (m-80) REVERT: D 272 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6225 (ptt-90) REVERT: D 319 LYS cc_start: 0.6038 (mtpp) cc_final: 0.5791 (mmmt) REVERT: D 551 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.5794 (p90) REVERT: D 564 ARG cc_start: 0.7480 (tpp-160) cc_final: 0.7249 (tpp-160) REVERT: D 730 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8549 (mm) REVERT: D 1007 TRP cc_start: 0.6515 (t60) cc_final: 0.6092 (t60) REVERT: D 1364 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6127 (pt0) REVERT: D 2480 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8656 (tp40) REVERT: D 2491 PHE cc_start: 0.7137 (m-10) cc_final: 0.6914 (m-10) REVERT: D 2776 GLU cc_start: 0.1133 (OUTLIER) cc_final: 0.0681 (tp30) REVERT: D 3694 MET cc_start: 0.8777 (mtp) cc_final: 0.8571 (mtm) REVERT: D 4187 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8623 (pp) REVERT: D 4574 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8347 (mp) REVERT: D 4645 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6471 (p0) REVERT: D 4922 MET cc_start: 0.8705 (ttt) cc_final: 0.8385 (ttt) REVERT: D 4942 MET cc_start: 0.8587 (mmm) cc_final: 0.8143 (mtt) outliers start: 474 outliers final: 310 residues processed: 1542 average time/residue: 0.9677 time to fit residues: 2658.8848 Evaluate side-chains 1457 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 1107 time to evaluate : 9.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1309 GLU Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1646 THR Chi-restraints excluded: chain A residue 1668 LEU Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1737 ILE Chi-restraints excluded: chain A residue 1831 ILE Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2203 CYS Chi-restraints excluded: chain A residue 2206 SER Chi-restraints excluded: chain A residue 2215 ASP Chi-restraints excluded: chain A residue 2236 SER Chi-restraints excluded: chain A residue 2276 CYS Chi-restraints excluded: chain A residue 2320 VAL Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2761 LEU Chi-restraints excluded: chain A residue 2776 GLU Chi-restraints excluded: chain A residue 2877 THR Chi-restraints excluded: chain A residue 2901 VAL Chi-restraints excluded: chain A residue 3628 ILE Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3771 THR Chi-restraints excluded: chain A residue 3800 SER Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3867 VAL Chi-restraints excluded: chain A residue 4034 TYR Chi-restraints excluded: chain A residue 4055 LYS Chi-restraints excluded: chain A residue 4124 VAL Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4509 PHE Chi-restraints excluded: chain A residue 4574 LEU Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4645 ASP Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4714 THR Chi-restraints excluded: chain A residue 4781 THR Chi-restraints excluded: chain A residue 4799 ASP Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4847 ILE Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 713 TRP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1199 ASP Chi-restraints excluded: chain B residue 1212 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1261 VAL Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 1309 GLU Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1572 PHE Chi-restraints excluded: chain B residue 1620 VAL Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1646 THR Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1737 ILE Chi-restraints excluded: chain B residue 1831 ILE Chi-restraints excluded: chain B residue 1921 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2106 THR Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2206 SER Chi-restraints excluded: chain B residue 2215 ASP Chi-restraints excluded: chain B residue 2236 SER Chi-restraints excluded: chain B residue 2276 CYS Chi-restraints excluded: chain B residue 2320 VAL Chi-restraints excluded: chain B residue 2334 LEU Chi-restraints excluded: chain B residue 2389 THR Chi-restraints excluded: chain B residue 2761 LEU Chi-restraints excluded: chain B residue 2776 GLU Chi-restraints excluded: chain B residue 2877 THR Chi-restraints excluded: chain B residue 2901 VAL Chi-restraints excluded: chain B residue 3628 ILE Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3771 THR Chi-restraints excluded: chain B residue 3800 SER Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3867 VAL Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 4124 VAL Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4509 PHE Chi-restraints excluded: chain B residue 4574 LEU Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4714 THR Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4799 ASP Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4847 ILE Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 713 TRP Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1164 CYS Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1224 LEU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain C residue 1300 MET Chi-restraints excluded: chain C residue 1309 GLU Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1364 GLU Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1620 VAL Chi-restraints excluded: chain C residue 1646 THR Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1737 ILE Chi-restraints excluded: chain C residue 1921 ILE Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2106 THR Chi-restraints excluded: chain C residue 2110 VAL Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2206 SER Chi-restraints excluded: chain C residue 2215 ASP Chi-restraints excluded: chain C residue 2236 SER Chi-restraints excluded: chain C residue 2276 CYS Chi-restraints excluded: chain C residue 2320 VAL Chi-restraints excluded: chain C residue 2334 LEU Chi-restraints excluded: chain C residue 2389 THR Chi-restraints excluded: chain C residue 2425 LEU Chi-restraints excluded: chain C residue 2761 LEU Chi-restraints excluded: chain C residue 2776 GLU Chi-restraints excluded: chain C residue 2877 THR Chi-restraints excluded: chain C residue 2901 VAL Chi-restraints excluded: chain C residue 3628 ILE Chi-restraints excluded: chain C residue 3676 THR Chi-restraints excluded: chain C residue 3771 THR Chi-restraints excluded: chain C residue 3800 SER Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3867 VAL Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 4092 ASP Chi-restraints excluded: chain C residue 4124 VAL Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4187 LEU Chi-restraints excluded: chain C residue 4509 PHE Chi-restraints excluded: chain C residue 4574 LEU Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4714 THR Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4799 ASP Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4847 ILE Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 270 HIS Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 784 ILE Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1164 CYS Chi-restraints excluded: chain D residue 1199 ASP Chi-restraints excluded: chain D residue 1261 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1364 GLU Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1646 THR Chi-restraints excluded: chain D residue 1668 LEU Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 1737 ILE Chi-restraints excluded: chain D residue 1921 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2106 THR Chi-restraints excluded: chain D residue 2110 VAL Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2206 SER Chi-restraints excluded: chain D residue 2215 ASP Chi-restraints excluded: chain D residue 2236 SER Chi-restraints excluded: chain D residue 2276 CYS Chi-restraints excluded: chain D residue 2320 VAL Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2480 GLN Chi-restraints excluded: chain D residue 2761 LEU Chi-restraints excluded: chain D residue 2776 GLU Chi-restraints excluded: chain D residue 2877 THR Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 2901 VAL Chi-restraints excluded: chain D residue 3628 ILE Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3771 THR Chi-restraints excluded: chain D residue 3800 SER Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3867 VAL Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 4124 VAL Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4187 LEU Chi-restraints excluded: chain D residue 4509 PHE Chi-restraints excluded: chain D residue 4574 LEU Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4714 THR Chi-restraints excluded: chain D residue 4781 THR Chi-restraints excluded: chain D residue 4799 ASP Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 95 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1333 optimal weight: 30.0000 chunk 908 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 1191 optimal weight: 5.9990 chunk 660 optimal weight: 30.0000 chunk 1365 optimal weight: 10.0000 chunk 1106 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 817 optimal weight: 1.9990 chunk 1436 optimal weight: 8.9990 chunk 403 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 ASN A1685 GLN A1973 ASN ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2463 HIS ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3900 GLN ** A3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4054 HIS A4107 HIS A4578 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 HIS B 971 GLN ** B1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1602 ASN ** B1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1632 HIS B1685 GLN ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2463 HIS ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3900 GLN ** B3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 HIS B4107 HIS B4578 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 HIS C 731 HIS ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1602 ASN C1685 GLN C1973 ASN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2463 HIS ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3900 GLN ** C3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4054 HIS C4107 HIS C4578 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1602 ASN D1685 GLN ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1919 HIS D1973 ASN ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2463 HIS D2480 GLN ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3900 GLN ** D3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4107 HIS D4578 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 125876 Z= 0.406 Angle : 0.656 10.202 170664 Z= 0.337 Chirality : 0.042 0.207 19404 Planarity : 0.004 0.052 22256 Dihedral : 5.003 57.852 17726 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.59 % Allowed : 19.71 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.07), residues: 13424 helix: 0.40 (0.06), residues: 6436 sheet: -1.79 (0.14), residues: 1336 loop : -2.48 (0.08), residues: 5652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B4479 HIS 0.008 0.001 HIS A1680 PHE 0.030 0.002 PHE B1740 TYR 0.024 0.002 TYR D1777 ARG 0.008 0.001 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1665 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 542 poor density : 1123 time to evaluate : 9.