Starting phenix.real_space_refine on Sun Feb 18 19:55:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/02_2024/7ngl_12315_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/02_2024/7ngl_12315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/02_2024/7ngl_12315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/02_2024/7ngl_12315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/02_2024/7ngl_12315_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/02_2024/7ngl_12315_trim_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 162 5.16 5 C 23442 2.51 5 N 6426 2.21 5 O 6978 1.98 5 H 37715 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "B ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 706": "OE1" <-> "OE2" Residue "B ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 781": "OE1" <-> "OE2" Residue "C ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 897": "OE1" <-> "OE2" Residue "D ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 441": "OE1" <-> "OE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D GLU 583": "OE1" <-> "OE2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 897": "OE1" <-> "OE2" Residue "E ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 441": "OE1" <-> "OE2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "E GLU 495": "OE1" <-> "OE2" Residue "E GLU 583": "OE1" <-> "OE2" Residue "E GLU 614": "OE1" <-> "OE2" Residue "E ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 897": "OE1" <-> "OE2" Residue "F ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 583": "OE1" <-> "OE2" Residue "F ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 812": "OE1" <-> "OE2" Residue "F ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 937": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 74735 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "B" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "C" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "D" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "E" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "F" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.83, per 1000 atoms: 0.33 Number of scatterers: 74735 At special positions: 0 Unit cell: (143.763, 146.256, 224.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 162 16.00 P 12 15.00 O 6978 8.00 N 6426 7.00 C 23442 6.00 H 37715 1.00 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: 45.43 Conformation dependent library (CDL) restraints added in 5.8 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 188 helices and 36 sheets defined 43.7% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.57 Creating SS restraints... Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.832A pdb=" N VAL A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 306 removed outlier: 3.681A pdb=" N GLU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.746A pdb=" N LEU A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 355 through 406 removed outlier: 3.952A pdb=" N LEU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 427 removed outlier: 3.814A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 4.208A pdb=" N ASP A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 495 through 508 Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.695A pdb=" N LEU A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 618 removed outlier: 3.660A pdb=" N ASN A 618 " --> pdb=" O GLN A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 618' Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 663 through 673 removed outlier: 3.998A pdb=" N LEU A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG A 672 " --> pdb=" O ALA A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 681 Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 710 through 728 Processing helix chain 'A' and resid 742 through 746 Processing helix chain 'A' and resid 808 through 828 removed outlier: 4.028A pdb=" N MET A 826 " --> pdb=" O ARG A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 869 Proline residue: A 854 - end of helix removed outlier: 4.397A pdb=" N CYS A 858 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 861 " --> pdb=" O CYS A 858 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A 869 " --> pdb=" O SER A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 919 through 922 Processing helix chain 'A' and resid 925 through 928 No H-bonds generated for 'chain 'A' and resid 925 through 928' Processing helix chain 'A' and resid 939 through 944 Processing helix chain 'B' and resid 149 through 155 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.772A pdb=" N VAL B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.849A pdb=" N GLU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 328 through 338 removed outlier: 4.077A pdb=" N LEU B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 355 through 388 Processing helix chain 'B' and resid 393 through 405 Processing helix chain 'B' and resid 414 through 427 Processing helix chain 'B' and resid 432 through 447 Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 495 through 508 Processing helix chain 'B' and resid 529 through 540 removed outlier: 3.713A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 559 Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.743A pdb=" N LEU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 618 removed outlier: 3.687A pdb=" N ASN B 618 " --> pdb=" O GLN B 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 615 through 618' Processing helix chain 'B' and resid 647 through 650 No H-bonds generated for 'chain 'B' and resid 647 through 650' Processing helix chain 'B' and resid 665 through 673 removed outlier: 4.072A pdb=" N ARG B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 681 Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 710 through 728 Processing helix chain 'B' and resid 739 through 746 removed outlier: 4.252A pdb=" N GLN B 743 " --> pdb=" O PRO B 739 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 828 removed outlier: 3.594A pdb=" N MET B 826 " --> pdb=" O ARG B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 869 Proline residue: B 854 - end of helix removed outlier: 4.219A pdb=" N CYS B 858 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 861 " --> pdb=" O CYS B 858 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET B 869 " --> pdb=" O SER B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 914 through 922 removed outlier: 4.451A pdb=" N LYS B 918 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE B 920 " --> pdb=" O LYS B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 928 No H-bonds generated for 'chain 'B' and resid 925 through 928' Processing helix chain 'B' and resid 939 through 944 Processing helix chain 'C' and resid 149 through 155 Processing helix chain 'C' and resid 175 through 180 removed outlier: 3.741A pdb=" N VAL C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 306 removed outlier: 3.682A pdb=" N GLU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 328 through 338 removed outlier: 3.836A pdb=" N LEU