Starting phenix.real_space_refine on Tue Feb 13 17:31:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fop_29353/02_2024/8fop_29353.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fop_29353/02_2024/8fop_29353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fop_29353/02_2024/8fop_29353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fop_29353/02_2024/8fop_29353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fop_29353/02_2024/8fop_29353.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fop_29353/02_2024/8fop_29353.pdb" } resolution = 3.2 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= 0.006 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 348 5.16 5 C 34702 2.51 5 N 9380 2.21 5 O 11054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 34": "OD1" <-> "OD2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "E ASP 86": "OD1" <-> "OD2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ASP 93": "OD1" <-> "OD2" Residue "G ASP 18": "OD1" <-> "OD2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G ASP 93": "OD1" <-> "OD2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "G ASP 111": "OD1" <-> "OD2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "I ASP 86": "OD1" <-> "OD2" Residue "J ASP 93": "OD1" <-> "OD2" Residue "J GLU 106": "OE1" <-> "OE2" Residue "J ASP 111": "OD1" <-> "OD2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ASP 34": "OD1" <-> "OD2" Residue "K ASP 35": "OD1" <-> "OD2" Residue "K ASP 86": "OD1" <-> "OD2" Residue "K ASP 93": "OD1" <-> "OD2" Residue "K ASP 111": "OD1" <-> "OD2" Residue "L TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 86": "OD1" <-> "OD2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "M GLU 31": "OE1" <-> "OE2" Residue "M TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 86": "OD1" <-> "OD2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "N PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N ASP 86": "OD1" <-> "OD2" Residue "N GLU 90": "OE1" <-> "OE2" Residue "N ASP 93": "OD1" <-> "OD2" Residue "N GLU 106": "OE1" <-> "OE2" Residue "N ASP 111": "OD1" <-> "OD2" Residue "N GLU 123": "OE1" <-> "OE2" Residue "O ASP 34": "OD1" <-> "OD2" Residue "O GLU 101": "OE1" <-> "OE2" Residue "P ASP 20": "OD1" <-> "OD2" Residue "P ASP 34": "OD1" <-> "OD2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "Q ASP 18": "OD1" <-> "OD2" Residue "Q ASP 93": "OD1" <-> "OD2" Residue "Q ASP 111": "OD1" <-> "OD2" Residue "R ASP 18": "OD1" <-> "OD2" Residue "R ASP 34": "OD1" <-> "OD2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R ASP 111": "OD1" <-> "OD2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S GLU 106": "OE1" <-> "OE2" Residue "T TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 37": "OD1" <-> "OD2" Residue "a TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 307": "OE1" <-> "OE2" Residue "a ASP 439": "OD1" <-> "OD2" Residue "a PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 227": "OD1" <-> "OD2" Residue "c PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 373": "OD1" <-> "OD2" Residue "c TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 400": "OE1" <-> "OE2" Residue "f PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 449": "OD1" <-> "OD2" Residue "g ASP 8": "OD1" <-> "OD2" Residue "g PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 439": "OD1" <-> "OD2" Residue "i ASP 267": "OD1" <-> "OD2" Residue "j TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 55484 Number of models: 1 Model: "" Number of chains: 30 Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 989 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 121} Chain: "C" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "D" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 989 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 121} Chain: "E" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "F" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 989 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 121} Chain: "G" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "J" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "K" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "L" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "M" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "N" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "O" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "P" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "Q" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "R" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 995 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 122} Chain: "S" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 989 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 121} Chain: "T" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3369 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 5 Chain: "U" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3485 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 24, 'TRANS': 435} Chain breaks: 5 Chain: "W" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3216 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 23, 'TRANS': 399} Chain breaks: 4 Chain: "X" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3418 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 23, 'TRANS': 425} Chain breaks: 5 Chain: "Z" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2115 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain breaks: 4 Chain: "a" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3076 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 379} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "c" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3113 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 21, 'TRANS': 386} Chain breaks: 3 Chain: "d" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3331 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 1 Chain: "f" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3030 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 20, 'TRANS': 376} Chain breaks: 2 Chain: "g" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2890 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 21, 'TRANS': 354} Chain breaks: 2 Chain: "i" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2868 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 20, 'TRANS': 352} Chain breaks: 2 Chain: "j" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3687 Classifications: {'peptide': 490} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 464} Chain breaks: 1 Time building chain proxies: 21.02, per 1000 atoms: 0.38 Number of scatterers: 55484 At special positions: 0 Unit cell: (208.44, 210.6, 142.