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8249 (m-80) cc_final: 0.7415 (m-80) REVERT: A 272 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.6230 (ptt-90) REVERT: A 506 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6649 (m-70) REVERT: A 1050 LEU cc_start: 0.2819 (OUTLIER) cc_final: 0.2509 (mm) REVERT: A 1232 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 1364 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5806 (pt0) REVERT: A 2222 GLU cc_start: 0.6968 (tp30) cc_final: 0.6665 (tp30) REVERT: A 2335 ARG cc_start: 0.6672 (ttp80) cc_final: 0.6358 (tmt-80) REVERT: A 2776 GLU cc_start: 0.0866 (OUTLIER) cc_final: 0.0459 (tp30) REVERT: A 3905 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8373 (t80) REVERT: A 4574 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8312 (mp) REVERT: A 4645 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7281 (p0) REVERT: A 4942 MET cc_start: 0.8693 (mmm) cc_final: 0.8198 (mtt) REVERT: G 50 ARG cc_start: 0.7058 (mtp-110) cc_final: 0.6583 (mtp-110) REVERT: G 75 LEU cc_start: 0.8466 (mp) cc_final: 0.8084 (mt) REVERT: B 191 TYR cc_start: 0.8242 (m-80) cc_final: 0.7558 (m-80) REVERT: B 506 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.6894 (m-70) REVERT: B 981 MET cc_start: 0.2327 (ppp) cc_final: 0.1984 (ppp) REVERT: B 1050 LEU cc_start: 0.2739 (OUTLIER) cc_final: 0.2470 (mm) REVERT: B 1224 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.5063 (mp) REVERT: B 1232 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8119 (tt) REVERT: B 1364 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5802 (pt0) REVERT: B 1606 LYS cc_start: 0.8052 (tmtt) cc_final: 0.7827 (tptm) REVERT: B 2718 TYR cc_start: 0.3891 (OUTLIER) cc_final: 0.3331 (m-80) REVERT: B 2776 GLU cc_start: 0.0937 (OUTLIER) cc_final: 0.0507 (tp30) REVERT: B 3694 MET cc_start: 0.8779 (mtp) cc_final: 0.8569 (mtm) REVERT: B 4187 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8668 (pp) REVERT: B 4574 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8330 (mp) REVERT: B 4645 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7248 (p0) REVERT: H 33 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8671 (p0) REVERT: H 50 ARG cc_start: 0.7039 (mtp-110) cc_final: 0.6566 (mtp-110) REVERT: C 191 TYR cc_start: 0.8235 (m-80) cc_final: 0.7552 (m-80) REVERT: C 272 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6229 (ptt-90) REVERT: C 506 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.6907 (m-70) REVERT: C 1050 LEU cc_start: 0.2742 (OUTLIER) cc_final: 0.2474 (mm) REVERT: C 1224 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5271 (mp) REVERT: C 1232 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8196 (tt) REVERT: C 1364 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5796 (pt0) REVERT: C 2222 GLU cc_start: 0.6979 (tp30) cc_final: 0.6675 (tp30) REVERT: C 2718 TYR cc_start: 0.3836 (OUTLIER) cc_final: 0.3330 (m-80) REVERT: C 2776 GLU cc_start: 0.0909 (OUTLIER) cc_final: 0.0489 (tp30) REVERT: C 3694 MET cc_start: 0.8802 (mtp) cc_final: 0.8590 (mtm) REVERT: C 4187 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8711 (pp) REVERT: C 4574 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8336 (mp) REVERT: C 4645 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7306 (p0) REVERT: C 4942 MET cc_start: 0.8666 (mmm) cc_final: 0.8142 (mtt) REVERT: I 33 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8659 (p0) REVERT: D 191 TYR cc_start: 0.8266 (m-80) cc_final: 0.7498 (m-80) REVERT: D 564 ARG cc_start: 0.7476 (tpp-160) cc_final: 0.5649 (tpp80) REVERT: D 1050 LEU cc_start: 0.2772 (OUTLIER) cc_final: 0.2496 (mm) REVERT: D 1232 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8127 (tt) REVERT: D 1364 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5807 (pt0) REVERT: D 2222 GLU cc_start: 0.6948 (tp30) cc_final: 0.6653 (tp30) REVERT: D 2718 TYR cc_start: 0.3819 (OUTLIER) cc_final: 0.3313 (m-80) REVERT: D 2776 GLU cc_start: 0.0929 (OUTLIER) cc_final: 0.0495 (tp30) REVERT: D 3694 MET cc_start: 0.8782 (mtp) cc_final: 0.8580 (mtm) REVERT: D 3905 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8342 (t80) REVERT: D 4574 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8402 (mp) REVERT: D 4645 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7260 (p0) REVERT: D 4942 MET cc_start: 0.8704 (mmm) cc_final: 0.8162 (mtt) REVERT: J 75 LEU cc_start: 0.8469 (mp) cc_final: 0.8083 (mt) outliers start: 542 outliers final: 369 residues processed: 1571 average time/residue: 0.9685 time to fit residues: 2724.4089 Evaluate side-chains 1483 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 409 poor density : 1074 time to evaluate : 9.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1309 GLU Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1372 ASN Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1646 THR Chi-restraints excluded: chain A residue 1668 LEU Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1737 ILE Chi-restraints excluded: chain A residue 1843 ILE Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2215 ASP Chi-restraints excluded: chain A residue 2236 SER Chi-restraints excluded: chain A residue 2276 CYS Chi-restraints excluded: chain A residue 2320 VAL Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2761 LEU Chi-restraints excluded: chain A residue 2776 GLU Chi-restraints excluded: chain A residue 2877 THR Chi-restraints excluded: chain A residue 2891 ILE Chi-restraints excluded: chain A residue 2901 VAL Chi-restraints excluded: chain A residue 3628 ILE Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3771 THR Chi-restraints excluded: chain A residue 3800 SER Chi-restraints excluded: chain A residue 3818 MET Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3867 VAL Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3966 LEU Chi-restraints excluded: chain A residue 4012 ILE Chi-restraints excluded: chain A residue 4117 PHE Chi-restraints excluded: chain A residue 4124 VAL Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4559 VAL Chi-restraints excluded: chain A residue 4574 LEU Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4645 ASP Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4714 THR Chi-restraints excluded: chain A residue 4781 THR Chi-restraints excluded: chain A residue 4799 ASP Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain A residue 4881 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 577 CYS Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 713 TRP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1199 ASP Chi-restraints excluded: chain B residue 1212 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1261 VAL Chi-restraints excluded: chain B residue 1309 GLU Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1372 ASN Chi-restraints excluded: chain B residue 1572 PHE Chi-restraints excluded: chain B residue 1620 VAL Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1646 THR Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1737 ILE Chi-restraints excluded: chain B residue 1843 ILE Chi-restraints excluded: chain B residue 1921 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2106 THR Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2215 ASP Chi-restraints excluded: chain B residue 2236 SER Chi-restraints excluded: chain B residue 2276 CYS Chi-restraints excluded: chain B residue 2320 VAL Chi-restraints excluded: chain B residue 2334 LEU Chi-restraints excluded: chain B residue 2389 THR Chi-restraints excluded: chain B residue 2718 TYR Chi-restraints excluded: chain B residue 2776 GLU Chi-restraints excluded: chain B residue 2877 THR Chi-restraints excluded: chain B residue 2891 ILE Chi-restraints excluded: chain B residue 2901 VAL Chi-restraints excluded: chain B residue 3628 ILE Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3771 THR Chi-restraints excluded: chain B residue 3800 SER Chi-restraints excluded: chain B residue 3818 MET Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3864 ASN Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3867 VAL Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3966 LEU Chi-restraints excluded: chain B residue 4012 ILE Chi-restraints excluded: chain B residue 4117 PHE Chi-restraints excluded: chain B residue 4124 VAL Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4559 VAL Chi-restraints excluded: chain B residue 4574 LEU Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4714 THR Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4799 ASP Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 506 HIS Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 577 CYS Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain C residue 713 TRP Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1050 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1164 CYS Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1224 LEU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1300 MET Chi-restraints excluded: chain C residue 1309 GLU Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1364 GLU Chi-restraints excluded: chain C residue 1372 ASN Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1620 VAL Chi-restraints excluded: chain C residue 1646 THR Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1737 ILE Chi-restraints excluded: chain C residue 1843 ILE Chi-restraints excluded: chain C residue 1921 ILE Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2079 LEU Chi-restraints excluded: chain C residue 2106 THR Chi-restraints excluded: chain C residue 2110 VAL Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2215 ASP Chi-restraints excluded: chain C residue 2236 SER Chi-restraints excluded: chain C residue 2276 CYS Chi-restraints excluded: chain C residue 2320 VAL Chi-restraints excluded: chain C residue 2334 LEU Chi-restraints excluded: chain C residue 2389 THR Chi-restraints excluded: chain C residue 2718 TYR Chi-restraints excluded: chain C residue 2761 LEU Chi-restraints excluded: chain C residue 2776 GLU Chi-restraints excluded: chain C residue 2877 THR Chi-restraints excluded: chain C residue 2891 ILE Chi-restraints excluded: chain C residue 2901 VAL Chi-restraints excluded: chain C residue 3628 ILE Chi-restraints excluded: chain C residue 3676 THR Chi-restraints excluded: chain C residue 3771 THR Chi-restraints excluded: chain C residue 3818 MET Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3864 ASN Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3867 VAL Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3966 LEU Chi-restraints excluded: chain C residue 4117 PHE Chi-restraints excluded: chain C residue 4124 VAL Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4187 LEU Chi-restraints excluded: chain C residue 4509 PHE Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4559 VAL Chi-restraints excluded: chain C residue 4574 LEU Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4714 THR Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4799 ASP Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 270 HIS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 577 CYS Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 784 ILE Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1161 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1164 CYS Chi-restraints excluded: chain D residue 1199 ASP Chi-restraints excluded: chain D residue 1212 VAL Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1261 VAL Chi-restraints excluded: chain D residue 1273 ILE Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1364 GLU Chi-restraints excluded: chain D residue 1372 ASN Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1646 THR Chi-restraints excluded: chain D residue 1668 LEU Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 1737 ILE Chi-restraints excluded: chain D residue 1843 ILE Chi-restraints excluded: chain D residue 1921 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2079 LEU Chi-restraints excluded: chain D residue 2106 THR Chi-restraints excluded: chain D residue 2110 VAL Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2215 ASP Chi-restraints excluded: chain D residue 2236 SER Chi-restraints excluded: chain D residue 2276 CYS Chi-restraints excluded: chain D residue 2320 VAL Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2718 TYR Chi-restraints excluded: chain D residue 2761 LEU Chi-restraints excluded: chain D residue 2776 GLU Chi-restraints excluded: chain D residue 2877 THR Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 2901 VAL Chi-restraints excluded: chain D residue 3628 ILE Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3771 THR Chi-restraints excluded: chain D residue 3800 SER Chi-restraints excluded: chain D residue 3818 MET Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3867 VAL Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3966 LEU Chi-restraints excluded: chain D residue 4117 PHE Chi-restraints excluded: chain D residue 4124 VAL Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4187 LEU Chi-restraints excluded: chain D residue 4509 PHE Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4559 VAL Chi-restraints excluded: chain D residue 4574 LEU Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4714 THR Chi-restraints excluded: chain D residue 4781 THR Chi-restraints excluded: chain D residue 4799 ASP Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain D residue 4881 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 95 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 538 optimal weight: 9.9990 chunk 1441 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 939 optimal weight: 8.9990 chunk 395 optimal weight: 2.9990 chunk 1602 optimal weight: 1.9990 chunk 1330 optimal weight: 8.9990 chunk 741 optimal weight: 0.9990 chunk 133 optimal weight: 30.0000 chunk 530 optimal weight: 0.5980 chunk 841 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4054 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1973 ASN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4054 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 HIS ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1973 ASN ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 125876 Z= 0.227 Angle : 0.563 8.357 170664 Z= 0.289 Chirality : 0.038 0.185 19404 Planarity : 0.004 0.052 22256 Dihedral : 4.822 59.382 17726 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.20 % Allowed : 20.86 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.07), residues: 13424 helix: 0.65 (0.07), residues: 6460 sheet: -1.71 (0.13), residues: 1404 loop : -2.38 (0.08), residues: 5560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP B4479 HIS 0.008 0.001 HIS B3731 PHE 0.022 0.001 PHE B1740 TYR 0.020 0.001 TYR A4034 ARG 0.006 0.000 ARG C2326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1647 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 496 poor density : 1151 time to evaluate : 9.