C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 355 through 405 removed outlier: 3.599A pdb=" N LEU C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS C 393 " --> pdb=" O GLN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 427 Processing helix chain 'C' and resid 432 through 447 Processing helix chain 'C' and resid 453 through 466 Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 495 through 510 removed outlier: 3.721A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 540 Processing helix chain 'C' and resid 555 through 559 Processing helix chain 'C' and resid 572 through 580 Processing helix chain 'C' and resid 592 through 594 No H-bonds generated for 'chain 'C' and resid 592 through 594' Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.694A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 removed outlier: 3.738A pdb=" N ASN C 618 " --> pdb=" O GLN C 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 615 through 618' Processing helix chain 'C' and resid 647 through 650 No H-bonds generated for 'chain 'C' and resid 647 through 650' Processing helix chain 'C' and resid 663 through 673 removed outlier: 3.979A pdb=" N LEU C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG C 672 " --> pdb=" O ALA C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 682 Processing helix chain 'C' and resid 693 through 702 Processing helix chain 'C' and resid 710 through 728 Processing helix chain 'C' and resid 739 through 746 removed outlier: 3.967A pdb=" N GLN C 743 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 828 removed outlier: 3.801A pdb=" N MET C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 869 Proline residue: C 854 - end of helix removed outlier: 4.318A pdb=" N CYS C 858 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 861 " --> pdb=" O CYS C 858 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET C 869 " --> pdb=" O SER C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 914 through 916 No H-bonds generated for 'chain 'C' and resid 914 through 916' Processing helix chain 'C' and resid 919 through 922 Processing helix chain 'C' and resid 925 through 928 No H-bonds generated for 'chain 'C' and resid 925 through 928' Processing helix chain 'C' and resid 939 through 944 Processing helix chain 'D' and resid 148 through 155 removed outlier: 3.820A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 291 through 306 removed outlier: 3.554A pdb=" N GLU D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 328 through 338 removed outlier: 3.915A pdb=" N LEU D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 355 through 388 Processing helix chain 'D' and resid 392 through 404 Processing helix chain 'D' and resid 414 through 427 Processing helix chain 'D' and resid 432 through 447 Processing helix chain 'D' and resid 453 through 467 Processing helix chain 'D' and resid 480 through 488 Processing helix chain 'D' and resid 495 through 510 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 592 through 594 No H-bonds generated for 'chain 'D' and resid 592 through 594' Processing helix chain 'D' and resid 603 through 611 removed outlier: 4.125A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 650 No H-bonds generated for 'chain 'D' and resid 647 through 650' Processing helix chain 'D' and resid 663 through 673 removed outlier: 3.997A pdb=" N LEU D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG D 672 " --> pdb=" O ALA D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 681 Processing helix chain 'D' and resid 693 through 702 Processing helix chain 'D' and resid 710 through 728 Processing helix chain 'D' and resid 742 through 746 Processing helix chain 'D' and resid 808 through 828 removed outlier: 3.560A pdb=" N MET D 826 " --> pdb=" O ARG D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 869 Proline residue: D 854 - end of helix removed outlier: 4.316A pdb=" N CYS D 858 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 861 " --> pdb=" O CYS D 858 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET D 869 " --> pdb=" O SER D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 914 through 916 No H-bonds generated for 'chain 'D' and resid 914 through 916' Processing helix chain 'D' and resid 919 through 922 Processing helix chain 'D' and resid 925 through 928 No H-bonds generated for 'chain 'D' and resid 925 through 928' Processing helix chain 'D' and resid 939 through 944 Processing helix chain 'E' and resid 148 through 155 removed outlier: 3.661A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 removed outlier: 3.616A pdb=" N VAL E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 306 Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 328 through 338 removed outlier: 4.013A pdb=" N LEU E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 351 Processing helix chain 'E' and resid 355 through 404 removed outlier: 3.867A pdb=" N LEU E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 427 Processing helix chain 'E' and resid 432 through 447 removed outlier: 3.789A pdb=" N GLY E 446 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 466 removed outlier: 3.686A pdb=" N VAL E 457 " --> pdb=" O SER E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 488 Processing helix chain 'E' and resid 495 through 511 removed outlier: 3.753A pdb=" N ARG E 511 " --> pdb=" O VAL E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 540 Processing helix chain 'E' and resid 555 through 558 Processing helix chain 'E' and resid 572 through 580 Processing helix chain 'E' and resid 592 through 594 No H-bonds generated for 'chain 'E' and resid 592 through 594' Processing helix chain 'E' and resid 603 through 611 removed outlier: 3.808A pdb=" N LEU E 608 " --> pdb=" O SER E 604 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 618 Processing helix chain 'E' and resid 647 through 650 No H-bonds generated for 'chain 'E' and resid 647 through 650' Processing helix chain 'E' and resid 663 through 673 removed outlier: 4.252A pdb=" N ARG E 672 " --> pdb=" O ALA E 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 682 Processing helix chain 'E' and resid 693 through 702 Processing helix chain 'E' and resid 710 through 728 Processing helix chain 'E' and resid 742 through 746 Processing helix chain 'E' and resid 808 through 828 removed outlier: 3.891A pdb=" N MET E 826 " --> pdb=" O ARG E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 850 through 869 Proline residue: E 854 - end of helix removed outlier: 4.404A pdb=" N CYS E 858 " --> pdb=" O SER E 855 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 861 " --> pdb=" O CYS E 858 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 865 " --> pdb=" O THR E 862 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET E 869 " --> pdb=" O SER E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 904 Processing helix chain 'E' and resid 914 through 916 No H-bonds generated for 'chain 'E' and resid 914 through 916' Processing helix chain 'E' and resid 919 through 922 Processing helix chain 'E' and resid 925 through 928 