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 348 16.00 O 11054 8.00 N 9380 7.00 C 34702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=67, symmetry=0 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS Q 82 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS E 43 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS R 82 " distance=2.03 Simple disulfide: pdb=" SG CYS C 82 " - pdb=" SG CYS F 43 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS S 82 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS G 43 " distance=2.03 Simple disulfide: pdb=" SG CYS E 82 " - pdb=" SG CYS H 43 " distance=2.03 Simple disulfide: pdb=" SG CYS G 82 " - pdb=" SG CYS J 43 " distance=2.03 Simple disulfide: pdb=" SG CYS H 82 " - pdb=" SG CYS K 43 " distance=2.03 Simple disulfide: pdb=" SG CYS I 82 " - pdb=" SG CYS L 43 " distance=2.03 Simple disulfide: pdb=" SG CYS J 82 " - pdb=" SG CYS M 43 " distance=2.03 Simple disulfide: pdb=" SG CYS K 82 " - pdb=" SG CYS N 43 " distance=2.03 Simple disulfide: pdb=" SG CYS L 82 " - pdb=" SG CYS O 43 " distance=2.03 Simple disulfide: pdb=" SG CYS M 82 " - pdb=" SG CYS P 43 " distance=2.03 Simple disulfide: pdb=" SG CYS N 82 " - pdb=" SG CYS Q 43 " distance=2.03 Simple disulfide: pdb=" SG CYS O 82 " - pdb=" SG CYS R 43 " distance=2.03 Simple disulfide: pdb=" SG CYS P 82 " - pdb=" SG CYS S 43 " distance=2.03 Simple disulfide: pdb=" SG CYS T 26 " - pdb=" SG CYS T 303 " distance=2.03 Simple disulfide: pdb=" SG CYS T 73 " - pdb=" SG CYS T 320 " distance=2.03 Simple disulfide: pdb=" SG CYS T 75 " - pdb=" SG CYS T 300 " distance=2.02 Simple disulfide: pdb=" SG CYS T 216 " - pdb=" SG CYS U 327 " distance=2.03 Simple disulfide: pdb=" SG CYS T 217 " - pdb=" SG CYS T 249 " distance=2.03 Simple disulfide: pdb=" SG CYS T 244 " - pdb=" SG CYS j 14 " distance=2.03 Simple disulfide: pdb=" SG CYS U 14 " - pdb=" SG CYS W 244 " distance=2.03 Simple disulfide: pdb=" SG CYS U 26 " - pdb=" SG CYS U 303 " distance=2.03 Simple disulfide: pdb=" SG CYS U 73 " - pdb=" SG CYS U 320 " distance=2.03 Simple disulfide: pdb=" SG CYS U 75 " - pdb=" SG CYS U 300 " distance=2.03 Simple disulfide: pdb=" SG CYS U 217 " - pdb=" SG CYS U 249 " distance=2.04 Simple disulfide: pdb=" SG CYS W 26 " - pdb=" SG CYS W 303 " distance=2.03 Simple disulfide: pdb=" SG CYS W 73 " - pdb=" SG CYS W 320 " distance=2.03 Simple disulfide: pdb=" SG CYS W 75 " - pdb=" SG CYS W 300 " distance=2.02 Simple disulfide: pdb=" SG CYS W 216 " - pdb=" SG CYS X 327 " distance=2.03 Simple disulfide: pdb=" SG CYS W 217 " - pdb=" SG CYS W 249 " distance=2.03 Simple disulfide: pdb=" SG CYS X 26 " - pdb=" SG CYS X 303 " distance=2.03 Simple disulfide: pdb=" SG CYS X 73 " - pdb=" SG CYS X 320 " distance=2.03 Simple disulfide: pdb=" SG CYS X 75 " - pdb=" SG CYS X 300 " distance=2.02 Simple disulfide: pdb=" SG CYS X 217 " - pdb=" SG CYS X 249 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 26 " - pdb=" SG CYS Z 303 " distance=2.03 Simple disulfide: pdb=" SG CYS a 26 " - pdb=" SG CYS a 303 " distance=2.03 Simple disulfide: pdb=" SG CYS a 73 " - pdb=" SG CYS a 320 " distance=2.03 Simple disulfide: pdb=" SG CYS a 75 " - pdb=" SG CYS a 300 " distance=2.03 Simple disulfide: pdb=" SG CYS a 217 " - pdb=" SG CYS a 249 " distance=2.03 Simple disulfide: pdb=" SG CYS c 26 " - pdb=" SG CYS c 303 " distance=2.03 Simple disulfide: pdb=" SG CYS c 73 " - pdb=" SG CYS c 320 " distance=2.03 Simple disulfide: pdb=" SG CYS c 75 " - pdb=" SG CYS c 300 " distance=2.02 Simple disulfide: pdb=" SG CYS c 217 " - pdb=" SG CYS c 249 " distance=2.03 Simple disulfide: pdb=" SG CYS d 26 " - pdb=" SG CYS d 303 " distance=2.03 Simple disulfide: pdb=" SG CYS d 73 " - pdb=" SG CYS d 320 " distance=2.03 Simple disulfide: pdb=" SG CYS d 75 " - pdb=" SG CYS d 300 " distance=2.02 Simple disulfide: pdb=" SG CYS d 217 " - pdb=" SG CYS d 249 " distance=2.03 Simple disulfide: pdb=" SG CYS f 26 " - pdb=" SG CYS f 303 " distance=2.03 Simple disulfide: pdb=" SG CYS f 73 " - pdb=" SG CYS f 320 " distance=2.03 Simple disulfide: pdb=" SG CYS f 75 " - pdb=" SG CYS f 300 " distance=2.02 Simple disulfide: pdb=" SG CYS f 217 " - pdb=" SG CYS f 249 " distance=2.03 Simple disulfide: pdb=" SG CYS g 26 " - pdb=" SG CYS g 303 " distance=2.03 Simple disulfide: pdb=" SG CYS g 73 " - pdb=" SG CYS g 320 " distance=2.03 Simple disulfide: pdb=" SG CYS g 75 " - pdb=" SG CYS g 300 " distance=2.04 Simple disulfide: pdb=" SG CYS g 217 " - pdb=" SG CYS g 249 " distance=2.04 Simple disulfide: pdb=" SG CYS i 26 " - pdb=" SG CYS i 303 " distance=2.03 Simple disulfide: pdb=" SG CYS i 73 " - pdb=" SG CYS i 320 " distance=2.04 Simple disulfide: pdb=" SG CYS i 75 " - pdb=" SG CYS i 300 " distance=2.03 Simple disulfide: pdb=" SG CYS i 216 " - pdb=" SG CYS j 327 " distance=2.03 Simple disulfide: pdb=" SG CYS i 217 " - pdb=" SG CYS i 249 " distance=2.03 Simple disulfide: pdb=" SG CYS j 26 " - pdb=" SG CYS j 303 " distance=2.03 Simple disulfide: pdb=" SG CYS j 73 " - pdb=" SG CYS j 320 " distance=2.03 Simple disulfide: pdb=" SG CYS j 75 " - pdb=" SG CYS j 300 " distance=2.04 Simple disulfide: pdb=" SG CYS j 217 " - pdb=" SG CYS j 249 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.43 Conformation dependent library (CDL) restraints added in 7.7 seconds 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13480 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 113 sheets defined 24.7% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'C' and resid 50 through 54 removed outlier: 4.294A pdb=" N GLY C 53 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C 54 " --> pdb=" O THR C 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 50 through 54' Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'E' and