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8278 (m-80) cc_final: 0.7513 (m-80) REVERT: A 272 ARG cc_start: 0.6475 (OUTLIER) cc_final: 0.6250 (ptt-90) REVERT: A 506 HIS cc_start: 0.7342 (OUTLIER) cc_final: 0.6776 (m-70) REVERT: A 651 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.8272 (m-70) REVERT: A 1232 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8214 (tt) REVERT: A 1364 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6185 (pt0) REVERT: A 2222 GLU cc_start: 0.6921 (tp30) cc_final: 0.6615 (tp30) REVERT: A 2335 ARG cc_start: 0.6771 (ttp80) cc_final: 0.6464 (tmt-80) REVERT: A 2506 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5906 (pp) REVERT: A 2776 GLU cc_start: 0.0872 (OUTLIER) cc_final: 0.0466 (tp30) REVERT: A 4084 LYS cc_start: 0.8455 (mptt) cc_final: 0.8232 (mmtt) REVERT: A 4108 MET cc_start: 0.7550 (tpt) cc_final: 0.7345 (tpt) REVERT: A 4125 LEU cc_start: 0.8961 (tp) cc_final: 0.8759 (tp) REVERT: A 4574 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 4645 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7123 (p0) REVERT: A 4942 MET cc_start: 0.8625 (mmm) cc_final: 0.8099 (mtt) REVERT: B 191 TYR cc_start: 0.8218 (m-80) cc_final: 0.7500 (m-80) REVERT: B 202 HIS cc_start: 0.5759 (m90) cc_final: 0.5244 (m90) REVERT: B 506 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6845 (m-70) REVERT: B 564 ARG cc_start: 0.7068 (tpt170) cc_final: 0.6336 (tpp-160) REVERT: B 651 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8234 (m-70) REVERT: B 981 MET cc_start: 0.2500 (ppp) cc_final: 0.2189 (ppp) REVERT: B 1050 LEU cc_start: 0.2717 (OUTLIER) cc_final: 0.2461 (mm) REVERT: B 1224 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5350 (mp) REVERT: B 1232 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8125 (tt) REVERT: B 1606 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7814 (tptm) REVERT: B 2222 GLU cc_start: 0.6921 (tp30) cc_final: 0.6625 (tp30) REVERT: B 2506 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5867 (pp) REVERT: B 2776 GLU cc_start: 0.0765 (OUTLIER) cc_final: 0.0357 (tp30) REVERT: B 3694 MET cc_start: 0.8742 (mtp) cc_final: 0.8540 (mtm) REVERT: B 3905 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8123 (t80) REVERT: B 4574 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B 4645 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7039 (p0) REVERT: H 33 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8616 (p0) REVERT: H 75 LEU cc_start: 0.8401 (mp) cc_final: 0.8008 (mt) REVERT: C 191 TYR cc_start: 0.8218 (m-80) cc_final: 0.7456 (m-80) REVERT: C 202 HIS cc_start: 0.5752 (m90) cc_final: 0.5248 (m90) REVERT: C 272 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6200 (ptt-90) REVERT: C 319 LYS cc_start: 0.5875 (mtpp) cc_final: 0.5593 (mmmt) REVERT: C 506 HIS cc_start: 0.7331 (OUTLIER) cc_final: 0.6747 (m-70) REVERT: C 651 HIS cc_start: 0.8483 (OUTLIER) cc_final: 0.8264 (m-70) REVERT: C 1050 LEU cc_start: 0.2722 (OUTLIER) cc_final: 0.2465 (mm) REVERT: C 1224 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5396 (mp) REVERT: C 1232 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8199 (tt) REVERT: C 1364 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.6174 (pt0) REVERT: C 2222 GLU cc_start: 0.6939 (tp30) cc_final: 0.6629 (tp30) REVERT: C 2425 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7843 (mp) REVERT: C 2506 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5865 (pp) REVERT: C 2718 TYR cc_start: 0.3860 (OUTLIER) cc_final: 0.3357 (m-80) REVERT: C 2776 GLU cc_start: 0.0842 (OUTLIER) cc_final: 0.0447 (tp30) REVERT: C 3905 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8169 (t80) REVERT: C 4084 LYS cc_start: 0.8809 (mptt) cc_final: 0.8566 (mmtt) REVERT: C 4574 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8377 (mp) REVERT: C 4645 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7177 (p0) REVERT: C 4942 MET cc_start: 0.8688 (mmm) cc_final: 0.8137 (mtt) REVERT: I 33 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8602 (p0) REVERT: D 191 TYR cc_start: 0.8246 (m-80) cc_final: 0.7470 (m-80) REVERT: D 319 LYS cc_start: 0.5895 (mtpp) cc_final: 0.5616 (mmmt) REVERT: D 564 ARG cc_start: 0.7460 (tpp-160) cc_final: 0.5910 (tpp80) REVERT: D 566 GLU cc_start: 0.7443 (pm20) cc_final: 0.7237 (pp20) REVERT: D 651 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.8256 (m-70) REVERT: D 1050 LEU cc_start: 0.2748 (OUTLIER) cc_final: 0.2484 (mm) REVERT: D 1232 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8142 (tt) REVERT: D 1364 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.6211 (pt0) REVERT: D 2506 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5953 (pp) REVERT: D 4574 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8370 (mp) REVERT: D 4645 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7129 (p0) REVERT: D 4898 ASP cc_start: 0.8261 (m-30) cc_final: 0.7872 (m-30) REVERT: D 4942 MET cc_start: 0.8653 (mmm) cc_final: 0.8073 (mtt) outliers start: 496 outliers final: 357 residues processed: 1548 average time/residue: 0.9714 time to fit residues: 2679.0804 Evaluate side-chains 1504 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 399 poor density : 1105 time to evaluate : 9.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1309 GLU Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1646 THR Chi-restraints excluded: chain A residue 1668 LEU Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1737 ILE Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2215 ASP Chi-restraints excluded: chain A residue 2236 SER Chi-restraints excluded: chain A residue 2276 CYS Chi-restraints excluded: chain A residue 2320 VAL Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain A residue 2735 LYS Chi-restraints excluded: chain A residue 2761 LEU Chi-restraints excluded: chain A residue 2776 GLU Chi-restraints excluded: chain A residue 2848 HIS Chi-restraints excluded: chain A residue 2877 THR Chi-restraints excluded: chain A residue 2891 ILE Chi-restraints excluded: chain A residue 2901 VAL Chi-restraints excluded: chain A residue 3628 ILE Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3771 THR Chi-restraints excluded: chain A residue 3800 SER Chi-restraints excluded: chain A residue 3818 MET Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3864 ASN Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3867 VAL Chi-restraints excluded: chain A residue 4055 LYS Chi-restraints excluded: chain A residue 4092 ASP Chi-restraints excluded: chain A residue 4124 VAL Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4509 PHE Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4559 VAL Chi-restraints excluded: chain A residue 4574 LEU Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4645 ASP Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4714 THR Chi-restraints excluded: chain A residue 4781 THR Chi-restraints excluded: chain A residue 4799 ASP Chi-restraints excluded: chain A residue 4803 MET Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 713 TRP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1161 VAL Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1199 ASP Chi-restraints excluded: chain B residue 1212 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1309 GLU Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1572 PHE Chi-restraints excluded: chain B residue 1620 VAL Chi-restraints excluded: chain B residue 1646 THR Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1737 ILE Chi-restraints excluded: chain B residue 1921 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2106 THR Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2215 ASP Chi-restraints excluded: chain B residue 2236 SER Chi-restraints excluded: chain B residue 2276 CYS Chi-restraints excluded: chain B residue 2320 VAL Chi-restraints excluded: chain B residue 2334 LEU Chi-restraints excluded: chain B residue 2389 THR Chi-restraints excluded: chain B residue 2506 LEU Chi-restraints excluded: chain B residue 2761 LEU Chi-restraints excluded: chain B residue 2776 GLU Chi-restraints excluded: chain B residue 2871 VAL Chi-restraints excluded: chain B residue 2877 THR Chi-restraints excluded: chain B residue 2891 ILE Chi-restraints excluded: chain B residue 2901 VAL Chi-restraints excluded: chain B residue 3628 ILE Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3771 THR Chi-restraints excluded: chain B residue 3818 MET Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3866 THR Chi-restraints excluded: chain B residue 3867 VAL Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3966 LEU Chi-restraints excluded: chain B residue 4092 ASP Chi-restraints excluded: chain B residue 4124 VAL Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4509 PHE Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4574 LEU Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4714 THR Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4799 ASP Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 506 HIS Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 713 TRP Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1050 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1164 CYS Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1224 LEU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1300 MET Chi-restraints excluded: chain C residue 1309 GLU Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1364 GLU Chi-restraints excluded: chain C residue 1376 TYR Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1620 VAL Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1646 THR Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1737 ILE Chi-restraints excluded: chain C residue 1831 ILE Chi-restraints excluded: chain C residue 1921 ILE Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2079 LEU Chi-restraints excluded: chain C residue 2106 THR Chi-restraints excluded: chain C residue 2110 VAL Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2215 ASP Chi-restraints excluded: chain C residue 2236 SER Chi-restraints excluded: chain C residue 2276 CYS Chi-restraints excluded: chain C residue 2320 VAL Chi-restraints excluded: chain C residue 2389 THR Chi-restraints excluded: chain C residue 2425 LEU Chi-restraints excluded: chain C residue 2506 LEU Chi-restraints excluded: chain C residue 2718 TYR Chi-restraints excluded: chain C residue 2761 LEU Chi-restraints excluded: chain C residue 2776 GLU Chi-restraints excluded: chain C residue 2877 THR Chi-restraints excluded: chain C residue 2891 ILE Chi-restraints excluded: chain C residue 2901 VAL Chi-restraints excluded: chain C residue 3628 ILE Chi-restraints excluded: chain C residue 3676 THR Chi-restraints excluded: chain C residue 3771 THR Chi-restraints excluded: chain C residue 3800 SER Chi-restraints excluded: chain C residue 3818 MET Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 3867 VAL Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3966 LEU Chi-restraints excluded: chain C residue 4077 LEU Chi-restraints excluded: chain C residue 4124 VAL Chi-restraints excluded: chain C residue 4140 SER Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4187 LEU Chi-restraints excluded: chain C residue 4509 PHE Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4574 LEU Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4714 THR Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4799 ASP Chi-restraints excluded: chain C residue 4803 MET Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 270 HIS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 713 TRP Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 784 ILE Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1164 CYS Chi-restraints excluded: chain D residue 1199 ASP Chi-restraints excluded: chain D residue 1212 VAL Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1364 GLU Chi-restraints excluded: chain D residue 1376 TYR Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1646 THR Chi-restraints excluded: chain D residue 1668 LEU Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 1737 ILE Chi-restraints excluded: chain D residue 1831 ILE Chi-restraints excluded: chain D residue 1843 ILE Chi-restraints excluded: chain D residue 1921 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2079 LEU Chi-restraints excluded: chain D residue 2106 THR Chi-restraints excluded: chain D residue 2110 VAL Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2215 ASP Chi-restraints excluded: chain D residue 2236 SER Chi-restraints excluded: chain D residue 2276 CYS Chi-restraints excluded: chain D residue 2320 VAL Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2761 LEU Chi-restraints excluded: chain D residue 2877 THR Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 3628 ILE Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3771 THR Chi-restraints excluded: chain D residue 3818 MET Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3864 ASN Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3866 THR Chi-restraints excluded: chain D residue 3867 VAL Chi-restraints excluded: chain D residue 3966 LEU Chi-restraints excluded: chain D residue 4077 LEU Chi-restraints excluded: chain D residue 4092 ASP Chi-restraints excluded: chain D residue 4124 VAL Chi-restraints excluded: chain D residue 4140 SER Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4187 LEU Chi-restraints excluded: chain D residue 4509 PHE Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4574 LEU Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4714 THR Chi-restraints excluded: chain D residue 4781 THR Chi-restraints excluded: chain D residue 4799 ASP Chi-restraints excluded: chain D residue 4803 MET Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 95 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1544 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 912 optimal weight: 9.9990 chunk 1170 optimal weight: 2.9990 chunk 906 optimal weight: 20.0000 chunk 1348 optimal weight: 9.9990 chunk 894 optimal weight: 9.9990 chunk 1596 optimal weight: 1.9990 chunk 998 optimal weight: 7.9990 chunk 973 optimal weight: 1.9990 chunk 736 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4054 HIS A4486 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4054 HIS C4486 GLN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 HIS ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1973 ASN ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 125876 Z= 0.178 Angle : 0.538 9.273 170664 Z= 0.275 Chirality : 0.037 0.236 19404 Planarity : 0.004 0.057 22256 Dihedral : 4.631 59.621 17721 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.90 % Allowed : 21.60 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.07), residues: 13424 helix: 0.85 (0.07), residues: 6488 sheet: -1.54 (0.14), residues: 1380 loop : -2.31 (0.08), residues: 5556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.001 TRP B4479 HIS 0.010 0.001 HIS D 202 PHE 0.020 0.001 PHE C4064 TYR 0.014 0.001 TYR B3876 ARG 0.014 0.000 ARG B2326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1641 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 460 poor density : 1181 time to evaluate : 9.