No H-bonds generated for 'chain 'E' and resid 925 through 928' Processing helix chain 'E' and resid 939 through 945 Processing helix chain 'F' and resid 150 through 155 Processing helix chain 'F' and resid 175 through 180 removed outlier: 3.807A pdb=" N VAL F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 306 removed outlier: 3.793A pdb=" N GLU F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 328 through 338 removed outlier: 3.935A pdb=" N LEU F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 351 Processing helix chain 'F' and resid 355 through 388 Processing helix chain 'F' and resid 392 through 404 Processing helix chain 'F' and resid 414 through 425 removed outlier: 4.271A pdb=" N LYS F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE F 421 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 removed outlier: 3.844A pdb=" N GLY F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU F 447 " --> pdb=" O SER F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 480 through 488 Processing helix chain 'F' and resid 495 through 508 Processing helix chain 'F' and resid 529 through 540 Processing helix chain 'F' and resid 555 through 559 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 592 through 594 No H-bonds generated for 'chain 'F' and resid 592 through 594' Processing helix chain 'F' and resid 603 through 611 removed outlier: 3.730A pdb=" N LEU F 608 " --> pdb=" O SER F 604 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU F 609 " --> pdb=" O SER F 605 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 618 removed outlier: 3.863A pdb=" N ASN F 618 " --> pdb=" O GLN F 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 615 through 618' Processing helix chain 'F' and resid 647 through 650 No H-bonds generated for 'chain 'F' and resid 647 through 650' Processing helix chain 'F' and resid 663 through 673 removed outlier: 4.072A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG F 672 " --> pdb=" O ALA F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 681 Processing helix chain 'F' and resid 686 through 688 No H-bonds generated for 'chain 'F' and resid 686 through 688' Processing helix chain 'F' and resid 693 through 702 Processing helix chain 'F' and resid 710 through 728 Processing helix chain 'F' and resid 739 through 746 removed outlier: 4.278A pdb=" N GLN F 743 " --> pdb=" O PRO F 739 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 828 removed outlier: 4.083A pdb=" N MET F 826 " --> pdb=" O ARG F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 869 Proline residue: F 854 - end of helix removed outlier: 4.398A pdb=" N CYS F 858 " --> pdb=" O SER F 855 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 861 " --> pdb=" O CYS F 858 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET F 869 " --> pdb=" O SER F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 904 Processing helix chain 'F' and resid 914 through 922 removed outlier: 4.214A pdb=" N LYS F 918 " --> pdb=" O GLU F 915 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE F 920 " --> pdb=" O LYS F 917 " (cutoff:3.500A) Processing helix chain 'F' and resid 925 through 928 No H-bonds generated for 'chain 'F' and resid 925 through 928' Processing helix chain 'F' and resid 939 through 944 Processing sheet with id= A, first strand: chain 'A' and resid 140 through 142 Processing sheet with id= B, first strand: chain 'A' and resid 164 through 166 Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.324A pdb=" N CYS A 637 " --> pdb=" O PHE A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.532A pdb=" N LEU A 586 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE A 547 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 588 " --> pdb=" O PHE A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 689 through 691 removed outlier: 7.061A pdb=" N VAL A 735 " --> pdb=" O LYS A 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 764 through 766 Processing sheet with id= G, first strand: chain 'B' and resid 140 through 142 Processing sheet with id= H, first strand: chain 'B' and resid 188 through 191 Processing sheet with id= I, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.182A pdb=" N CYS B 637 " --> pdb=" O PHE B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 544 through 548 removed outlier: 6.516A pdb=" N LEU B 586 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE B 547 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 588 " --> pdb=" O PHE B 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 764 through 766 Processing sheet with id= L, first strand: chain 'B' and resid 910 through 913 removed outlier: 3.640A pdb=" N LEU B 912 " --> pdb=" O HIS B 934 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 140 through 142 Processing sheet with id= N, first strand: chain 'C' and resid 164 through 167 Processing sheet with id= O, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.233A pdb=" N CYS C 637 " --> pdb=" O PHE C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 544 through 548 removed outlier: 6.457A pdb=" N LEU C 586 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE C 547 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU C 588 " --> pdb=" O PHE C 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 764 through 766 Processing sheet with id= R, first strand: chain 'C' and resid 910 through 913 removed outlier: 3.587A pdb=" N LEU C 912 " --> pdb=" O HIS C 934 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 140 through 142 Processing sheet with id= T, first strand: chain 'D' and resid 163 through 167 Processing sheet with id= U, first strand: chain 'D' and resid 544 through 548 removed outlier: 7.156A pdb=" N LEU D 586 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE D 547 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU D 588 " --> pdb=" O PHE D 547 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE D 636 " --> pdb=" O ILE D 589 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 764 through 766 Processing sheet with id= W, first strand: chain 'D' and resid 910 through 913 Processing sheet with id= X, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= Y, first strand: chain 'E' and resid 164 through 166 Processing sheet with id= Z, first strand: chain 'E' and resid 519 through 522 removed outlier: 6.034A pdb=" N GLU E 654 " --> pdb=" O CYS E 520 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TYR E 522 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE E 656 " --> pdb=" O TYR E 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.454A pdb=" N LEU E 586 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE E 547 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU E 588 " --> pdb=" O PHE E 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.844A pdb=" N VAL E 735 " --> pdb=" O LYS E 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 780 through 784 Processing sheet with id= AD, first strand: chain 'E' and resid 910 through 913 Processing sheet with id= AE, first strand: chain 'F' and resid 140 through 142 Processing sheet with id= AF, first strand: chain 'F' and resid 188 through 191 Processing sheet with id= AG, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.172A pdb=" N CYS F 637 " --> pdb=" O PHE F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.664A pdb=" N LEU F 586 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE F 547 " --> pdb=" O LEU F 586 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU F 588 " --> pdb=" O PHE F 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 689 through 691 removed outlier: 6.938A pdb=" N VAL F 735 " --> pdb=" O LYS F 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 764 through 766 1319 hydrogen bonds defined for protein. 