resid 75 through 81 removed outlier: 3.940A pdb=" N GLY E 81 " --> pdb=" O PHE E 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 81 removed outlier: 4.219A pdb=" N GLY F 81 " --> pdb=" O PHE F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 81 removed outlier: 4.199A pdb=" N GLY G 81 " --> pdb=" O PHE G 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 54 removed outlier: 4.124A pdb=" N GLY H 53 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'I' and resid 51 through 53 No H-bonds generated for 'chain 'I' and resid 51 through 53' Processing helix chain 'I' and resid 75 through 80 Processing helix chain 'J' and resid 75 through 80 Processing helix chain 'K' and resid 75 through 81 removed outlier: 4.131A pdb=" N GLY K 81 " --> pdb=" O PHE K 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 80 Processing helix chain 'M' and resid 75 through 81 removed outlier: 4.179A pdb=" N GLY M 81 " --> pdb=" O PHE M 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 81 removed outlier: 4.300A pdb=" N GLY N 81 " --> pdb=" O PHE N 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 80 Processing helix chain 'P' and resid 75 through 80 Processing helix chain 'Q' and resid 75 through 80 removed outlier: 4.104A pdb=" N TYR Q 79 " --> pdb=" O PRO Q 75 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN Q 80 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 75 through 80' Processing helix chain 'R' and resid 75 through 80 Processing helix chain 'S' and resid 75 through 80 Processing helix chain 'T' and resid 54 through 59 Processing helix chain 'T' and resid 62 through 75 Processing helix chain 'T' and resid 117 through 121 Processing helix chain 'T' and resid 133 through 143 Processing helix chain 'T' and resid 166 through 172 removed outlier: 3.747A pdb=" N GLY T 169 " --> pdb=" O GLY T 166 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU T 172 " --> pdb=" O GLY T 169 " (cutoff:3.500A) Processing helix chain 'T' and resid 208 through 213 Processing helix chain 'T' and resid 227 through 242 Processing helix chain 'T' and resid 260 through 268 removed outlier: 3.801A pdb=" N LEU T 265 " --> pdb=" O LEU T 261 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA T 266 " --> pdb=" O GLY T 262 " (cutoff:3.500A) Processing helix chain 'T' and resid 286 through 303 removed outlier: 3.512A pdb=" N THR T 290 " --> pdb=" O LEU T 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 316 Processing helix chain 'T' and resid 332 through 342 Processing helix chain 'T' and resid 384 through 402 removed outlier: 4.263A pdb=" N ARG T 388 " --> pdb=" O ASP T 384 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG T 389 " --> pdb=" O ALA T 385 " (cutoff:3.500A) Processing helix chain 'T' and resid 403 through 406 Processing helix chain 'T' and resid 425 through 440 Processing helix chain 'T' and resid 450 through 454 Processing helix chain 'U' and resid 52 through 59 removed outlier: 4.401A pdb=" N GLU U 56 " --> pdb=" O LEU U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 75 Processing helix chain 'U' and resid 117 through 121 Processing helix chain 'U' and resid 131 through 143 Processing helix chain 'U' and resid 166 through 170 removed outlier: 3.829A pdb=" N GLY U 169 " --> pdb=" O GLY U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 208 through 213 Processing helix chain 'U' and resid 227 through 242 removed outlier: 3.696A pdb=" N TRP U 242 " --> pdb=" O ILE U 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 260 through 267 removed outlier: 3.606A pdb=" N ALA U 266 " --> pdb=" O GLY U 262 " (cutoff:3.500A) Processing helix chain 'U' and resid 286 through 303 removed outlier: 3.537A pdb=" N THR U 290 " --> pdb=" O LEU U 286 " (cutoff:3.500A) Processing helix chain 'U' and resid 311 through 316 Processing helix chain 'U' and resid 332 through 342 Processing helix chain 'U' and resid 384 through 402 removed outlier: 3.947A pdb=" N ARG U 388 " --> pdb=" O ASP U 384 " (cutoff:3.500A) Processing helix chain 'U' and resid 403 through 406 Processing helix chain 'U' and resid 425 through 440 Processing helix chain 'U' and resid 450 through 454 Processing helix chain 'W' and resid 53 through 59 Processing helix chain 'W' and resid 62 through 75 Processing helix chain 'W' and resid 134 through 141 Processing helix chain 'W' and resid 166 through 172 removed outlier: 3.949A pdb=" N GLY W 169 " --> pdb=" O GLY W 166 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS W 171 " --> pdb=" O ILE W 168 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU W 172 " --> pdb=" O GLY W 169 " (cutoff:3.500A) Processing helix chain 'W' and resid 208 through 213 Processing helix chain 'W' and resid 227 through 242 Processing helix chain 'W' and resid 260 through 267 removed outlier: 3.672A pdb=" N ALA W 266 " --> pdb=" O GLY W 262 " (cutoff:3.500A) Processing helix chain 'W' and resid 286 through 303 removed outlier: 3.839A pdb=" N THR W 290 " --> pdb=" O LEU W 286 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 316 Processing helix chain 'W' and resid 332 through 342 Processing helix chain 'W' and resid 384 through 403 removed outlier: 3.955A pdb=" N ARG W 388 " --> pdb=" O ASP W 384 " (cutoff:3.500A) Processing helix chain 'W' and resid 404 through 406 No H-bonds generated for 'chain 'W' and resid 404 through 406' Processing helix chain 'W' and resid 425 through 440 Processing helix chain 'W' and resid 450 through 454 Processing helix chain 'X' and resid 53 through 59 Processing helix chain 'X' and resid 62 through 75 Processing helix chain 'X' and resid 117 through 121 Processing helix chain 'X' and resid 131 through 143 Processing helix chain 'X' and resid 166 through 171 removed outlier: 3.868A pdb=" N GLY X 169 " --> pdb=" O GLY X 166 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS X 171 " --> pdb=" O ILE X 168 " (cutoff:3.500A) Processing helix chain 'X' and resid 208 through 213 Processing helix chain 'X' and resid 227 through 242 removed outlier: 3.595A pdb=" N TRP X 242 " --> pdb=" O ILE X 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 260 through 267 removed outlier: 3.570A pdb=" N ALA X 266 " --> pdb=" O GLY X 262 " (cutoff:3.500A) Processing