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7680 (mmmt) cc_final: 0.7428 (mmmt) REVERT: A 176 ARG cc_start: 0.8358 (mpp80) cc_final: 0.8096 (mpp80) REVERT: A 191 TYR cc_start: 0.8251 (m-80) cc_final: 0.7490 (m-80) REVERT: A 272 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.6291 (ptt90) REVERT: A 506 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.6701 (m-70) REVERT: A 651 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.8146 (m-70) REVERT: A 1232 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 2191 MET cc_start: 0.8314 (tpp) cc_final: 0.8004 (tpt) REVERT: A 2222 GLU cc_start: 0.6906 (tp30) cc_final: 0.6602 (tp30) REVERT: A 2335 ARG cc_start: 0.6749 (ttp80) cc_final: 0.6445 (tmt-80) REVERT: A 2776 GLU cc_start: 0.0986 (OUTLIER) cc_final: 0.0552 (tp30) REVERT: A 3905 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8112 (t80) REVERT: A 4034 TYR cc_start: 0.5907 (t80) cc_final: 0.5471 (t80) REVERT: A 4108 MET cc_start: 0.7533 (tpt) cc_final: 0.7302 (tpt) REVERT: A 4574 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8365 (mp) REVERT: A 4645 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7138 (p0) REVERT: G 50 ARG cc_start: 0.7232 (mtp-110) cc_final: 0.6967 (mtp85) REVERT: B 56 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7420 (mmmt) REVERT: B 191 TYR cc_start: 0.8216 (m-80) cc_final: 0.7460 (m-80) REVERT: B 506 HIS cc_start: 0.7267 (OUTLIER) cc_final: 0.6811 (m-70) REVERT: B 651 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.8194 (m-70) REVERT: B 1050 LEU cc_start: 0.2709 (OUTLIER) cc_final: 0.2448 (mm) REVERT: B 1232 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8118 (tt) REVERT: B 1606 LYS cc_start: 0.7984 (tmtt) cc_final: 0.7773 (tptm) REVERT: B 2191 MET cc_start: 0.8300 (tpp) cc_final: 0.7986 (tpt) REVERT: B 2335 ARG cc_start: 0.6701 (ttp80) cc_final: 0.6410 (tmt-80) REVERT: B 2718 TYR cc_start: 0.3925 (OUTLIER) cc_final: 0.3359 (m-80) REVERT: B 2756 MET cc_start: 0.3002 (mmt) cc_final: 0.2084 (mmt) REVERT: B 2776 GLU cc_start: 0.0721 (OUTLIER) cc_final: 0.0322 (tp30) REVERT: B 2891 ILE cc_start: -0.3307 (OUTLIER) cc_final: -0.3557 (pt) REVERT: B 3905 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8075 (t80) REVERT: B 4034 TYR cc_start: 0.6088 (t80) cc_final: 0.5608 (t80) REVERT: B 4574 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 4645 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7103 (p0) REVERT: B 4898 ASP cc_start: 0.8131 (m-30) cc_final: 0.7650 (m-30) REVERT: H 50 ARG cc_start: 0.7230 (mtp-110) cc_final: 0.7012 (mtp85) REVERT: C 56 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7412 (mmmt) REVERT: C 191 TYR cc_start: 0.8198 (m-80) cc_final: 0.7440 (m-80) REVERT: C 506 HIS cc_start: 0.7287 (OUTLIER) cc_final: 0.6823 (m-70) REVERT: C 651 HIS cc_start: 0.8428 (OUTLIER) cc_final: 0.8157 (m-70) REVERT: C 1050 LEU cc_start: 0.2713 (OUTLIER) cc_final: 0.2459 (mm) REVERT: C 1232 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8215 (tt) REVERT: C 2191 MET cc_start: 0.8335 (tpp) cc_final: 0.8033 (tpt) REVERT: C 2222 GLU cc_start: 0.6919 (tp30) cc_final: 0.6603 (tp30) REVERT: C 2335 ARG cc_start: 0.6774 (ttp80) cc_final: 0.6422 (tmt-80) REVERT: C 2425 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7887 (mp) REVERT: C 2506 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5858 (pp) REVERT: C 2718 TYR cc_start: 0.3862 (OUTLIER) cc_final: 0.3352 (m-80) REVERT: C 2756 MET cc_start: 0.3004 (mmt) cc_final: 0.2064 (mmt) REVERT: C 2776 GLU cc_start: 0.0774 (OUTLIER) cc_final: 0.0398 (tp30) REVERT: C 3905 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8092 (t80) REVERT: C 4034 TYR cc_start: 0.6051 (t80) cc_final: 0.5577 (t80) REVERT: C 4574 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8398 (mp) REVERT: C 4645 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7177 (p0) REVERT: C 4898 ASP cc_start: 0.8166 (m-30) cc_final: 0.7678 (m-30) REVERT: C 4942 MET cc_start: 0.8683 (mmm) cc_final: 0.8104 (mtt) REVERT: I 33 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8604 (p0) REVERT: D 191 TYR cc_start: 0.8223 (m-80) cc_final: 0.7449 (m-80) REVERT: D 202 HIS cc_start: 0.5591 (m90) cc_final: 0.5262 (m90) REVERT: D 319 LYS cc_start: 0.5871 (mtpp) cc_final: 0.5612 (mmmt) REVERT: D 564 ARG cc_start: 0.7512 (tpp-160) cc_final: 0.5854 (tpp80) REVERT: D 651 HIS cc_start: 0.8437 (OUTLIER) cc_final: 0.8153 (m-70) REVERT: D 691 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7710 (p) REVERT: D 1050 LEU cc_start: 0.2735 (OUTLIER) cc_final: 0.2473 (mm) REVERT: D 1232 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8128 (tt) REVERT: D 1344 GLU cc_start: 0.4860 (tt0) cc_final: 0.4625 (tt0) REVERT: D 2335 ARG cc_start: 0.6663 (ttp80) cc_final: 0.6370 (tmt-80) REVERT: D 2718 TYR cc_start: 0.3848 (OUTLIER) cc_final: 0.3348 (m-80) REVERT: D 2776 GLU cc_start: 0.0874 (OUTLIER) cc_final: 0.0482 (tp30) REVERT: D 3905 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8096 (t80) REVERT: D 4034 TYR cc_start: 0.6135 (t80) cc_final: 0.5626 (t80) REVERT: D 4574 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8386 (mp) REVERT: D 4645 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7118 (p0) REVERT: D 4942 MET cc_start: 0.8637 (mmm) cc_final: 0.8084 (mmm) outliers start: 460 outliers final: 317 residues processed: 1545 average time/residue: 0.9742 time to fit residues: 2676.4146 Evaluate side-chains 1464 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 1108 time to evaluate : 9.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1309 GLU Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1372 ASN Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1646 THR Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1737 ILE Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2197 ARG Chi-restraints excluded: chain A residue 2236 SER Chi-restraints excluded: chain A residue 2276 CYS Chi-restraints excluded: chain A residue 2320 VAL Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2776 GLU Chi-restraints excluded: chain A residue 2848 HIS Chi-restraints excluded: chain A residue 2877 THR Chi-restraints excluded: chain A residue 2891 ILE Chi-restraints excluded: chain A residue 3628 ILE Chi-restraints excluded: chain A residue 3771 THR Chi-restraints excluded: chain A residue 3800 SER Chi-restraints excluded: chain A residue 3818 MET Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3864 ASN Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 3966 LEU Chi-restraints excluded: chain A residue 4055 LYS Chi-restraints excluded: chain A residue 4077 LEU Chi-restraints excluded: chain A residue 4092 ASP Chi-restraints excluded: chain A residue 4124 VAL Chi-restraints excluded: chain A residue 4140 SER Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4509 PHE Chi-restraints excluded: chain A residue 4559 VAL Chi-restraints excluded: chain A residue 4574 LEU Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4645 ASP Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4781 THR Chi-restraints excluded: chain A residue 4799 ASP Chi-restraints excluded: chain A residue 4803 MET Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4847 ILE Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 713 TRP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1161 VAL Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1199 ASP Chi-restraints excluded: chain B residue 1212 VAL Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1309 GLU Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1372 ASN Chi-restraints excluded: chain B residue 1620 VAL Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1646 THR Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1737 ILE Chi-restraints excluded: chain B residue 1921 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2106 THR Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2215 ASP Chi-restraints excluded: chain B residue 2236 SER Chi-restraints excluded: chain B residue 2276 CYS Chi-restraints excluded: chain B residue 2320 VAL Chi-restraints excluded: chain B residue 2389 THR Chi-restraints excluded: chain B residue 2718 TYR Chi-restraints excluded: chain B residue 2776 GLU Chi-restraints excluded: chain B residue 2877 THR Chi-restraints excluded: chain B residue 2891 ILE Chi-restraints excluded: chain B residue 2901 VAL Chi-restraints excluded: chain B residue 3628 ILE Chi-restraints excluded: chain B residue 3771 THR Chi-restraints excluded: chain B residue 3800 SER Chi-restraints excluded: chain B residue 3818 MET Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3864 ASN Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3866 THR Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 4077 LEU Chi-restraints excluded: chain B residue 4092 ASP Chi-restraints excluded: chain B residue 4124 VAL Chi-restraints excluded: chain B residue 4140 SER Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4509 PHE Chi-restraints excluded: chain B residue 4574 LEU Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4799 ASP Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4847 ILE Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 506 HIS Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 713 TRP Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1050 LEU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1300 MET Chi-restraints excluded: chain C residue 1309 GLU Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1372 ASN Chi-restraints excluded: chain C residue 1589 VAL Chi-restraints excluded: chain C residue 1620 VAL Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1646 THR Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1737 ILE Chi-restraints excluded: chain C residue 1831 ILE Chi-restraints excluded: chain C residue 1921 ILE Chi-restraints excluded: chain C residue 1975 LEU Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2079 LEU Chi-restraints excluded: chain C residue 2110 VAL Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2236 SER Chi-restraints excluded: chain C residue 2276 CYS Chi-restraints excluded: chain C residue 2320 VAL Chi-restraints excluded: chain C residue 2425 LEU Chi-restraints excluded: chain C residue 2506 LEU Chi-restraints excluded: chain C residue 2718 TYR Chi-restraints excluded: chain C residue 2776 GLU Chi-restraints excluded: chain C residue 2877 THR Chi-restraints excluded: chain C residue 2891 ILE Chi-restraints excluded: chain C residue 2901 VAL Chi-restraints excluded: chain C residue 3628 ILE Chi-restraints excluded: chain C residue 3771 THR Chi-restraints excluded: chain C residue 3800 SER Chi-restraints excluded: chain C residue 3818 MET Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3864 ASN Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 4077 LEU Chi-restraints excluded: chain C residue 4092 ASP Chi-restraints excluded: chain C residue 4124 VAL Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4187 LEU Chi-restraints excluded: chain C residue 4509 PHE Chi-restraints excluded: chain C residue 4574 LEU Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4799 ASP Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 270 HIS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 713 TRP Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 784 ILE Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1164 CYS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1212 VAL Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1273 ILE Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1372 ASN Chi-restraints excluded: chain D residue 1376 