3600 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: 25.03 Time building geometry restraints manager: 48.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 37673 1.02 - 1.22: 159 1.22 - 1.42: 14911 1.42 - 1.62: 22333 1.62 - 1.82: 283 Bond restraints: 75359 Sorted by residual: bond pdb=" CG GLU E 665 " pdb=" CD GLU E 665 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.34e+01 bond pdb=" CG GLU A 665 " pdb=" CD GLU A 665 " ideal model delta sigma weight residual 1.516 1.427 0.089 2.50e-02 1.60e+03 1.28e+01 bond pdb=" CG GLU C 665 " pdb=" CD GLU C 665 " ideal model delta sigma weight residual 1.516 1.428 0.088 2.50e-02 1.60e+03 1.25e+01 bond pdb=" CG GLU B 665 " pdb=" CD GLU B 665 " ideal model delta sigma weight residual 1.516 1.433 0.083 2.50e-02 1.60e+03 1.11e+01 bond pdb=" CB ILE D 403 " pdb=" CG2 ILE D 403 " ideal model delta sigma weight residual 1.521 1.629 -0.108 3.30e-02 9.18e+02 1.07e+01 ... (remaining 75354 not shown) Histogram of bond angle deviations from ideal: 94.39 - 102.70: 225 102.70 - 111.00: 80189 111.00 - 119.31: 29232 119.31 - 127.62: 26939 127.62 - 135.93: 386 Bond angle restraints: 136971 Sorted by residual: angle pdb=" N GLY F 601 " pdb=" CA GLY F 601 " pdb=" C GLY F 601 " ideal model delta sigma weight residual 113.18 94.39 18.79 2.37e+00 1.78e-01 6.29e+01 angle pdb=" N GLY D 601 " pdb=" CA GLY D 601 " pdb=" C GLY D 601 " ideal model delta sigma weight residual 113.18 95.96 17.22 2.37e+00 1.78e-01 5.28e+01 angle pdb=" N GLY E 601 " pdb=" CA GLY E 601 " pdb=" C GLY E 601 " ideal model delta sigma weight residual 113.18 97.91 15.27 2.37e+00 1.78e-01 4.15e+01 angle pdb=" N GLY C 601 " pdb=" CA GLY C 601 " pdb=" C GLY C 601 " ideal model delta sigma weight residual 113.18 98.76 14.42 2.37e+00 1.78e-01 3.70e+01 angle pdb=" N GLY B 210 " pdb=" CA GLY B 210 " pdb=" C GLY B 210 " ideal model delta sigma weight residual 113.18 100.17 13.01 2.37e+00 1.78e-01 3.01e+01 ... (remaining 136966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 33809 31.27 - 62.53: 1033 62.53 - 93.80: 62 93.80 - 125.07: 1 125.07 - 156.34: 3 Dihedral angle restraints: 34908 sinusoidal: 19668 harmonic: 15240 Sorted by residual: dihedral pdb=" O1B ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PB ADP D1001 " pdb=" PA ADP D1001 " ideal model delta sinusoidal sigma weight residual 300.00 143.66 156.34 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 69.25 -129.25 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 66.43 -126.43 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 34905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4739 0.093 - 0.185: 1015 0.185 - 0.278: 70 0.278 - 0.371: 6 0.371 - 0.463: 2 Chirality restraints: 5832 Sorted by residual: chirality pdb=" CB ILE D 558 " pdb=" CA ILE D 558 " pdb=" CG1 ILE D 558 " pdb=" CG2 ILE D 558 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CG LEU C 462 " pdb=" CB LEU C 462 " pdb=" CD1 LEU C 462 " pdb=" CD2 LEU C 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE B 185 " pdb=" CA ILE B 185 " pdb=" CG1 ILE B 185 " pdb=" CG2 ILE B 185 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 5829 not shown) Planarity restraints: 10980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 491 " -0.038 2.00e-02 2.50e+03 3.41e-02 2.62e+01 pdb=" CG HIS E 491 " 0.085 2.00e-02 2.50e+03 pdb=" ND1 HIS E 491 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS E 491 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS E 491 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS E 491 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 HIS E 491 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 HIS E 491 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS E 491 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 615 " 0.024 2.00e-02 2.50e+03 4.80e-02 2.30e+01 pdb=" C GLN E 615 " -0.083 2.00e-02 2.50e+03 pdb=" O GLN E 615 " 0.031 2.00e-02 2.50e+03 pdb=" N ASN E 616 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 861 " -0.024 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C VAL D 861 " 0.082 2.00e-02 2.50e+03 pdb=" O VAL D 861 " -0.031 2.00e-02 2.50e+03 pdb=" N THR D 862 " -0.028 2.00e-02 2.50e+03 ... (remaining 10977 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 7275 2.23 - 2.82: 162404 2.82 - 3.41: 193316 3.41 - 4.01: 243454 4.01 - 4.60: 382428 Nonbonded interactions: 988877 Sorted by model distance: nonbonded pdb=" O GLU E 543 " pdb=" H LEU E 586 " model vdw 1.636 1.850 nonbonded pdb=" O PHE C 619 " pdb=" H VAL C 628 " model vdw 1.649 1.850 nonbonded pdb=" O ASP B 852 " pdb=" HG SER B 855 " model vdw 1.651 1.850 nonbonded pdb=" O ALA C 556 " pdb=" H GLY C 560 " model vdw 1.652 1.850 nonbonded pdb=" O ALA F 556 " pdb=" H GLY F 560 " model vdw 1.653 1.850 ... (remaining 988872 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'B' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'C' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'D' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = chain 'E' selection = (chain 'F' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.800 Extract box with map and model: 15.390 Check model and map are aligned: 0.850 Set scattering table: 0.530 Process input model: 177.740 Find NCS groups from input model: 2.970 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.012 0.134 37644 Z= 0.771 Angle : 1.497 18.792 50856 Z= 0.830 Chirality : 0.072 0.463 5832 Planarity : 0.009 0.055 6528 Dihedral : 13.267 156.335 14466 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.22 % Favored : 90.76 % Rotamer: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.12), residues: 4632 helix: -2.07 (0.09), residues: 1874 sheet: -3.71 (0.18), residues: 567 loop : -0.47 (0.15), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.006 TRP D 464 HIS 0.051 0.004 HIS E 491 PHE 0.049 0.005 PHE E 504 TYR 0.041 0.005 TYR C 623 ARG 0.017 0.001 ARG D 786 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 397 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 396 time to evaluate : 4.548 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: 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 197 MET cc_start: 0.0070 (mtp) cc_final: -0.0179 (mmm) REVERT: A 206 MET cc_start: 0.4321 (ttp) cc_final: 0.3916 (tmm) REVERT: A 317 MET cc_start: 0.1116 (mmp) cc_final: 0.0023 (ptt) REVERT: A 651 ASP cc_start: 0.8101 (t0) cc_final: 0.7857 (t0) REVERT: A 773 MET