helix chain 'X' and resid 286 through 302 removed outlier: 3.592A pdb=" N THR X 290 " --> pdb=" O LEU X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 316 removed outlier: 3.651A pdb=" N PHE X 315 " --> pdb=" O GLN X 311 " (cutoff:3.500A) Processing helix chain 'X' and resid 332 through 342 Processing helix chain 'X' and resid 384 through 402 removed outlier: 3.874A pdb=" N ARG X 388 " --> pdb=" O ASP X 384 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG X 389 " --> pdb=" O ALA X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 403 through 405 No H-bonds generated for 'chain 'X' and resid 403 through 405' Processing helix chain 'X' and resid 425 through 440 Processing helix chain 'X' and resid 450 through 454 Processing helix chain 'X' and resid 461 through 463 No H-bonds generated for 'chain 'X' and resid 461 through 463' Processing helix chain 'Z' and resid 53 through 59 Processing helix chain 'Z' and resid 62 through 73 removed outlier: 3.572A pdb=" N ARG Z 69 " --> pdb=" O THR Z 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 227 through 242 Processing helix chain 'Z' and resid 289 through 303 Processing helix chain 'Z' and resid 311 through 316 removed outlier: 3.578A pdb=" N PHE Z 315 " --> pdb=" O GLN Z 311 " (cutoff:3.500A) Processing helix chain 'Z' and resid 332 through 342 Processing helix chain 'Z' and resid 384 through 403 removed outlier: 3.776A pdb=" N ARG Z 388 " --> pdb=" O ASP Z 384 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN Z 403 " --> pdb=" O ALA Z 399 " (cutoff:3.500A) Processing helix chain 'Z' and resid 404 through 406 No H-bonds generated for 'chain 'Z' and resid 404 through 406' Processing helix chain 'Z' and resid 425 through 440 Processing helix chain 'Z' and resid 450 through 454 Processing helix chain 'Z' and resid 461 through 463 No H-bonds generated for 'chain 'Z' and resid 461 through 463' Processing helix chain 'a' and resid 53 through 59 Processing helix chain 'a' and resid 62 through 74 Processing helix chain 'a' and resid 166 through 170 removed outlier: 3.692A pdb=" N GLY a 169 " --> pdb=" O GLY a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 213 Processing helix chain 'a' and resid 227 through 241 Processing helix chain 'a' and resid 260 through 265 Processing helix chain 'a' and resid 286 through 303 removed outlier: 3.665A pdb=" N THR a 290 " --> pdb=" O LEU a 286 " (cutoff:3.500A) Processing helix chain 'a' and resid 311 through 316 removed outlier: 3.556A pdb=" N PHE a 315 " --> pdb=" O GLN a 311 " (cutoff:3.500A) Processing helix chain 'a' and resid 332 through 341 Processing helix chain 'a' and resid 379 through 383 removed outlier: 3.822A pdb=" N PHE a 382 " --> pdb=" O ASN a 379 " (cutoff:3.500A) Processing helix chain 'a' and resid 384 through 403 removed outlier: 3.790A pdb=" N ARG a 388 " --> pdb=" O ASP a 384 " (cutoff:3.500A) Processing helix chain 'a' and resid 404 through 406 No H-bonds generated for 'chain 'a' and resid 404 through 406' Processing helix chain 'a' and resid 425 through 440 Processing helix chain 'a' and resid 450 through 454 Processing helix chain 'a' and resid 460 through 464 Processing helix chain 'c' and resid 53 through 58 Processing helix chain 'c' and resid 62 through 75 Processing helix chain 'c' and resid 166 through 170 removed outlier: 4.069A pdb=" N GLY c 169 " --> pdb=" O GLY c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 208 through 213 Processing helix chain 'c' and resid 227 through 242 Processing helix chain 'c' and resid 260 through 268 removed outlier: 3.691A pdb=" N GLY c 268 " --> pdb=" O VAL c 264 " (cutoff:3.500A) Processing helix chain 'c' and resid 286 through 303 removed outlier: 3.563A pdb=" N THR c 290 " --> pdb=" O LEU c 286 " (cutoff:3.500A) Processing helix chain 'c' and resid 311 through 316 removed outlier: 3.631A pdb=" N PHE c 315 " --> pdb=" O GLN c 311 " (cutoff:3.500A) Processing helix chain 'c' and resid 332 through 342 Processing helix chain 'c' and resid 384 through 403 removed outlier: 4.133A pdb=" N ARG c 388 " --> pdb=" O ASP c 384 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG c 389 " --> pdb=" O ALA c 385 " (cutoff:3.500A) Processing helix chain 'c' and resid 404 through 406 No H-bonds generated for 'chain 'c' and resid 404 through 406' Processing helix chain 'c' and resid 425 through 440 Processing helix chain 'c' and resid 450 through 454 Processing helix chain 'c' and resid 460 through 464 removed outlier: 3.768A pdb=" N GLN c 464 " --> pdb=" O ASP c 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 460 through 464' Processing helix chain 'd' and resid 51 through 59 removed outlier: 4.284A pdb=" N ILE d 55 " --> pdb=" O GLU d 51 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU d 56 " --> pdb=" O LEU d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 75 Processing helix chain 'd' and resid 166 through 171 removed outlier: 3.500A pdb=" N GLY d 169 " --> pdb=" O GLY d 166 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS d 171 " --> pdb=" O ILE d 168 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 185 removed outlier: 3.953A pdb=" N VAL d 185 " --> pdb=" O CYS d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 208 through 213 Processing helix chain 'd' and resid 227 through 242 removed outlier: 3.636A pdb=" N TRP d 242 " --> pdb=" O ILE d 238 " (cutoff:3.500A) Processing helix chain 'd' and resid 260 through 268 removed outlier: 3.677A pdb=" N LEU d 265 " --> pdb=" O LEU d 261 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA d 266 " --> pdb=" O GLY d 262 " (cutoff:3.500A) Processing helix chain 'd' and resid 286 through 303 removed outlier: 3.545A pdb=" N THR d 290 " --> pdb=" O LEU d 286 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 316 Processing helix chain 'd' and resid 332 through 342 Processing helix chain 'd' and resid 379 through 383 removed outlier: 4.265A pdb=" N PHE d 382 " --> pdb=" O ASN d 379 " (cutoff:3.500A) Processing helix chain 'd' and resid 384 through 402 removed outlier: 3.807A pdb=" N ARG d 388 " --> pdb=" O ASP d 384 " (cutoff:3.500A) Processing helix chain 'd' and resid 403 through 406 Processing helix chain 'd' and resid 425 through 440 Processing helix