TYR Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1646 THR Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 1737 ILE Chi-restraints excluded: chain D residue 1831 ILE Chi-restraints excluded: chain D residue 1921 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2079 LEU Chi-restraints excluded: chain D residue 2110 VAL Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2215 ASP Chi-restraints excluded: chain D residue 2236 SER Chi-restraints excluded: chain D residue 2276 CYS Chi-restraints excluded: chain D residue 2320 VAL Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2718 TYR Chi-restraints excluded: chain D residue 2776 GLU Chi-restraints excluded: chain D residue 2877 THR Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 2901 VAL Chi-restraints excluded: chain D residue 3628 ILE Chi-restraints excluded: chain D residue 3771 THR Chi-restraints excluded: chain D residue 3800 SER Chi-restraints excluded: chain D residue 3818 MET Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3864 ASN Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 4077 LEU Chi-restraints excluded: chain D residue 4092 ASP Chi-restraints excluded: chain D residue 4124 VAL Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4187 LEU Chi-restraints excluded: chain D residue 4509 PHE Chi-restraints excluded: chain D residue 4574 LEU Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4781 THR Chi-restraints excluded: chain D residue 4799 ASP Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4847 ILE Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 95 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 987 optimal weight: 10.0000 chunk 637 optimal weight: 20.0000 chunk 953 optimal weight: 8.9990 chunk 480 optimal weight: 10.0000 chunk 313 optimal weight: 3.9990 chunk 309 optimal weight: 0.9980 chunk 1014 optimal weight: 4.9990 chunk 1087 optimal weight: 40.0000 chunk 789 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 1254 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4054 HIS A4486 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2848 HIS ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3774 GLN ** B3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 HIS B4486 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1973 ASN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4054 HIS C4486 GLN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1973 ASN ** D2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4486 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 125876 Z= 0.322 Angle : 0.611 8.694 170664 Z= 0.313 Chirality : 0.040 0.237 19404 Planarity : 0.004 0.062 22256 Dihedral : 4.834 59.134 17708 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.18 % Allowed : 21.89 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.07), residues: 13424 helix: 0.71 (0.07), residues: 6452 sheet: -1.59 (0.14), residues: 1376 loop : -2.33 (0.08), residues: 5596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP C4479 HIS 0.009 0.001 HIS D 270 PHE 0.025 0.002 PHE B1740 TYR 0.021 0.002 TYR D1777 ARG 0.015 0.000 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1590 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 493 poor density : 1097 time to evaluate : 9.310 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: A 191 TYR cc_start: 0.8259 (m-80) cc_final: 0.7334 (m-80) REVERT: A 201 TRP cc_start: 0.5903 (m100) cc_final: 0.5415 (m100) REVERT: A 506 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.6828 (m-70) REVERT: A 651 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8231 (m-70) REVERT: A 691 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7681 (p) REVERT: A 1224 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5587 (mp) REVERT: A 1232 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8271 (tt) REVERT: A 2222 GLU cc_start: 0.7121 (tp30) cc_final: 0.6818 (tp30) REVERT: A 2335 ARG cc_start: 0.6759 (ttp80) cc_final: 0.6455 (tmt-80) REVERT: A 2756 MET cc_start: 0.2572 (mmt) cc_final: 0.1920 (tpp) REVERT: A 2776 GLU cc_start: 0.0857 (OUTLIER) cc_final: 0.0464 (tp30) REVERT: A 2843 MET cc_start: 0.0738 (tpp) cc_final: 0.0477 (tpt) REVERT: A 3905 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8283 (t80) REVERT: A 4108 MET cc_start: 0.7601 (tpt) cc_final: 0.7365 (tpt) REVERT: A 4574 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 4645 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7331 (p0) REVERT: A 4942 MET cc_start: 0.8650 (mmm) cc_final: 0.8081 (mtt) REVERT: B 191 TYR cc_start: 0.8268 (m-80) cc_final: 0.7467 (m-80) REVERT: B 506 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.6847 (m-70) REVERT: B 651 HIS cc_start: 0.8450 (OUTLIER) cc_final: 0.8208 (m-70) REVERT: B 691 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7740 (p) REVERT: B 1050 LEU cc_start: 0.2713 (OUTLIER) cc_final: 0.2449 (mm) REVERT: B 1224 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5526 (mp) REVERT: B 1232 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8208 (tt) REVERT: B 1606 LYS cc_start: 0.8022 (tmtt) cc_final: 0.7816 (tptm) REVERT: B 2222 GLU cc_start: 0.6975 (tp30) cc_final: 0.6689 (tp30) REVERT: B 2335 ARG cc_start: 0.6753 (ttp80) cc_final: 0.6465 (tmt-80) REVERT: B 2718 TYR cc_start: 0.3973 (OUTLIER) cc_final: 0.3419 (m-80) REVERT: B 2756 MET cc_start: 0.2206 (mmt) cc_final: 0.1613 (tpp) REVERT: B 2776 GLU cc_start: 0.0736 (OUTLIER) cc_final: 0.0340 (tp30) REVERT: B 2891 ILE cc_start: -0.3293 (OUTLIER) cc_final: -0.3580 (pt) REVERT: B 3905 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8212 (t80) REVERT: B 4574 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8342 (mp) REVERT: B 4645 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7297 (p0) REVERT: H 33 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8537 (p0) REVERT: C 191 TYR cc_start: 0.8244 (m-80) cc_final: 0.7342 (m-80) REVERT: C 506 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6863 (m-70) REVERT: C 651 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.8246 (m-70) REVERT: C 691 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7717 (p) REVERT: C 1050 LEU cc_start: 0.2724 (OUTLIER) cc_final: 0.2464 (mm) REVERT: C 1224 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5537 (mp) REVERT: C 1232 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8258 (tt) REVERT: C 2222 GLU cc_start: 0.6974 (tp30) cc_final: 0.6669 (tp30) REVERT: C 2335 ARG cc_start: 0.6742 (ttp80) cc_final: 0.6441 (tmt-80) REVERT: C 2506 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5800 (pp) REVERT: C 2718 TYR cc_start: 0.3966 (OUTLIER) cc_final: 0.3473 (m-80) REVERT: C 2756 MET cc_start: 0.2607 (mmt) cc_final: 0.2088 (tpp) REVERT: C 2776 GLU cc_start: 0.0706 (OUTLIER) cc_final: 0.0312 (tp30) REVERT: C 3905 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8235 (t80) REVERT: C 4574 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8371 (mp) REVERT: C 4645 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7370 (p0) REVERT: C 4942 MET cc_start: 0.8693 (mmm) cc_final: 0.8180 (mtt) REVERT: I 33 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8593 (p0) REVERT: D 56 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7464 (mmmt) REVERT: D 191 TYR cc_start: 0.8279 (m-80) cc_final: 0.7433 (m-80) REVERT: D 319 LYS cc_start: 0.5869 (mtpp) cc_final: 0.5603 (mmmt) REVERT: D 564 ARG cc_start: 0.7576 (tpp-160) cc_final: 0.6349 (tpp-160) REVERT: D 651 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.8241 (m-70) REVERT: D 691 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7715 (p) REVERT: D 981 MET cc_start: 0.2304 (ppp) cc_final: 0.1990 (ppp) REVERT: D 1050 LEU cc_start: 0.2741 (OUTLIER) cc_final: 0.2472 (mm) REVERT: D 1232 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8199 (tt) REVERT: D 2222 GLU cc_start: 0.6967 (tp30) cc_final: 0.6676 (tp30) REVERT: D 2335 ARG cc_start: 0.6724 (ttp80) cc_final: 0.6433 (tmt-80) REVERT: D 2718 TYR cc_start: 0.3962 (OUTLIER) cc_final: 0.3476 (m-80) REVERT: D 2756 MET cc_start: 0.2550 (mmt) cc_final: 0.1933 (tpp) REVERT: D 2776 GLU cc_start: 0.0907 (OUTLIER) cc_final: 0.0480 (tp30) REVERT: D 2891 ILE cc_start: -0.3305 (OUTLIER) cc_final: -0.3599 (pt) REVERT: D 3905 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8281 (t80) REVERT: D 4084 LYS cc_start: 0.8648 (mptt) cc_final: 0.8408 (mmtt) REVERT: D 4574 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8401 (mp) REVERT: D 4645 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7311 (p0) REVERT: D 4942 MET cc_start: 0.8662 (mmm) cc_final: 0.8111 (mtt) outliers start: 493 outliers final: 386 residues processed: 1494 average time/residue: 0.9519 time to fit residues: 2539.8563 Evaluate side-chains 1503 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 431 poor density : 1072 time to evaluate : 9.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1646 THR Chi-restraints excluded: chain A residue 1668 LEU Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1737 ILE Chi-restraints excluded: chain A residue 1843 ILE Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2197 ARG Chi-restraints excluded: chain A residue 2236 SER Chi-restraints excluded: chain A residue 2276 CYS Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2320 VAL Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2776 GLU Chi-restraints excluded: chain A residue 2848 HIS Chi-restraints excluded: chain A residue 2877 THR Chi-restraints excluded: chain A residue 3628 ILE Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3771 THR Chi-restraints excluded: chain A residue 3800 SER Chi-restraints excluded: chain A residue 3818 MET Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3864 ASN Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3867 VAL Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 3966 LEU Chi-restraints excluded: chain A residue 4055 LYS Chi-restraints excluded: chain A residue 4077 LEU Chi-restraints excluded: chain A residue 4092 ASP Chi-restraints excluded: chain A residue 4124 VAL Chi-restraints excluded: chain A residue 4140 SER Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4486 GLN Chi-restraints excluded: chain A residue 4509 PHE Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4559 VAL Chi-restraints excluded: chain A residue 4574 LEU Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4645 ASP Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4781 THR Chi-restraints excluded: chain A residue 4799 ASP Chi-restraints excluded: chain A residue 4803 MET Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4847 ILE Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain A residue 4881 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 577 CYS Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 713 TRP Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1161 VAL Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1199 ASP Chi-restraints excluded: chain B residue 1212 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1572 PHE Chi-restraints excluded: chain B residue 1589 VAL Chi-restraints excluded: chain B residue 1620 VAL Chi-restraints excluded: chain B residue 1646 THR Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1737 ILE Chi-restraints excluded: chain B residue 1843 ILE Chi-restraints excluded: chain B residue 1921 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2106 THR Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2215 ASP Chi-restraints excluded: chain B residue 2236 SER Chi-restraints excluded: chain B residue 2276 CYS Chi-restraints excluded: chain B residue 2292 VAL Chi-restraints excluded: chain B residue 2320 VAL Chi-restraints excluded: chain B residue 2389 THR Chi-restraints excluded: chain B residue 2718 TYR Chi-restraints excluded: chain B residue 2776 GLU Chi-restraints excluded: chain B residue 2877 THR Chi-restraints excluded: chain B residue 2891 ILE Chi-restraints excluded: chain B residue 2901 VAL Chi-restraints excluded: chain B residue 3628 ILE Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3771 THR Chi-restraints excluded: chain B residue 3800 SER Chi-restraints excluded: chain B residue 3818 MET Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3864 ASN Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3866 THR Chi-restraints excluded: chain B residue 3867 VAL Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3947 LEU Chi-restraints excluded: chain B residue 4077 LEU Chi-restraints excluded: chain B residue 4124 VAL Chi-restraints excluded: chain B residue 4140 SER Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4509 PHE Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4559 VAL Chi-restraints excluded: chain B residue 4574 LEU Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4799 ASP Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain B residue 4881 GLU Chi-restraints excluded: chain B residue 4942 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 506 HIS Chi-restraints excluded: chain C residue 577 CYS Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 713 TRP Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1050 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1164 CYS Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1224 