cc_start: 0.8674 (ppp) cc_final: 0.8167 (ppp) REVERT: B 317 MET cc_start: 0.3181 (mmp) cc_final: 0.2907 (mtt) REVERT: B 490 ASP cc_start: 0.8184 (p0) cc_final: 0.7502 (t0) REVERT: B 496 ASP cc_start: 0.8181 (t0) cc_final: 0.7757 (t0) REVERT: B 773 MET cc_start: 0.8212 (ppp) cc_final: 0.7898 (ppp) REVERT: C 197 MET cc_start: 0.2022 (mtp) cc_final: 0.1553 (pmm) REVERT: C 488 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7448 (tt0) REVERT: C 543 GLU cc_start: 0.6207 (tm-30) cc_final: 0.5902 (mt-10) REVERT: D 327 ASN cc_start: 0.7266 (m-40) cc_final: 0.6982 (t0) REVERT: D 397 GLN cc_start: 0.7896 (mt0) cc_final: 0.7518 (tp40) REVERT: D 653 MET cc_start: 0.6111 (ptm) cc_final: 0.5854 (ptm) REVERT: D 756 MET cc_start: 0.5772 (mpp) cc_final: 0.5249 (ptm) REVERT: D 773 MET cc_start: 0.5128 (mmm) cc_final: 0.4318 (mpp) REVERT: D 810 MET cc_start: 0.8795 (mmt) cc_final: 0.8230 (mtt) REVERT: E 406 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7663 (pp20) REVERT: E 655 MET cc_start: 0.7735 (mpp) cc_final: 0.7441 (mmm) REVERT: E 685 ASP cc_start: 0.8323 (t0) cc_final: 0.7511 (p0) REVERT: E 896 LYS cc_start: 0.6784 (tttt) cc_final: 0.6580 (tttt) REVERT: F 272 MET cc_start: 0.0654 (ptp) cc_final: 0.0450 (ptp) REVERT: F 609 GLU cc_start: 0.8588 (pt0) cc_final: 0.8222 (tp30) outliers start: 1 outliers final: 1 residues processed: 397 average time/residue: 0.9770 time to fit residues: 622.3528 Evaluate side-chains 245 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 10.0000 chunk 350 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 187 optimal weight: 0.9990 chunk 362 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 269 optimal weight: 20.0000 chunk 419 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 916 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37644 Z= 0.196 Angle : 0.657 7.728 50856 Z= 0.339 Chirality : 0.040 0.159 5832 Planarity : 0.004 0.049 6528 Dihedral : 7.115 158.379 5132 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.47 % Allowed : 8.37 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4632 helix: -0.65 (0.11), residues: 1908 sheet: -3.37 (0.18), residues: 583 loop : -0.73 (0.14), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 464 HIS 0.014 0.001 HIS F 433 PHE 0.019 0.001 PHE F 191 TYR 0.030 0.001 TYR A 360 ARG 0.006 0.001 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 259 time to evaluate : 4.552 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: 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 206 MET cc_start: 0.4594 (ttp) cc_final: 0.4331 (tpp) REVERT: A 317 MET cc_start: 0.1080 (mmp) cc_final: -0.0216 (ttp) REVERT: A 318 MET cc_start: -0.4834 (mtm) cc_final: -0.5086 (mtp) REVERT: A 424 ARG cc_start: 0.8979 (mtt-85) cc_final: 0.8307 (ttm-80) REVERT: A 669 ILE cc_start: 0.8190 (mt) cc_final: 0.7864 (mt) REVERT: A 773 MET cc_start: 0.8633 (ppp) cc_final: 0.8052 (ppp) REVERT: B 490 ASP cc_start: 0.8053 (p0) cc_final: 0.7454 (t0) REVERT: B 741 ASN cc_start: 0.8005 (t0) cc_final: 0.7767 (t0) REVERT: B 773 MET cc_start: 0.8192 (ppp) cc_final: 0.7938 (ppp) REVERT: C 197 MET cc_start: 0.2068 (mtp) cc_final: 0.1617 (pmm) REVERT: C 653 MET cc_start: 0.8145 (ptp) cc_final: 0.7904 (ptp) REVERT: C 806 LEU cc_start: 0.8118 (pt) cc_final: 0.7813 (pp) REVERT: D 327 ASN cc_start: 0.7264 (m-40) cc_final: 0.7003 (t0) REVERT: D 397 GLN cc_start: 0.8029 (mt0) cc_final: 0.7612 (tp40) REVERT: D 756 MET cc_start: 0.5935 (mpp) cc_final: 0.5359 (ptm) REVERT: D 773 MET cc_start: 0.4770 (mmm) cc_final: 0.4127 (mpp) REVERT: D 810 MET cc_start: 0.8779 (mmt) cc_final: 0.8235 (mtt) REVERT: D 879 MET cc_start: 0.6958 (pmm) cc_final: 0.6700 (pmm) REVERT: E 406 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7687 (pp20) REVERT: E 441 GLU cc_start: 0.6283 (mm-30) cc_final: 0.5823 (mm-30) REVERT: E 653 MET cc_start: 0.7969 (pmm) cc_final: 0.6954 (pmm) REVERT: E 685 ASP cc_start: 0.8256 (t0) cc_final: 0.7729 (p0) REVERT: E 731 GLU cc_start: 0.7139 (mp0) cc_final: 0.6128 (pm20) REVERT: E 783 SER cc_start: 0.8979 (t) cc_final: 0.8568 (p) REVERT: F 272 MET cc_start: 0.0309 (ptp) cc_final: 0.0053 (ptp) REVERT: F 669 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.8009 (mt) REVERT: F 671 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7800 (tm-30) outliers start: 19 outliers final: 14 residues processed: 272 average time/residue: 0.9341 time to fit residues: 418.1151 Evaluate side-chains 243 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 228 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 895 ILE Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 651 ASP Chi-restraints excluded: chain F residue 669 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 349 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 420 optimal weight: 0.3980 chunk 454 optimal weight: 2.9990 chunk 374 optimal weight: 6.9990 chunk 416 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 337 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37644 Z= 0.238 Angle : 0.591 7.368 50856 Z= 0.300 Chirality : 0.039 0.152 5832 Planarity : 0.004 0.042 6528 Dihedral : 6.638 144.404 5132 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.44 % Allowed : 9.58 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.12), residues: 4632 helix: -0.08 (0.11), residues: 1930 sheet: -3.16 (0.20), residues: 602 loop : -0.86 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 770 HIS 0.008 0.001 HIS F 433 PHE 0.014 0.001 PHE B 421 TYR 0.025 0.001 TYR A 360 ARG 0.011 0.000 ARG C 597 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 239 time to evaluate : 4.522 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.4337 (ttp) cc_final: 0.4061 (tmm) REVERT: A 317 MET cc_start: 0.1158 (mmp) cc_final: -0.0122 (ttp) REVERT: A 773 MET cc_start: 0.8671 (ppp) cc_final: 0.8061 (ppp) REVERT: B 490 ASP cc_start: 0.8074 (p0) cc_final: 0.7521 (t0) REVERT: B 741 ASN cc_start: 0.7956 (t0) cc_final: 0.7696 (t0) REVERT: B 773 MET cc_start: 0.8180 (ppp) cc_final: 0.7887 (ppp) REVERT: C 653 MET cc_start: 0.8183 (ptp) cc_final: 0.7893 (ptp) REVERT: C 806 LEU cc_start: 0.8045 (pt) cc_final: 0.7706 (pp) REVERT: D 327 ASN cc_start: 0.7272 (m-40) cc_final: 0.7002 (t0) REVERT: D 397 GLN cc_start: 0.8017 (mt0) cc_final: 0.7618 (tp40) REVERT: D 756 MET cc_start: 0.5959 (mpp) cc_final: 0.5532 (ptm) REVERT: D 773 MET cc_start: 0.4676 (mmm) cc_final: 0.4010 (mpp) REVERT: D 810 MET cc_start: 0.8811 (mmt) cc_final: 0.8212 (mtt) REVERT: D 879 MET cc_start: 0.7165 (pmm) cc_final: 0.6880 (pmm) REVERT: E 406 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7738 (pp20) REVERT: E 441 GLU cc_start: 0.6282 (mm-30) cc_final: 0.5857 (mm-30) REVERT: E 653 MET cc_start: 0.7864 (pmm) cc_final: 0.6972 (pmm) REVERT: E 685 ASP cc_start: 0.8305 (t0) cc_final: 0.7658 (p0) REVERT: E 783 SER cc_start: 0.8972 (t) cc_final: 0.8617 (p) REVERT: F 272 MET cc_start: 0.0582 (ptp) cc_final: 0.0324 (ptp) REVERT: F 435 MET cc_start: 0.8370 (tmm) cc_final: 0.8033 (tmm) REVERT: F 669 ILE cc_start: 0.8195 (mt) cc_final: 0.7989 (mt) REVERT: F 671 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7800 (tm-30) outliers start: 18 outliers final: 16 residues processed: 249 average time/residue: 0.9392 time to fit residues: 384.0089 Evaluate side-chains 232 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 216 time to evaluate : 4.