chain 'd' and resid 450 through 454 Processing helix chain 'f' and resid 50 through 52 No H-bonds generated for 'chain 'f' and resid 50 through 52' Processing helix chain 'f' and resid 53 through 59 Processing helix chain 'f' and resid 62 through 75 Processing helix chain 'f' and resid 166 through 170 removed outlier: 3.583A pdb=" N GLY f 169 " --> pdb=" O GLY f 166 " (cutoff:3.500A) Processing helix chain 'f' and resid 208 through 213 Processing helix chain 'f' and resid 227 through 241 Processing helix chain 'f' and resid 262 through 267 Processing helix chain 'f' and resid 286 through 303 removed outlier: 3.636A pdb=" N THR f 290 " --> pdb=" O LEU f 286 " (cutoff:3.500A) Processing helix chain 'f' and resid 332 through 342 Processing helix chain 'f' and resid 384 through 403 removed outlier: 4.110A pdb=" N ARG f 388 " --> pdb=" O ASP f 384 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG f 389 " --> pdb=" O ALA f 385 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN f 403 " --> pdb=" O ALA f 399 " (cutoff:3.500A) Processing helix chain 'f' and resid 404 through 406 No H-bonds generated for 'chain 'f' and resid 404 through 406' Processing helix chain 'f' and resid 425 through 440 Processing helix chain 'f' and resid 450 through 455 removed outlier: 3.893A pdb=" N ILE f 455 " --> pdb=" O ILE f 451 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 464 Processing helix chain 'g' and resid 63 through 75 Processing helix chain 'g' and resid 208 through 213 Processing helix chain 'g' and resid 227 through 242 Processing helix chain 'g' and resid 260 through 265 Processing helix chain 'g' and resid 286 through 293 removed outlier: 3.662A pdb=" N THR g 290 " --> pdb=" O LEU g 286 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA g 292 " --> pdb=" O TYR g 288 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA g 293 " --> pdb=" O LEU g 289 " (cutoff:3.500A) Processing helix chain 'g' and resid 296 through 302 Processing helix chain 'g' and resid 333 through 342 removed outlier: 3.764A pdb=" N ALA g 341 " --> pdb=" O THR g 337 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN g 342 " --> pdb=" O GLN g 338 " (cutoff:3.500A) Processing helix chain 'g' and resid 384 through 402 removed outlier: 4.184A pdb=" N ARG g 388 " --> pdb=" O ASP g 384 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG g 389 " --> pdb=" O ALA g 385 " (cutoff:3.500A) Processing helix chain 'g' and resid 425 through 440 Processing helix chain 'g' and resid 450 through 454 Processing helix chain 'i' and resid 53 through 59 Processing helix chain 'i' and resid 62 through 75 Processing helix chain 'i' and resid 208 through 213 Processing helix chain 'i' and resid 227 through 242 Processing helix chain 'i' and resid 260 through 265 removed outlier: 3.664A pdb=" N LEU i 265 " --> pdb=" O LEU i 261 " (cutoff:3.500A) Processing helix chain 'i' and resid 286 through 303 removed outlier: 3.767A pdb=" N THR i 290 " --> pdb=" O LEU i 286 " (cutoff:3.500A) Processing helix chain 'i' and resid 311 through 316 removed outlier: 3.723A pdb=" N PHE i 315 " --> pdb=" O GLN i 311 " (cutoff:3.500A) Processing helix chain 'i' and resid 332 through 341 Processing helix chain 'i' and resid 384 through 403 removed outlier: 4.202A pdb=" N ARG i 388 " --> pdb=" O ASP i 384 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG i 389 " --> pdb=" O ALA i 385 " (cutoff:3.500A) Processing helix chain 'i' and resid 404 through 406 No H-bonds generated for 'chain 'i' and resid 404 through 406' Processing helix chain 'i' and resid 425 through 440 Processing helix chain 'i' and resid 450 through 454 Processing helix chain 'j' and resid 53 through 59 Processing helix chain 'j' and resid 62 through 75 Processing helix chain 'j' and resid 117 through 121 Processing helix chain 'j' and resid 131 through 143 Processing helix chain 'j' and resid 166 through 171 removed outlier: 3.643A pdb=" N GLY j 169 " --> pdb=" O GLY j 166 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS j 171 " --> pdb=" O ILE j 168 " (cutoff:3.500A) Processing helix chain 'j' and resid 208 through 213 Processing helix chain 'j' and resid 227 through 242 Processing helix chain 'j' and resid 260 through 268 removed outlier: 3.669A pdb=" N LEU j 265 " --> pdb=" O LEU j 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA j 266 " --> pdb=" O GLY j 262 " (cutoff:3.500A) Processing helix chain 'j' and resid 286 through 303 removed outlier: 3.625A pdb=" N THR j 290 " --> pdb=" O LEU j 286 " (cutoff:3.500A) Processing helix chain 'j' and resid 311 through 316 removed outlier: 3.808A pdb=" N PHE j 315 " --> pdb=" O GLN j 311 " (cutoff:3.500A) Processing helix chain 'j' and resid 332 through 342 Processing helix chain 'j' and resid 384 through 402 removed outlier: 3.749A pdb=" N ARG j 388 " --> pdb=" O ASP j 384 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG j 389 " --> pdb=" O ALA j 385 " (cutoff:3.500A) Processing helix chain 'j' and resid 403 through 406 Processing helix chain 'j' and resid 425 through 440 Processing helix chain 'j' and resid 450 through 454 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 24 through 29 removed outlier: 6.177A pdb=" N ILE B 14 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 29 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 12 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 40 Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'C' and resid 24 through 29 removed outlier: 5.585A pdb=" N ILE C 14 " --> pdb=" O PRO C 27 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER C 29 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 12 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 24 through 29 removed outlier: 5.585A pdb=" N ILE C 14 " --> pdb=" O PRO C 27 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER C 29 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 12 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU C 90 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE C 12 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN C 88 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 39 through 40 removed outlier: 3.619A pdb=" N ALA C 121 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AB1, first