LEU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1309 GLU Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1589 VAL Chi-restraints excluded: chain C residue 1620 VAL Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1646 THR Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1737 ILE Chi-restraints excluded: chain C residue 1843 ILE Chi-restraints excluded: chain C residue 1921 ILE Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2079 LEU Chi-restraints excluded: chain C residue 2106 THR Chi-restraints excluded: chain C residue 2110 VAL Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2236 SER Chi-restraints excluded: chain C residue 2276 CYS Chi-restraints excluded: chain C residue 2292 VAL Chi-restraints excluded: chain C residue 2320 VAL Chi-restraints excluded: chain C residue 2389 THR Chi-restraints excluded: chain C residue 2506 LEU Chi-restraints excluded: chain C residue 2718 TYR Chi-restraints excluded: chain C residue 2776 GLU Chi-restraints excluded: chain C residue 2848 HIS Chi-restraints excluded: chain C residue 2877 THR Chi-restraints excluded: chain C residue 2891 ILE Chi-restraints excluded: chain C residue 2901 VAL Chi-restraints excluded: chain C residue 3628 ILE Chi-restraints excluded: chain C residue 3676 THR Chi-restraints excluded: chain C residue 3771 THR Chi-restraints excluded: chain C residue 3800 SER Chi-restraints excluded: chain C residue 3818 MET Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3864 ASN Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 3867 VAL Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3947 LEU Chi-restraints excluded: chain C residue 4092 ASP Chi-restraints excluded: chain C residue 4124 VAL Chi-restraints excluded: chain C residue 4140 SER Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4187 LEU Chi-restraints excluded: chain C residue 4486 GLN Chi-restraints excluded: chain C residue 4509 PHE Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4559 VAL Chi-restraints excluded: chain C residue 4574 LEU Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4799 ASP Chi-restraints excluded: chain C residue 4847 ILE Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain C residue 4881 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 577 CYS Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 713 TRP Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 784 ILE Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1164 CYS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1199 ASP Chi-restraints excluded: chain D residue 1212 VAL Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1273 ILE Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1376 TYR Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1646 THR Chi-restraints excluded: chain D residue 1668 LEU Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 1737 ILE Chi-restraints excluded: chain D residue 1843 ILE Chi-restraints excluded: chain D residue 1921 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2079 LEU Chi-restraints excluded: chain D residue 2106 THR Chi-restraints excluded: chain D residue 2110 VAL Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2215 ASP Chi-restraints excluded: chain D residue 2236 SER Chi-restraints excluded: chain D residue 2276 CYS Chi-restraints excluded: chain D residue 2292 VAL Chi-restraints excluded: chain D residue 2320 VAL Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2481 ASP Chi-restraints excluded: chain D residue 2718 TYR Chi-restraints excluded: chain D residue 2776 GLU Chi-restraints excluded: chain D residue 2848 HIS Chi-restraints excluded: chain D residue 2877 THR Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 2901 VAL Chi-restraints excluded: chain D residue 3628 ILE Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3771 THR Chi-restraints excluded: chain D residue 3800 SER Chi-restraints excluded: chain D residue 3818 MET Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3864 ASN Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3866 THR Chi-restraints excluded: chain D residue 3867 VAL Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3947 LEU Chi-restraints excluded: chain D residue 4077 LEU Chi-restraints excluded: chain D residue 4092 ASP Chi-restraints excluded: chain D residue 4124 VAL Chi-restraints excluded: chain D residue 4140 SER Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4187 LEU Chi-restraints excluded: chain D residue 4509 PHE Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4559 VAL Chi-restraints excluded: chain D residue 4574 LEU Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4781 THR Chi-restraints excluded: chain D residue 4799 ASP Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4847 ILE Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain D residue 4881 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 95 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1451 optimal weight: 0.8980 chunk 1529 optimal weight: 30.0000 chunk 1395 optimal weight: 0.6980 chunk 1487 optimal weight: 20.0000 chunk 1528 optimal weight: 20.0000 chunk 895 optimal weight: 3.9990 chunk 647 optimal weight: 10.0000 chunk 1167 optimal weight: 0.3980 chunk 456 optimal weight: 5.9990 chunk 1344 optimal weight: 8.9990 chunk 1406 optimal weight: 8.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4054 HIS A4486 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 HIS B4486 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1973 ASN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4054 HIS C4486 GLN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1973 ASN ** D2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4486 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 125876 Z= 0.259 Angle : 0.585 9.776 170664 Z= 0.299 Chirality : 0.039 0.225 19404 Planarity : 0.004 0.063 22256 Dihedral : 4.736 58.540 17708 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.04 % Allowed : 22.36 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.07), residues: 13424 helix: 0.77 (0.07), residues: 6472 sheet: -1.49 (0.14), residues: 1360 loop : -2.33 (0.08), residues: 5592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.001 TRP D4479 HIS 0.018 0.001 HIS D 270 PHE 0.022 0.002 PHE C1740 TYR 0.021 0.002 TYR C4079 ARG 0.015 0.000 ARG C2326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1587 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 477 poor density : 1110 time to evaluate : 9.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7407 (mmmt) REVERT: A 176 ARG cc_start: 0.8400 (mpp80) cc_final: 0.8196 (mpp80) REVERT: A 191 TYR cc_start: 0.8256 (m-80) cc_final: 0.7349 (m-80) REVERT: A 201 TRP cc_start: 0.5771 (m100) cc_final: 0.5123 (m100) REVERT: A 506 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.6871 (m-70) REVERT: A 644 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8750 (tp) REVERT: A 651 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.8199 (m-70) REVERT: A 691 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7647 (p) REVERT: A 1232 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8278 (tt) REVERT: A 2222 GLU cc_start: 0.7112 (tp30) cc_final: 0.6809 (tp30) REVERT: A 2335 ARG cc_start: 0.6740 (ttp80) cc_final: 0.6423 (tmt-80) REVERT: A 2756 MET cc_start: 0.2749 (mmt) cc_final: 0.2181 (tpp) REVERT: A 2776 GLU cc_start: 0.0861 (OUTLIER) cc_final: 0.0473 (tp30) REVERT: A 3905 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8258 (t80) REVERT: A 4051 MET cc_start: 0.5604 (ptm) cc_final: 0.5355 (ptm) REVERT: A 4108 MET cc_start: 0.7601 (tpt) cc_final: 0.7350 (tpt) REVERT: A 4574 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 4645 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7334 (p0) REVERT: A 4898 ASP cc_start: 0.8271 (m-30) cc_final: 0.7983 (m-30) REVERT: A 4942 MET cc_start: 0.8610 (mmm) cc_final: 0.7986 (mtt) REVERT: B 191 TYR cc_start: 0.8263 (m-80) cc_final: 0.7431 (m-80) REVERT: B 506 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6796 (m-70) REVERT: B 691 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7721 (p) REVERT: B 1050 LEU cc_start: 0.2946 (OUTLIER) cc_final: 0.2621 (mm) REVERT: B 1224 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5599 (mp) REVERT: B 1232 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8222 (tt) REVERT: B 1606 LYS cc_start: 0.8002 (tmtt) cc_final: 0.7796 (tptm) REVERT: B 2191 MET cc_start: 0.8267 (tpp) cc_final: 0.7924 (tpt) REVERT: B 2222 GLU cc_start: 0.6965 (tp30) cc_final: 0.6678 (tp30) REVERT: B 2335 ARG cc_start: 0.6737 (ttp80) cc_final: 0.6446 (tmt-80) REVERT: B 2718 TYR cc_start: 0.3982 (OUTLIER) cc_final: 0.3424 (m-80) REVERT: B 2756 MET cc_start: 0.2473 (mmt) cc_final: 0.2022 (tpp) REVERT: B 2776 GLU cc_start: 0.0717 (OUTLIER) cc_final: 0.0322 (tp30) REVERT: B 3905 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8191 (t80) REVERT: B 4574 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8380 (mp) REVERT: B 4645 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7294 (p0) REVERT: H 33 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8512 (p0) REVERT: H 75 LEU cc_start: 0.8407 (mp) cc_final: 0.8013 (mt) REVERT: C 191 TYR cc_start: 0.8288 (m-80) cc_final: 0.7475 (m-80) REVERT: C 506 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.6843 (m-70) REVERT: C 644 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8734 (tp) REVERT: C 651 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.8207 (m-70) REVERT: C 691 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7705 (p) REVERT: C 1050 LEU cc_start: 0.2947 (OUTLIER) cc_final: 0.2632 (mm) REVERT: C 1232 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8264 (tt) REVERT: C 2191 MET cc_start: 0.8301 (tpp) cc_final: 0.7969 (tpt) REVERT: C 2222 GLU cc_start: 0.6962 (tp30) cc_final: 0.6656 (tp30) REVERT: C 2335 ARG cc_start: 0.6803 (ttp80) cc_final: 0.6502 (tmt-80) REVERT: C 2425 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7847 (mp) REVERT: C 2506 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5827 (pp) REVERT: C 2718 TYR cc_start: 0.3971 (OUTLIER) cc_final: 0.3476 (m-80) REVERT: C 2756 MET cc_start: 0.2638 (mmt) cc_final: 0.2177 (tpp) REVERT: C 2776 GLU cc_start: 0.0694 (OUTLIER) cc_final: 0.0301 (tp30) REVERT: C 3905 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8250 (t80) REVERT: C 4051 MET cc_start: 0.5608 (ptm) cc_final: 0.5405 (ptm) REVERT: C 4574 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8379 (mp) REVERT: C 4645 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7365 (p0) REVERT: C 4942 MET cc_start: 0.8677 (mmm) cc_final: 0.8137 (mtt) REVERT: I 33 ASN cc_start: 0.9085 (OUTLIER) cc_final: 0.8542 (p0) REVERT: I 75 LEU cc_start: 0.8418 (mp) cc_final: 0.8036 (mt) REVERT: D 56 LYS cc_start: 0.7713 (mmmt) cc_final: 0.7459 (mmmt) REVERT: D 191 TYR cc_start: 0.8307 (m-80) cc_final: 0.7483 (m-80) REVERT: D 319 LYS cc_start: 0.5890 (mtpp) cc_final: 0.5612 (mmmt) REVERT: D 564 ARG cc_start: 0.7284 (tpp-160) cc_final: 0.5691 (tpp80) REVERT: D 651 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.8214 (m-70) REVERT: D 691 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7701 (p) REVERT: D 1050 LEU cc_start: 0.2726 (OUTLIER) cc_final: 0.2454 (mm) REVERT: D 1232 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8276 (tt) REVERT: D 2222 GLU cc_start: 0.6954 (tp30) cc_final: 0.6678 (tp30) REVERT: D 2335 ARG cc_start: 0.6711 (ttp80) cc_final: 0.6413 (tmt-80) REVERT: D 2718 TYR cc_start: 0.3966 (OUTLIER) cc_final: 0.3480 (m-80) REVERT: D 2756 MET cc_start: 0.2627 (mmt) cc_final: 0.2145 (tpp) REVERT: D 2776 GLU cc_start: 0.0907 (OUTLIER) cc_final: 0.0483 (tp30) REVERT: D 2891 ILE cc_start: -0.3002 (OUTLIER) cc_final: -0.3253 (pt) REVERT: D 3905 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8244 (t80) REVERT: D 4084 LYS cc_start: 0.8622 (mptt) cc_final: 0.8380 (mmtt) REVERT: D 4574 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8374 (mp) REVERT: D 4645 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7298 (p0) REVERT: D 4898 ASP cc_start: 0.8271 (m-30) cc_final: 0.7874 (m-30) REVERT: D 4942 MET cc_start: 0.8634 (mmm) cc_final: 0.8119 (mtt) outliers start: 477 outliers final: 384 residues processed: 1497 average time/residue: 0.9606 time to fit residues: 2560.5013 Evaluate side-chains 1513 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 428 poor density : 1085 time to evaluate : 11.