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 727 ILE Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 197 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 421 optimal weight: 2.9990 chunk 446 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 399 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 HIS B 477 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37644 Z= 0.221 Angle : 0.559 6.913 50856 Z= 0.282 Chirality : 0.039 0.147 5832 Planarity : 0.004 0.040 6528 Dihedral : 6.368 136.202 5132 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.77 % Allowed : 10.10 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.12), residues: 4632 helix: 0.16 (0.12), residues: 1946 sheet: -2.91 (0.21), residues: 574 loop : -1.03 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 770 HIS 0.005 0.001 HIS E 491 PHE 0.030 0.001 PHE B 421 TYR 0.021 0.001 TYR A 360 ARG 0.010 0.000 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 4.541 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: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.4250 (ttp) cc_final: 0.3966 (tmm) REVERT: A 317 MET cc_start: 0.1227 (mmp) cc_final: 0.0796 (tpt) REVERT: A 424 ARG cc_start: 0.8937 (mtt-85) cc_final: 0.8380 (ttm-80) REVERT: A 773 MET cc_start: 0.8695 (ppp) cc_final: 0.8102 (ppp) REVERT: B 490 ASP cc_start: 0.8147 (p0) cc_final: 0.7588 (t0) REVERT: B 741 ASN cc_start: 0.7899 (t0) cc_final: 0.7598 (t0) REVERT: B 773 MET cc_start: 0.8219 (ppp) cc_final: 0.7909 (ppp) REVERT: C 653 MET cc_start: 0.8170 (ptp) cc_final: 0.7831 (ptp) REVERT: C 806 LEU cc_start: 0.8050 (pt) cc_final: 0.7667 (pp) REVERT: D 327 ASN cc_start: 0.7284 (m-40) cc_final: 0.7006 (t0) REVERT: D 397 GLN cc_start: 0.8024 (mt0) cc_final: 0.7612 (tp40) REVERT: D 637 CYS cc_start: 0.9124 (m) cc_final: 0.8792 (t) REVERT: D 756 MET cc_start: 0.6038 (mpp) cc_final: 0.5565 (ptm) REVERT: D 773 MET cc_start: 0.4507 (mmm) cc_final: 0.3922 (mpp) REVERT: D 810 MET cc_start: 0.8824 (mmt) cc_final: 0.8260 (mtt) REVERT: D 879 MET cc_start: 0.7236 (pmm) cc_final: 0.6964 (pmm) REVERT: E 406 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7692 (pp20) REVERT: E 441 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6045 (mt-10) REVERT: E 653 MET cc_start: 0.7847 (pmm) cc_final: 0.6966 (pmm) REVERT: E 685 ASP cc_start: 0.8313 (t0) cc_final: 0.7584 (p0) REVERT: E 783 SER cc_start: 0.8962 (t) cc_final: 0.8634 (p) REVERT: F 435 MET cc_start: 0.8460 (tmm) cc_final: 0.7999 (tmm) REVERT: F 609 GLU cc_start: 0.8429 (pt0) cc_final: 0.8083 (tp30) REVERT: F 671 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7811 (tm-30) outliers start: 31 outliers final: 27 residues processed: 257 average time/residue: 0.9237 time to fit residues: 394.7409 Evaluate side-chains 246 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 219 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 727 ILE Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 490 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 0.8980 chunk 253 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 332 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 chunk 381 optimal weight: 5.9990 chunk 308 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 228 optimal weight: 0.6980 chunk 400 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37644 Z= 0.223 Angle : 0.550 6.869 50856 Z= 0.276 Chirality : 0.038 0.148 5832 Planarity : 0.003 0.055 6528 Dihedral : 6.183 126.591 5132 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.81 % Allowed : 10.67 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.12), residues: 4632 helix: 0.33 (0.12), residues: 1951 sheet: -2.88 (0.21), residues: 584 loop : -1.05 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 770 HIS 0.010 0.001 HIS F 433 PHE 0.025 0.001 PHE B 421 TYR 0.020 0.001 TYR A 360 ARG 0.008 0.000 ARG B 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 4.567 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.2364 (mmm) cc_final: 0.2075 (mmt) REVERT: A 206 MET cc_start: 0.4312 (ttp) cc_final: 0.4015 (tmm) REVERT: A 317 MET cc_start: 0.1213 (mmp) cc_final: 0.0792 (tpt) REVERT: A 424 ARG cc_start: 0.8930 (mtt-85) cc_final: 0.8375 (ttm-80) REVERT: A 773 MET cc_start: 0.8726 (ppp) cc_final: 0.8141 (ppp) REVERT: B 490 ASP cc_start: 0.8226 (p0) cc_final: 0.7654 (t0) REVERT: B 773 MET cc_start: 0.8189 (ppp) cc_final: 0.7874 (ppp) REVERT: C 653 MET cc_start: 0.8153 (ptp) cc_final: 0.7775 (ptp) REVERT: C 806 LEU cc_start: 0.8126 (pt) cc_final: 0.7745 (pp) REVERT: D 327 ASN cc_start: 0.7242 (m-40) cc_final: 0.6962 (t0) REVERT: D 397 GLN cc_start: 0.8022 (mt0) cc_final: 0.7612 (tp40) REVERT: D 637 CYS cc_start: 0.9157 (m) cc_final: 0.8826 (t) REVERT: D 756 MET cc_start: 0.6018 (mpp) cc_final: 0.5569 (ptm) REVERT: D 773 MET cc_start: 0.4583 (mmm) cc_final: 0.4121 (mpp) REVERT: D 810 MET cc_start: 0.8803 (mmt) cc_final: 0.8234 (mtt) REVERT: D 879 MET cc_start: 0.7291 (pmm) cc_final: 0.6982 (pmm) REVERT: E 406 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7686 (pp20) REVERT: E 441 GLU cc_start: 0.6332 (mm-30) cc_final: 0.6011 (mt-10) REVERT: E 653 MET cc_start: 0.7835 (pmm) cc_final: 0.6957 (pmm) REVERT: E 685 ASP cc_start: 0.8335 (t0) cc_final: 0.7640 (p0) REVERT: E 783 SER cc_start: 0.8972 (t) cc_final: 0.8637 (p) REVERT: F 671 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7819 (tm-30) outliers start: 33 outliers final: 30 residues processed: 249 average time/residue: 0.8996 time to fit residues: 373.0743 Evaluate side-chains 246 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 4.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 727 ILE Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 2.9990 chunk 402 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 262 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 447 optimal weight: 2.9990 chunk 371 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 37644 Z= 0.166 Angle : 0.521 8.414 50856 Z= 0.257 Chirality : 0.038 0.147 5832 Planarity : 0.003 0.041 6528 Dihedral : 5.980 117.086 5132 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.89 % Allowed : 11.09 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 4632 helix: 0.55 (0.12), residues: 1943 sheet: -2.66 (0.21), residues: 565 loop : -1.02 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 770 HIS 0.005 0.001 HIS F 433 PHE 0.021 0.001 PHE E 547 TYR 0.022 0.001 TYR E 394 ARG 0.004 0.000 ARG E 652 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 4.523 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.2435 (mmm) cc_final: 0.2151 (mmt) REVERT: A 206 MET cc_start: 0.4290 (ttp) cc_final: 0.3994 (tmm) REVERT: A 317 MET cc_start: 0.1257 (mmp) cc_final: 0.0843 (tpt) REVERT: A 424 ARG cc_start: 0.8928 (mtt-85) cc_final: 0.8361 (ttm-80) REVERT: A 773 MET cc_start: 0.8725 (ppp) cc_final: 