strand: chain 'D' and resid 24 through 29 removed outlier: 5.506A pdb=" N ILE D 14 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER D 29 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE D 12 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU D 90 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE D 12 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN D 88 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE D 14 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP D 86 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE D 16 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN D 84 " --> pdb=" O PHE D 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 40 Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AB4, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 29 removed outlier: 5.892A pdb=" N ILE E 14 " --> pdb=" O PRO E 27 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER E 29 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 12 " --> pdb=" O SER E 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 24 through 29 removed outlier: 5.892A pdb=" N ILE E 14 " --> pdb=" O PRO E 27 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER E 29 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 12 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU E 90 " --> pdb=" O LYS E 10 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE E 12 " --> pdb=" O GLN E 88 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN E 88 " --> pdb=" O ILE E 12 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 49 Processing sheet with id=AB9, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AC1, first strand: chain 'F' and resid 24 through 29 removed outlier: 5.486A pdb=" N ILE F 14 " --> pdb=" O PRO F 27 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER F 29 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE F 12 " --> pdb=" O SER F 29 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 24 through 29 removed outlier: 5.486A pdb=" N ILE F 14 " --> pdb=" O PRO F 27 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER F 29 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE F 12 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN F 11 " --> pdb=" O GLU F 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 39 through 41 removed outlier: 3.505A pdb=" N THR F 63 " --> pdb=" O LYS F 41 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 45 through 46 Processing sheet with id=AC5, first strand: chain 'G' and resid 25 through 29 removed outlier: 5.618A pdb=" N ILE G 14 " --> pdb=" O PRO G 27 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER G 29 " --> pdb=" O ILE G 12 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE G 12 " --> pdb=" O SER G 29 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 25 through 29 removed outlier: 5.618A pdb=" N ILE G 14 " --> pdb=" O PRO G 27 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER G 29 " --> pdb=" O ILE G 12 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE G 12 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU G 90 " --> pdb=" O LYS G 10 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE G 12 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN G 88 " --> pdb=" O ILE G 12 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AC8, first strand: chain 'G' and resid 45 through 46 Processing sheet with id=AC9, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AD1, first strand: chain 'H' and resid 24 through 29 removed outlier: 5.964A pdb=" N ILE H 14 " --> pdb=" O PRO H 27 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER H 29 " --> pdb=" O ILE H 12 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE H 12 " --> pdb=" O SER H 29 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 39 through 40 Processing sheet with id=AD3, first strand: chain 'H' and resid 45 through 46 Processing sheet with id=AD4, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AD5, first strand: chain 'I' and resid 24 through 29 removed outlier: 5.619A pdb=" N ILE I 14 " --> pdb=" O PRO I 27 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER I 29 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE I 12 " --> pdb=" O SER I 29 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 24 through 29 removed outlier: 5.619A pdb=" N ILE I 14 " --> pdb=" O PRO I 27 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER I 29 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE I 12 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU I 90 " --> pdb=" O LYS I 10 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE I 12 " --> pdb=" O GLN I 88 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN I 88 " --> pdb=" O ILE I 12 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 39 through 40 Processing sheet with id=AD8, first strand: chain 'J' and resid 24 through 29 removed outlier: 5.561A pdb=" N ILE J 14 " --> pdb=" O PRO J 27 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER J 29 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE J 12 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU J 90 " --> pdb=" O LYS J 10 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE J 12 " --> pdb=" O GLN J 88 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN J 88 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE J 14 " --> pdb=" O ASP J 86 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP J 86 " --> pdb=" O ILE J 14 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE J 16 " --> pdb=" O GLN J 84 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN J 84 " --> pdb=" O PHE J 16 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 39 through 40 removed outlier: 3.578A pdb=" N ALA J 121 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 45 through 46 removed outlier: 3.527A pdb=" N SER J 58 " --> pdb=" O THR J 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 6 through 7 Processing sheet with id=AE3, first strand: chain 'K' and resid 24 through 29 removed outlier: 5.839A pdb=" N ILE K 14 " --> pdb=" O PRO K 27 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER K 29 " --> pdb=" O ILE K 12 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE K 12 " --> pdb=" O SER K 29 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN K 11 " --> pdb=" O GLU K 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 39 through 41 removed outlier: 3.543A pdb=" N ALA K 62 " --> pdb=" O ALA K 121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 45 through 49 removed outlier: 3.502A pdb=" N SER K 58 " --> pdb=" O THR K 46 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 23 through 29 removed outlier: 3.761A pdb=" N GLU L 23 " --> pdb=" O ASP L 18 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE L 14 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER L 29 " --> pdb=" O ILE L 12 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE L 12 " --> pdb=" O SER L 29 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU L 90 " --> pdb=" O LYS L 10 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE L 12 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN L 88 " --> pdb=" O ILE L 12 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE L 14 " --> pdb=" O ASP L 86 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP L 86 " --> pdb=" O ILE L 14 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE L 16 " --> pdb=" O GLN L 84 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN L 84 " --> pdb=" O PHE L 16 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 39 through 40 Processing sheet with id=AE8, first strand: chain 'M' and resid 24 through 29 removed outlier: 5.899A pdb=" N ILE M 14 " --> pdb=" O PRO M 27 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER M 29 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE M 12 " --> pdb=" O SER M 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 24 through 29 removed outlier: 5.899A pdb=" N ILE M 14 " --> pdb=" O PRO M 27 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER M 29 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE M 12 " --> pdb=" O SER M 29 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 39 through 40 Processing sheet with id=AF2, first strand: chain 'M' and resid 45 through 46 Processing sheet with id=AF3, first strand: chain 'N' and resid 6 through 7 Processing sheet with id=AF4, first strand: chain 'N' and resid 24 through 29 removed outlier: 6.052A pdb=" N ILE N 14 " --> pdb=" O PRO N 27 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER N 29 " --> pdb=" O ILE N 12 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE N 12 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU N 90 " --> pdb=" O LYS N 10 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE N 12 " --> pdb=" O GLN N 88 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN N 88 " --> pdb=" O ILE N 12 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE N 14 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP N 86 " --> pdb=" O ILE N 14 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE N 16 " --> pdb=" O GLN N 84 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLN N 84 " --> pdb=" O PHE N 16 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 39 through 40 Processing sheet with id=AF6, first strand: chain 'N' and resid 45 through 49 Processing sheet with id=AF7, first strand: chain 'O' and resid 24 through 29 removed outlier: 6.090A pdb=" N ILE O 14 " --> pdb=" O PRO O 27 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER O 29 " --> pdb=" O ILE O 12 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE O 12 " --> pdb=" O SER O 29 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 39 through 40 Processing sheet with id=AF9, first strand: chain 'P' and resid 24 through 29 removed outlier: 5.632A pdb=" N ILE P 14 " --> pdb=" O PRO P 27 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER P 29 " --> pdb=" O ILE P 12 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE P 12 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU P 90 " --> pdb=" O LYS P 10 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE P 12 " --> pdb=" O GLN P 88 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN P 88 " --> pdb=" O ILE P 12 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE P 14 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP P 86 " --> pdb=" O ILE P 14 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE P 16 " --> pdb=" O GLN P 84 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN P 84 " --> pdb=" O PHE P 16 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 39 through 40 Processing sheet with id=AG2, first strand: chain 'P' and resid 45 through 49 Processing sheet with id=AG3, first strand: chain 'Q' and resid 6 through 7 removed outlier: 6.123A pdb=" N ASN Q 7 " --> pdb=" O ARG R 57 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ALA R 59 " --> pdb=" O ASN Q 7 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 24 through 29 removed outlier: 5.966A pdb=" N ILE Q 14 " --> pdb=" O PRO Q 27 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER Q 29 " --> pdb=" O ILE Q 12 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE Q 12 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU Q 90 " --> pdb=" O LYS Q 10 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE Q 12 " --> pdb=" O GLN Q 88 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN Q 88 " --> pdb=" O ILE Q 12 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE Q 14 " --> pdb=" O ASP Q 86 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP Q 86 " --> pdb=" O ILE Q 14 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE Q 16 " --> pdb=" O GLN Q 84 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN Q 84 " --> pdb=" O PHE Q 16 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR Q 98 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 39 through 40 Processing sheet with id=AG6, first strand: chain 'Q' and resid 45 through 49 removed outlier: 3.523A pdb=" N GLN Q 56 " --> pdb=" O THR Q 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 6 through 7 Processing sheet with id=AG8, first strand: chain 'R' and resid 24 through 29 removed outlier: 5.394A pdb=" N ILE R 14 " --> pdb=" O PRO R 27 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER R 29 " --> pdb=" O ILE R 12 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE R 12 