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1646 THR Chi-restraints excluded: chain A residue 1668 LEU Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1737 ILE Chi-restraints excluded: chain A residue 1843 ILE Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2197 ARG Chi-restraints excluded: chain A residue 2236 SER Chi-restraints excluded: chain A residue 2276 CYS Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2320 VAL Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2776 GLU Chi-restraints excluded: chain A residue 2848 HIS Chi-restraints excluded: chain A residue 2877 THR Chi-restraints excluded: chain A residue 3628 ILE Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3771 THR Chi-restraints excluded: chain A residue 3800 SER Chi-restraints excluded: chain A residue 3818 MET Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3864 ASN Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3867 VAL Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 3966 LEU Chi-restraints excluded: chain A residue 4055 LYS Chi-restraints excluded: chain A residue 4077 LEU Chi-restraints excluded: chain A residue 4092 ASP Chi-restraints excluded: chain A residue 4124 VAL Chi-restraints excluded: chain A residue 4140 SER Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4509 PHE Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4559 VAL Chi-restraints excluded: chain A residue 4574 LEU Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4645 ASP Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4781 THR Chi-restraints excluded: chain A residue 4799 ASP Chi-restraints excluded: chain A residue 4803 MET Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4847 ILE Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain A residue 4881 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 577 CYS Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 713 TRP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1161 VAL Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1199 ASP Chi-restraints excluded: chain B residue 1212 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1589 VAL Chi-restraints excluded: chain B residue 1620 VAL Chi-restraints excluded: chain B residue 1646 THR Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1737 ILE Chi-restraints excluded: chain B residue 1843 ILE Chi-restraints excluded: chain B residue 1921 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2106 THR Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2197 ARG Chi-restraints excluded: chain B residue 2215 ASP Chi-restraints excluded: chain B residue 2236 SER Chi-restraints excluded: chain B residue 2276 CYS Chi-restraints excluded: chain B residue 2292 VAL Chi-restraints excluded: chain B residue 2320 VAL Chi-restraints excluded: chain B residue 2389 THR Chi-restraints excluded: chain B residue 2718 TYR Chi-restraints excluded: chain B residue 2776 GLU Chi-restraints excluded: chain B residue 2877 THR Chi-restraints excluded: chain B residue 2901 VAL Chi-restraints excluded: chain B residue 3628 ILE Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3771 THR Chi-restraints excluded: chain B residue 3800 SER Chi-restraints excluded: chain B residue 3818 MET Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3864 ASN Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3866 THR Chi-restraints excluded: chain B residue 3867 VAL Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3947 LEU Chi-restraints excluded: chain B residue 3966 LEU Chi-restraints excluded: chain B residue 4077 LEU Chi-restraints excluded: chain B residue 4092 ASP Chi-restraints excluded: chain B residue 4124 VAL Chi-restraints excluded: chain B residue 4140 SER Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4486 GLN Chi-restraints excluded: chain B residue 4509 PHE Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4559 VAL Chi-restraints excluded: chain B residue 4574 LEU Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4799 ASP Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain B residue 4942 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 506 HIS Chi-restraints excluded: chain C residue 577 CYS Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 713 TRP Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1050 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1164 CYS Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1309 GLU Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1376 TYR Chi-restraints excluded: chain C residue 1589 VAL Chi-restraints excluded: chain C residue 1620 VAL Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1646 THR Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1737 ILE Chi-restraints excluded: chain C residue 1843 ILE Chi-restraints excluded: chain C residue 1921 ILE Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2079 LEU Chi-restraints excluded: chain C residue 2106 THR Chi-restraints excluded: chain C residue 2110 VAL Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2197 ARG Chi-restraints excluded: chain C residue 2236 SER Chi-restraints excluded: chain C residue 2276 CYS Chi-restraints excluded: chain C residue 2292 VAL Chi-restraints excluded: chain C residue 2320 VAL Chi-restraints excluded: chain C residue 2389 THR Chi-restraints excluded: chain C residue 2425 LEU Chi-restraints excluded: chain C residue 2506 LEU Chi-restraints excluded: chain C residue 2718 TYR Chi-restraints excluded: chain C residue 2776 GLU Chi-restraints excluded: chain C residue 2877 THR Chi-restraints excluded: chain C residue 2901 VAL Chi-restraints excluded: chain C residue 3628 ILE Chi-restraints excluded: chain C residue 3676 THR Chi-restraints excluded: chain C residue 3771 THR Chi-restraints excluded: chain C residue 3800 SER Chi-restraints excluded: chain C residue 3818 MET Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3864 ASN Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 3867 VAL Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3947 LEU Chi-restraints excluded: chain C residue 3966 LEU Chi-restraints excluded: chain C residue 4092 ASP Chi-restraints excluded: chain C residue 4124 VAL Chi-restraints excluded: chain C residue 4140 SER Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4187 LEU Chi-restraints excluded: chain C residue 4509 PHE Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4559 VAL Chi-restraints excluded: chain C residue 4574 LEU Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4799 ASP Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 713 TRP Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 784 ILE Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1199 ASP Chi-restraints excluded: chain D residue 1212 VAL Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1273 ILE Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1376 TYR Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1646 THR Chi-restraints excluded: chain D residue 1668 LEU Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 1737 ILE Chi-restraints excluded: chain D residue 1843 ILE Chi-restraints excluded: chain D residue 1921 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2079 LEU Chi-restraints excluded: chain D residue 2106 THR Chi-restraints excluded: chain D residue 2110 VAL Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2215 ASP Chi-restraints excluded: chain D residue 2236 SER Chi-restraints excluded: chain D residue 2276 CYS Chi-restraints excluded: chain D residue 2292 VAL Chi-restraints excluded: chain D residue 2320 VAL Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2481 ASP Chi-restraints excluded: chain D residue 2718 TYR Chi-restraints excluded: chain D residue 2776 GLU Chi-restraints excluded: chain D residue 2877 THR Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 2901 VAL Chi-restraints excluded: chain D residue 3628 ILE Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3771 THR Chi-restraints excluded: chain D residue 3800 SER Chi-restraints excluded: chain D residue 3818 MET Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3864 ASN Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3866 THR Chi-restraints excluded: chain D residue 3867 VAL Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3947 LEU Chi-restraints excluded: chain D residue 3966 LEU Chi-restraints excluded: chain D residue 4055 LYS Chi-restraints excluded: chain D residue 4077 LEU Chi-restraints excluded: chain D residue 4092 ASP Chi-restraints excluded: chain D residue 4124 VAL Chi-restraints excluded: chain D residue 4140 SER Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4486 GLN Chi-restraints excluded: chain D residue 4509 PHE Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4559 VAL Chi-restraints excluded: chain D residue 4574 LEU Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4781 THR Chi-restraints excluded: chain D residue 4799 ASP Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4847 ILE Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 95 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1482 optimal weight: 20.0000 chunk 976 optimal weight: 0.0270 chunk 1572 optimal weight: 8.9990 chunk 959 optimal weight: 20.0000 chunk 746 optimal weight: 0.9990 chunk 1093 optimal weight: 40.0000 chunk 1649 optimal weight: 10.0000 chunk 1518 optimal weight: 30.0000 chunk 1313 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 1014 optimal weight: 7.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN A1685 GLN ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4087 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS ** B1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1371 ASN ** B1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 HIS B4486 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1371 ASN C1685 GLN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4054 HIS C4087 HIS D 270 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1685 GLN ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1973 ASN ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4087 HIS D4486 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 125876 Z= 0.425 Angle : 0.679 9.632 170664 Z= 0.348 Chirality : 0.043 0.425 19404 Planarity : 0.005 0.072 22256 Dihedral : 4.934 58.497 17706 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 4.01 % Allowed : 22.40 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.07), residues: 13424 helix: 0.52 (0.06), residues: 6436 sheet: -1.54 (0.14), residues: 1328 loop : -2.39 (0.08), residues: 5660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C2772 HIS 0.011 0.001 HIS B2848 PHE 0.027 0.002 PHE D1740 TYR 0.026 0.002 TYR D1777 ARG 0.018 0.001 ARG A2326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 473 poor density : 1063 time to evaluate : 9.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7420 (mmmt) REVERT: A 191 TYR cc_start: 0.8315 (m-80) cc_final: 0.7462 (m-80) REVERT: A 201 TRP cc_start: 0.5851 (m100) cc_final: 0.5157 (m100) REVERT: A 506 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6822 (m-70) REVERT: A 644 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8851 (tp) REVERT: A 691 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7667 (p) REVERT: A 1232 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8345 (tt) REVERT: A 2222 GLU cc_start: 0.7184 (tp30) cc_final: 0.6878 (tp30) REVERT: A 2335 ARG cc_start: 0.6598 (ttp80) cc_final: 0.6359 (tmt-80) REVERT: A 2756 MET cc_start: 0.2718 (mmt) cc_final: 0.2024 (tpp) REVERT: A 2776 GLU cc_start: 0.0881 (OUTLIER) cc_final: 0.0462 (tp30) REVERT: A 3905 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8398 (t80) REVERT: A 4108 MET cc_start: 0.7738 (tpt) cc_final: 0.7529 (tpt) REVERT: A 4132 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8680 (pt) REVERT: A 4574 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8365 (mp) REVERT: A 4942 MET cc_start: 0.8630 (mmm) cc_final: 0.8135 (mtt) REVERT: G 75 LEU cc_start: 0.8454 (mp) cc_final: 0.8199 (mp) REVERT: B 191 TYR cc_start: 0.8308 (m-80) cc_final: 0.7476 (m-80) REVERT: B 506 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6795 (m-70) REVERT: B 651 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.7819 (m170) REVERT: B 691 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7713 (p) REVERT: B 995 MET cc_start: 0.4058 (tpt) cc_final: 0.3749 (tpp) REVERT: B 1050 LEU cc_start: 0.2727 (OUTLIER) cc_final: 0.2478 (mm) REVERT: B 1215 MET cc_start: 0.6539 (tpp) cc_final: 0.5925 (tpp) REVERT: B 1224 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5786 (mp) REVERT: B 1232 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8308 (tt) REVERT: B 2222 GLU cc_start: 0.7020 (tp30) cc_final: 0.6741 (tp30) REVERT: B 2335 ARG cc_start: 0.6714 (ttp80) cc_final: 0.6497 (tmt-80) REVERT: B 2718 TYR cc_start: 0.4034 (OUTLIER) cc_final: 0.3487 (m-80) REVERT: B 2756 MET cc_start: 0.2671 (mmt) cc_final: 0.2169 (tpp) REVERT: B 2776 GLU cc_start: 0.0612 (OUTLIER) cc_final: 0.0234 (tp30) REVERT: B 3905 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8352 (t80) REVERT: B 4574 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8393 (mp) REVERT: H 33 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8515 (p0) REVERT: H 75 LEU cc_start: 0.8437 (mp) cc_final: 0.8051 (mt) REVERT: C 191 TYR cc_start: 0.8299 (m-80) cc_final: 0.7471 (m-80) REVERT: C 506 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.6816 (m-70) REVERT: C 644 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8831 (tp) REVERT: C 691 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7708 (p) REVERT: C 995 MET cc_start: 0.4080 (tpt) cc_final: 0.3776 (tpp) REVERT: C 1050 LEU cc_start: 0.2738 (OUTLIER) cc_final: 0.2491 (mm) REVERT: C 1215 MET cc_start: 0.6522 (tpp) cc_final: 0.5905 (tpp) REVERT: C 1224 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5834 (mp) REVERT: C 1232 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8307 (tt) REVERT: C 2222 GLU cc_start: 0.7184 (tp30) cc_final: 0.6888 (tp30) REVERT: C 2335 ARG cc_start: 0.6694 (ttp80) cc_final: 