0.8149 (ppp) REVERT: B 490 ASP cc_start: 0.8260 (p0) cc_final: 0.7661 (t0) REVERT: B 773 MET cc_start: 0.8200 (ppp) cc_final: 0.7865 (ppp) REVERT: C 552 MET cc_start: 0.7726 (ppp) cc_final: 0.7380 (ppp) REVERT: C 653 MET cc_start: 0.8136 (ptp) cc_final: 0.7803 (ptp) REVERT: C 806 LEU cc_start: 0.8073 (pt) cc_final: 0.7686 (pp) REVERT: D 327 ASN cc_start: 0.7226 (m-40) cc_final: 0.6943 (t0) REVERT: D 397 GLN cc_start: 0.7977 (mt0) cc_final: 0.7573 (tp40) REVERT: D 637 CYS cc_start: 0.9176 (m) cc_final: 0.8842 (t) REVERT: D 756 MET cc_start: 0.6059 (mpp) cc_final: 0.5605 (ptm) REVERT: D 773 MET cc_start: 0.4298 (mmm) cc_final: 0.3972 (mpp) REVERT: D 810 MET cc_start: 0.8819 (mmt) cc_final: 0.8241 (mtt) REVERT: D 879 MET cc_start: 0.7289 (pmm) cc_final: 0.6978 (pmm) REVERT: E 406 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7703 (pp20) REVERT: E 441 GLU cc_start: 0.6355 (mm-30) cc_final: 0.6081 (mt-10) REVERT: E 653 MET cc_start: 0.7835 (pmm) cc_final: 0.6830 (pmm) REVERT: E 655 MET cc_start: 0.7620 (mpp) cc_final: 0.7356 (mpp) REVERT: E 685 ASP cc_start: 0.8312 (t0) cc_final: 0.7647 (p0) REVERT: E 783 SER cc_start: 0.8942 (t) cc_final: 0.8629 (p) REVERT: F 272 MET cc_start: 0.0931 (ptp) cc_final: 0.0408 (ptp) REVERT: F 435 MET cc_start: 0.8334 (tmm) cc_final: 0.8006 (ttm) REVERT: F 621 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7575 (p0) REVERT: F 669 ILE cc_start: 0.8208 (mt) cc_final: 0.7888 (mt) REVERT: F 671 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7807 (tm-30) outliers start: 36 outliers final: 29 residues processed: 253 average time/residue: 0.9317 time to fit residues: 393.9948 Evaluate side-chains 246 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 727 ILE Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 621 ASP Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 2.9990 chunk 50 optimal weight: 0.0040 chunk 254 optimal weight: 3.9990 chunk 326 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 376 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 445 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 205 optimal weight: 8.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37644 Z= 0.284 Angle : 0.563 6.852 50856 Z= 0.283 Chirality : 0.039 0.154 5832 Planarity : 0.003 0.038 6528 Dihedral : 6.023 116.988 5132 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.94 % Allowed : 11.51 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.12), residues: 4632 helix: 0.44 (0.12), residues: 1959 sheet: -2.68 (0.21), residues: 580 loop : -1.12 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 770 HIS 0.006 0.001 HIS E 491 PHE 0.019 0.001 PHE F 947 TYR 0.019 0.001 TYR C 544 ARG 0.005 0.000 ARG E 652 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 220 time to evaluate : 4.528 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.2474 (mmm) cc_final: 0.2178 (mmt) REVERT: A 206 MET cc_start: 0.4295 (ttp) cc_final: 0.3991 (tmm) REVERT: A 317 MET cc_start: 0.1239 (mmp) cc_final: 0.0853 (tpt) REVERT: A 773 MET cc_start: 0.8767 (ppp) cc_final: 0.8210 (ppp) REVERT: B 773 MET cc_start: 0.8201 (ppp) cc_final: 0.7861 (ppp) REVERT: C 552 MET cc_start: 0.7752 (ppp) cc_final: 0.7476 (ppp) REVERT: C 653 MET cc_start: 0.8100 (ptp) cc_final: 0.7728 (ptp) REVERT: C 806 LEU cc_start: 0.8104 (pt) cc_final: 0.7722 (pp) REVERT: D 327 ASN cc_start: 0.7170 (m-40) cc_final: 0.6878 (t0) REVERT: D 397 GLN cc_start: 0.7983 (mt0) cc_final: 0.7578 (tp40) REVERT: D 637 CYS cc_start: 0.9139 (m) cc_final: 0.8814 (t) REVERT: D 756 MET cc_start: 0.6066 (mpp) cc_final: 0.5617 (ptm) REVERT: D 773 MET cc_start: 0.4396 (mmm) cc_final: 0.4004 (mpp) REVERT: D 810 MET cc_start: 0.8839 (mmt) cc_final: 0.8317 (mtt) REVERT: D 879 MET cc_start: 0.7419 (pmm) cc_final: 0.7035 (pmm) REVERT: E 406 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7701 (pp20) REVERT: E 441 GLU cc_start: 0.6367 (mm-30) cc_final: 0.6092 (mt-10) REVERT: E 653 MET cc_start: 0.7834 (pmm) cc_final: 0.6782 (pmm) REVERT: E 655 MET cc_start: 0.7711 (mpp) cc_final: 0.7442 (mpp) REVERT: E 685 ASP cc_start: 0.8381 (t0) cc_final: 0.7602 (p0) REVERT: E 766 MET cc_start: 0.7121 (mmt) cc_final: 0.6806 (mmt) REVERT: E 783 SER cc_start: 0.8959 (t) cc_final: 0.8658 (p) REVERT: F 435 MET cc_start: 0.8359 (tmm) cc_final: 0.8137 (tmm) REVERT: F 621 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7579 (p0) REVERT: F 671 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7838 (tm-30) outliers start: 38 outliers final: 35 residues processed: 249 average time/residue: 0.9006 time to fit residues: 374.4763 Evaluate side-chains 251 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 5.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 727 ILE Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 621 ASP Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 30.0000 chunk 177 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 220 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 350 optimal weight: 10.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 HIS ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37644 Z= 0.277 Angle : 0.563 6.768 50856 Z= 0.283 Chirality : 0.039 0.154 5832 Planarity : 0.004 0.040 6528 Dihedral : 6.043 115.012 5132 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.06 % Allowed : 11.80 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.12), residues: 4632 helix: 0.46 (0.12), residues: 1952 sheet: -2.68 (0.21), residues: 574 loop : -1.16 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 770 HIS 0.006 0.001 HIS F 433 PHE 0.022 0.001 PHE B 421 TYR 0.019 0.001 TYR C 544 ARG 0.005 0.000 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 4.540 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.2503 (mmm) cc_final: 0.2206 (mmt) REVERT: A 206 MET cc_start: 0.4296 (ttp) cc_final: 0.4002 (tmm) REVERT: A 317 MET cc_start: 0.1258 (mmp) cc_final: 0.0874 (tpt) REVERT: A 773 MET cc_start: 0.8772 (ppp) cc_final: 0.8262 (ppp) REVERT: B 773 MET cc_start: 0.8272 (ppp) cc_final: 0.7928 (ppp) REVERT: C 552 MET cc_start: 0.7746 (ppp) cc_final: 0.7508 (ppp) REVERT: C 653 MET cc_start: 0.8065 (ptp) cc_final: 0.7761 (ptp) REVERT: C 806 LEU cc_start: 0.8132 (pt) cc_final: 0.7741 (pp) REVERT: D 327 ASN cc_start: 0.7184 (m-40) cc_final: 0.6885 (t0) REVERT: D 397 GLN cc_start: 0.7999 (mt0) cc_final: 0.7598 (tp40) REVERT: D 637 CYS cc_start: 0.9143 (m) cc_final: 0.8810 (t) REVERT: D 756 MET cc_start: 0.6003 (mpp) cc_final: 0.5608 (ptm) REVERT: D 810 MET cc_start: 0.8844 (mmt) cc_final: 0.8331 (mtt) REVERT: D 879 MET cc_start: 0.7445 (pmm) cc_final: 0.6988 (pmm) REVERT: E 406 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7694 (pp20) REVERT: E 441 GLU cc_start: 0.6395 (mm-30) cc_final: 0.6139 (mt-10) REVERT: E 653 MET cc_start: 0.7830 (pmm) cc_final: 0.6919 (pmm) REVERT: E 685 ASP cc_start: 0.8343 (t0) cc_final: 0.7541 (p0) REVERT: E 783 SER cc_start: 0.8971 (t) cc_final: 0.8677 (p) REVERT: F 435 MET cc_start: 0.8339 (tmm) cc_final: 0.7992 (ttm) REVERT: F 621 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7566 (p0) REVERT: F 671 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7844 (tm-30) outliers start: 43 outliers final: 38 residues processed: 248 average time/residue: 0.9087 time to fit residues: 375.7595 Evaluate side-chains 251 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 212 time to evaluate : 4.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 727 ILE Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 621 ASP Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 20.0000 chunk 426 optimal weight: 4.9990 chunk 389 optimal weight: 4.9990 chunk 414 optimal weight: 0.5980 chunk 249 optimal weight: 7.9990 chunk 180 optimal weight: 7.9990 chunk 325 optimal weight: 20.0000 chunk 127 optimal weight: 0.6980 chunk 374 optimal weight: 4.9990 chunk 392 optimal weight: 2.9990 chunk 413 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 37644 Z= 0.245 Angle : 0.548 6.911 50856 Z= 0.274 Chirality : 0.039 0.147 5832 Planarity : 0.003 0.040 6528 Dihedral : 5.936 113.757 5130 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.04 % Allowed : 11.93 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.12), residues: 4632 helix: 0.54 (0.12), residues: 1951 sheet: -2.66 (0.21), residues: 583 loop : -1.14 (0.14), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.006 0.001 HIS F 433 PHE 0.018 0.001 PHE F 947 TYR 0.017 0.001 TYR A 360 ARG 0.004 0.000 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 213 time to evaluate : 4.538 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.2391 (mmm) cc_final: 0.2085 (mmt) REVERT: A 206 MET cc_start: 0.4298 (ttp) cc_final: 0.4011 (tmm) REVERT: A 317 MET cc_start: 0.1216 (mmp) cc_final: 0.0837 (tpt) REVERT: A 773 MET cc_start: 0.8762 (ppp) cc_final: 0.8297 (ppp) REVERT: B 773 MET cc_start: 0.8269 (ppp) cc_final: 0.7941 (ppp) REVERT: C 653 MET cc_start: 0.8030 (ptp) cc_final: 0.7722 (ptp) REVERT: C 806 LEU cc_start: 0.8068 (pt) cc_final: 0.7669 (pp) REVERT: D 327 ASN cc_start: 0.7166 (m-40) cc_final: 0.6875 (t0) REVERT: D 397 GLN cc_start: 0.7980 (mt0) cc_final: 0.7592 (tp40) REVERT: D 637 CYS cc_start: 0.9140 (m) cc_final: 0.8797 (t) REVERT: D 756 MET cc_start: 0.6105 (mpp) cc_final: 0.5715 (ptm) REVERT: D 810 MET cc_start: 0.8847 (mmt) cc_final: 0.8335 (mtt) REVERT: D 879 MET cc_start: 0.7447 (pmm) cc_final: 0.6993 (pmm) REVERT: E 406 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7774 (pp20) REVERT: E 441 GLU cc_start: 0.6370 (mm-30) cc_final: 0.6126 (mt-10) REVERT: E 653 MET cc_start: 0.7845 (pmm) cc_final: 0.6924 (pmm) REVERT: E 685 ASP cc_start: 0.8337 (t0) cc_final: 0.7561 (p0) REVERT: E 783 SER cc_start: 0.8967 (t) cc_final: 0.8676 (p) REVERT: F 435 MET cc_start: 0.8359 (tmm) cc_final: 0.8019 (ttm) REVERT: F 609 GLU cc_start: 0.8468 (pt0) cc_final: 0.8023 (tp30) REVERT: F 671 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7796 (tm-30) outliers start: 42 outliers final: 38 residues processed: 245 average time/residue: 0.9024 time to fit residues: 370.4562 Evaluate side-chains 246 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 208 time to evaluate : 4.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 727 ILE Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 3.9990 chunk 438 optimal weight: 3.9990 chunk 267 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 305 optimal weight: 10.0000 chunk 460 optimal weight: 2.9990 chunk 423 optimal weight: 10.0000 chunk 366 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 37644 Z= 0.286 Angle : 0.645 59.199 50856 Z= 0.347 Chirality : 0.039 0.369 5832 Planarity : 0.003 0.049 6528 Dihedral : 5.934 113.754 5130 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.01 % Allowed : 12.00 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.12), residues: 4632 helix: 0.54 (0.12), residues: 1952 sheet: -2.65 (0.21), residues: 583 loop : -1.15 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.006 0.001 HIS F 433 PHE 0.016 0.001 PHE F 947 TYR 0.017 0.001 TYR A 360 ARG 0.004 0.000 ARG E 652 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 207 time to evaluate : 4.564 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.2417 (mmm) cc_final: 0.2115 (mmt) REVERT: A 206 MET cc_start: 0.4296 (ttp) cc_final: 0.4012 (tmm) REVERT: A 317 MET cc_start: 0.1217 (mmp) cc_final: 0.0838 (tpt) REVERT: A 773 MET cc_start: 0.8762 (ppp) cc_final: 0.8299 (ppp) REVERT: B 773 MET cc_start: 0.8272 (ppp) cc_final: 0.7943 (ppp) REVERT: C 653 MET cc_start: 0.8032 (ptp) cc_final: 0.7721 (ptp) REVERT: C 806 LEU cc_start: 0.8069 (pt) cc_final: 0.7669 (pp) REVERT: D 327 ASN cc_start: 0.7166 (m-40) cc_final: 0.6875 (t0) REVERT: D 397 GLN cc_start: 0.7980 (mt0) cc_final: 0.7592 (tp40) REVERT: D 637 CYS cc_start: 0.9139 (m) cc_final: 0.8798 (t) REVERT: D 756 MET cc_start: 0.6135 (mpp) cc_final: 0.5735 (ptm) REVERT: D 810 MET cc_start: 0.8847 (mmt) cc_final: 0.8337 (mtt) REVERT: D 879 MET cc_start: 0.7448 (pmm) cc_final: 0.6994 (pmm) REVERT: E 406 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7774 (pp20) REVERT: E 441 GLU cc_start: 0.6367 (mm-30) cc_final: 0.6126 (mt-10) REVERT: E 653 MET cc_start: 0.7846 (pmm) cc_final: 0.6924 (pmm) REVERT: E 685 ASP cc_start: 0.8340 (t0) cc_final: 0.7563 (p0) REVERT: E 783 SER cc_start: 0.8967 (t) cc_final: 0.8677 (p) REVERT: F 435 MET cc_start: 0.8358 (tmm) cc_final: 0.8019 (ttm) REVERT: F 609 GLU cc_start: 0.8468 (pt0) cc_final: 0.8025 (tp30) REVERT: F 671 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7799 (tm-30) outliers start: 41 outliers final: 40 residues processed: 238 average time/residue: 0.9151 time to fit residues: 365.3587 Evaluate side-chains 247 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 4.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 727 ILE Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 803 THR Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 30.0000 chunk 390 optimal weight: 0.2980 chunk 112 optimal weight: 0.0050 chunk 337 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 367 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 376 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.160121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.111006 restraints weight = 270905.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.112232 restraints weight = 150678.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.111286 restraints weight = 106767.295| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 37644 Z= 0.286 Angle : 0.645 59.199 50856 Z= 0.347 Chirality : 0.039 0.369 5832 Planarity : 0.003 0.049 6528 Dihedral : 5.934 113.754 5130 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.99 % Allowed : 12.00 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.12), residues: 4632 helix: 0.54 (0.12), residues: 1952 sheet: -2.65 (0.21), residues: 583 loop : -1.15 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.006 0.001 HIS F 433 PHE 0.016 0.001 PHE F 947 TYR 0.017 0.001 TYR A 360 ARG 0.004 0.000 ARG E 652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10020.06 seconds wall clock time: 175 minutes 59.46 seconds (10559.46 seconds total)