0.6464 (tmt-80) REVERT: C 2425 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7865 (mp) REVERT: C 2506 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5952 (pp) REVERT: C 2718 TYR cc_start: 0.4027 (OUTLIER) cc_final: 0.3546 (m-80) REVERT: C 2756 MET cc_start: 0.2658 (mmt) cc_final: 0.2155 (tpp) REVERT: C 2776 GLU cc_start: 0.0718 (OUTLIER) cc_final: 0.0332 (tp30) REVERT: C 2891 ILE cc_start: -0.2733 (OUTLIER) cc_final: -0.2979 (pt) REVERT: C 3905 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8402 (t80) REVERT: C 4574 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8358 (mp) REVERT: C 4942 MET cc_start: 0.8692 (mmm) cc_final: 0.8195 (mtt) REVERT: I 33 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8588 (p0) REVERT: I 75 LEU cc_start: 0.8451 (mp) cc_final: 0.8077 (mt) REVERT: D 56 LYS cc_start: 0.7712 (mmmt) cc_final: 0.7504 (mmmt) REVERT: D 191 TYR cc_start: 0.8306 (m-80) cc_final: 0.7478 (m-80) REVERT: D 319 LYS cc_start: 0.6159 (mtpp) cc_final: 0.5856 (mmmt) REVERT: D 564 ARG cc_start: 0.7366 (tpp-160) cc_final: 0.5580 (tpp80) REVERT: D 691 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7703 (p) REVERT: D 995 MET cc_start: 0.4066 (tpt) cc_final: 0.3738 (tpt) REVERT: D 1050 LEU cc_start: 0.2894 (OUTLIER) cc_final: 0.2636 (mm) REVERT: D 1232 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8296 (tt) REVERT: D 2222 GLU cc_start: 0.7015 (tp30) cc_final: 0.6740 (tp30) REVERT: D 2335 ARG cc_start: 0.6683 (ttp80) cc_final: 0.6460 (tmt-80) REVERT: D 2718 TYR cc_start: 0.4025 (OUTLIER) cc_final: 0.3470 (m-80) REVERT: D 2756 MET cc_start: 0.2653 (mmt) cc_final: 0.2132 (tpp) REVERT: D 2776 GLU cc_start: 0.1079 (OUTLIER) cc_final: 0.0639 (tp30) REVERT: D 2891 ILE cc_start: -0.3055 (OUTLIER) cc_final: -0.3297 (pt) REVERT: D 3905 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8433 (t80) REVERT: D 4084 LYS cc_start: 0.8628 (mptt) cc_final: 0.8370 (mmtt) REVERT: D 4574 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8422 (mp) REVERT: D 4645 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7806 (p0) REVERT: D 4898 ASP cc_start: 0.8343 (m-30) cc_final: 0.7968 (m-30) REVERT: D 4942 MET cc_start: 0.8700 (mmm) cc_final: 0.8168 (mtt) outliers start: 473 outliers final: 380 residues processed: 1439 average time/residue: 0.9683 time to fit residues: 2479.3938 Evaluate side-chains 1465 residues out of total 11932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 422 poor density : 1043 time to evaluate : 9.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1646 THR Chi-restraints excluded: chain A residue 1668 LEU Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1737 ILE Chi-restraints excluded: chain A residue 1843 ILE Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2197 ARG Chi-restraints excluded: chain A residue 2236 SER Chi-restraints excluded: chain A residue 2276 CYS Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2320 VAL Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2776 GLU Chi-restraints excluded: chain A residue 2848 HIS Chi-restraints excluded: chain A residue 3628 ILE Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3771 THR Chi-restraints excluded: chain A residue 3800 SER Chi-restraints excluded: chain A residue 3818 MET Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3864 ASN Chi-restraints excluded: chain A residue 3867 VAL Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 3966 LEU Chi-restraints excluded: chain A residue 4055 LYS Chi-restraints excluded: chain A residue 4077 LEU Chi-restraints excluded: chain A residue 4124 VAL Chi-restraints excluded: chain A residue 4132 LEU Chi-restraints excluded: chain A residue 4138 MET Chi-restraints excluded: chain A residue 4140 SER Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4509 PHE Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4559 VAL Chi-restraints excluded: chain A residue 4574 LEU Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4781 THR Chi-restraints excluded: chain A residue 4799 ASP Chi-restraints excluded: chain A residue 4803 MET Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain A residue 4881 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 577 CYS Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 713 TRP Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1161 VAL Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1199 ASP Chi-restraints excluded: chain B residue 1212 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1572 PHE Chi-restraints excluded: chain B residue 1589 VAL Chi-restraints excluded: chain B residue 1620 VAL Chi-restraints excluded: chain B residue 1646 THR Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1737 ILE Chi-restraints excluded: chain B residue 1843 ILE Chi-restraints excluded: chain B residue 1921 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2106 THR Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2197 ARG Chi-restraints excluded: chain B residue 2215 ASP Chi-restraints excluded: chain B residue 2236 SER Chi-restraints excluded: chain B residue 2276 CYS Chi-restraints excluded: chain B residue 2292 VAL Chi-restraints excluded: chain B residue 2320 VAL Chi-restraints excluded: chain B residue 2389 THR Chi-restraints excluded: chain B residue 2718 TYR Chi-restraints excluded: chain B residue 2776 GLU Chi-restraints excluded: chain B residue 2871 VAL Chi-restraints excluded: chain B residue 2877 THR Chi-restraints excluded: chain B residue 3628 ILE Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3771 THR Chi-restraints excluded: chain B residue 3800 SER Chi-restraints excluded: chain B residue 3818 MET Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3864 ASN Chi-restraints excluded: chain B residue 3867 VAL Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3947 LEU Chi-restraints excluded: chain B residue 3966 LEU Chi-restraints excluded: chain B residue 4077 LEU Chi-restraints excluded: chain B residue 4124 VAL Chi-restraints excluded: chain B residue 4140 SER Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4509 PHE Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4559 VAL Chi-restraints excluded: chain B residue 4574 LEU Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4799 ASP Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain B residue 4881 GLU Chi-restraints excluded: chain B residue 4942 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 506 HIS Chi-restraints excluded: chain C residue 577 CYS Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 713 TRP Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1050 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1164 CYS Chi-restraints excluded: chain C residue 1190 LEU Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1212 VAL Chi-restraints excluded: chain C residue 1224 LEU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1300 MET Chi-restraints excluded: chain C residue 1309 GLU Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1589 VAL Chi-restraints excluded: chain C residue 1620 VAL Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1646 THR Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1737 ILE Chi-restraints excluded: chain C residue 1843 ILE Chi-restraints excluded: chain C residue 1921 ILE Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2079 LEU Chi-restraints excluded: chain C residue 2106 THR Chi-restraints excluded: chain C residue 2110 VAL Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2197 ARG Chi-restraints excluded: chain C residue 2236 SER Chi-restraints excluded: chain C residue 2276 CYS Chi-restraints excluded: chain C residue 2292 VAL Chi-restraints excluded: chain C residue 2320 VAL Chi-restraints excluded: chain C residue 2389 THR Chi-restraints excluded: chain C residue 2425 LEU Chi-restraints excluded: chain C residue 2506 LEU Chi-restraints excluded: chain C residue 2718 TYR Chi-restraints excluded: chain C residue 2776 GLU Chi-restraints excluded: chain C residue 2848 HIS Chi-restraints excluded: chain C residue 2891 ILE Chi-restraints excluded: chain C residue 3628 ILE Chi-restraints excluded: chain C residue 3676 THR Chi-restraints excluded: chain C residue 3771 THR Chi-restraints excluded: chain C residue 3800 SER Chi-restraints excluded: chain C residue 3818 MET Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3864 ASN Chi-restraints excluded: chain C residue 3867 VAL Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3947 LEU Chi-restraints excluded: chain C residue 3966 LEU Chi-restraints excluded: chain C residue 4124 VAL Chi-restraints excluded: chain C residue 4140 SER Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4509 PHE Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4559 VAL Chi-restraints excluded: chain C residue 4574 LEU Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4799 ASP Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain C residue 4881 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 270 HIS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 577 CYS Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 713 TRP Chi-restraints excluded: chain D residue 721 ASP Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 784 ILE Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 851 LEU Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1199 ASP Chi-restraints excluded: chain D residue 1212 VAL Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1273 ILE Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1376 TYR Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1589 VAL Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1646 THR Chi-restraints excluded: chain D residue 1668 LEU Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 1737 ILE Chi-restraints excluded: chain D residue 1843 ILE Chi-restraints excluded: chain D residue 1921 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2079 LEU Chi-restraints excluded: chain D residue 2106 THR Chi-restraints excluded: chain D residue 2110 VAL Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2215 ASP Chi-restraints excluded: chain D residue 2236 SER Chi-restraints excluded: chain D residue 2276 CYS Chi-restraints excluded: chain D residue 2292 VAL Chi-restraints excluded: chain D residue 2320 VAL Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2481 ASP Chi-restraints excluded: chain D residue 2718 TYR Chi-restraints excluded: chain D residue 2776 GLU Chi-restraints excluded: chain D residue 2848 HIS Chi-restraints excluded: chain D residue 2877 THR Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 2901 VAL Chi-restraints excluded: chain D residue 3628 ILE Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3771 THR Chi-restraints excluded: chain D residue 3800 SER Chi-restraints excluded: chain D residue 3818 MET Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3864 ASN Chi-restraints excluded: chain D residue 3867 VAL Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3947 LEU Chi-restraints excluded: chain D residue 3966 LEU Chi-restraints excluded: chain D residue 4055 LYS Chi-restraints excluded: chain D residue 4077 LEU Chi-restraints excluded: chain D residue 4092 ASP Chi-restraints excluded: chain D residue 4124 VAL Chi-restraints excluded: chain D residue 4140 SER Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4509 PHE Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4559 VAL Chi-restraints excluded: chain D residue 4574 LEU Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4781 THR Chi-restraints excluded: chain D residue 4799 ASP Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 95 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 805 optimal weight: 1.9990 chunk 1043 optimal weight: 3.9990 chunk 1399 optimal weight: 1.9990 chunk 402 optimal weight: 0.7980 chunk 1211 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 365 optimal weight: 0.7980 chunk 1315 optimal weight: 9.9990 chunk 550 optimal weight: 1.9990 chunk 1351 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS ** B1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 HIS C 270 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1973 ASN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4054 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1973 ASN ** D2290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.169237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.139359 restraints weight = 231513.874| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.23 r_work: 0.3663 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 125876 Z= 0.170 Angle : 0.572 10.113 170664 Z= 0.292 Chirality : 0.038 0.271 19404 Planarity : 0.004 0.065 22256 Dihedral : 4.641 58.680 17696 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.01 % Allowed : 23.30 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.07), residues: 13424 helix: 0.88 (0.07), residues: 6456 sheet: -1.46 (0.14), residues: 1368 loop : -2.27 (0.08), residues: 5600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B4644 HIS 0.035 0.001 HIS A 651 PHE 0.019 0.001 PHE C4064 TYR 0.021 0.001 TYR C4079 ARG 0.015 0.000 ARG A2326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37577.35 seconds wall clock time: 651 minutes 2.03 seconds (39062.03 seconds total)