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLU R 90 " --> pdb=" O LYS R 10 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE R 12 " --> pdb=" O GLN R 88 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN R 88 " --> pdb=" O ILE R 12 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE R 14 " --> pdb=" O ASP R 86 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP R 86 " --> pdb=" O ILE R 14 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE R 16 " --> pdb=" O GLN R 84 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN R 84 " --> pdb=" O PHE R 16 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 39 through 40 removed outlier: 3.522A pdb=" N ALA R 121 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 24 through 29 removed outlier: 5.488A pdb=" N ILE S 14 " --> pdb=" O PRO S 27 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER S 29 " --> pdb=" O ILE S 12 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE S 12 " --> pdb=" O SER S 29 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU S 90 " --> pdb=" O LYS S 10 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE S 12 " --> pdb=" O GLN S 88 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN S 88 " --> pdb=" O ILE S 12 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE S 14 " --> pdb=" O ASP S 86 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP S 86 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE S 16 " --> pdb=" O GLN S 84 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN S 84 " --> pdb=" O PHE S 16 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 39 through 40 Processing sheet with id=AH3, first strand: chain 'S' and resid 45 through 46 Processing sheet with id=AH4, first strand: chain 'T' and resid 46 through 48 removed outlier: 4.185A pdb=" N VAL T 81 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE T 28 " --> pdb=" O TYR T 82 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU T 84 " --> pdb=" O ILE T 28 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL T 30 " --> pdb=" O LEU T 84 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ARG T 86 " --> pdb=" O VAL T 30 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY T 32 " --> pdb=" O ARG T 86 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR T 221 " --> pdb=" O TYR T 254 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N PHE T 256 " --> pdb=" O TYR T 221 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LEU T 223 " --> pdb=" O PHE T 256 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N LYS T 258 " --> pdb=" O LEU T 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL T 255 " --> pdb=" O SER T 275 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'T' and resid 96 through 98 Processing sheet with id=AH6, first strand: chain 'T' and resid 114 through 115 Processing sheet with id=AH7, first strand: chain 'T' and resid 347 through 349 Processing sheet with id=AH8, first strand: chain 'T' and resid 455 through 459 Processing sheet with id=AH9, first strand: chain 'U' and resid 46 through 47 removed outlier: 5.927A pdb=" N ILE U 28 " --> pdb=" O TYR U 82 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU U 84 " --> pdb=" O ILE U 28 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL U 30 " --> pdb=" O LEU U 84 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ARG U 86 " --> pdb=" O VAL U 30 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY U 32 " --> pdb=" O ARG U 86 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU U 223 " --> pdb=" O TYR U 254 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N PHE U 256 " --> pdb=" O LEU U 223 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL U 255 " --> pdb=" O SER U 275 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'U' and resid 149 through 151 removed outlier: 3.560A pdb=" N THR U 161 " --> pdb=" O ALA U 150 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'U' and resid 347 through 349 Processing sheet with id=AI3, first strand: chain 'U' and resid 455 through 459 Processing sheet with id=AI4, first strand: chain 'W' and resid 46 through 48 removed outlier: 3.888A pdb=" N VAL W 81 " --> pdb=" O VAL W 48 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE W 28 " --> pdb=" O TYR W 82 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU W 84 " --> pdb=" O ILE W 28 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL W 30 " --> pdb=" O LEU W 84 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ARG W 86 " --> pdb=" O VAL W 30 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY W 32 " --> pdb=" O ARG W 86 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU W 223 " --> pdb=" O TYR W 254 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N PHE W 256 " --> pdb=" O LEU W 223 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY W 253 " --> pdb=" O SER W 275 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU W 277 " --> pdb=" O GLY W 253 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL W 255 " --> pdb=" O LEU W 277 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU W 279 " --> pdb=" O VAL W 255 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN W 257 " --> pdb=" O LEU W 279 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'W' and resid 96 through 97 Processing sheet with id=AI6, first strand: chain 'W' and resid 347 through 349 Processing sheet with id=AI7, first strand: chain 'W' and resid 455 through 459 removed outlier: 8.052A pdb=" N ASN X 492 " --> pdb=" O PHE W 474 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU W 476 " --> pdb=" O ASN X 492 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'X' and resid 46 through 47 removed outlier: 3.762A pdb=" N GLY X 32 " --> pdb=" O LEU X 84 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR X 221 " --> pdb=" O TYR X 254 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N PHE X 256 " --> pdb=" O TYR X 221 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N LEU X 223 " --> pdb=" O PHE X 256 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N LYS X 258 " --> pdb=" O LEU X 223 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'X' and resid 96 through 98 removed outlier: 3.555A pdb=" N THR X 161 " --> pdb=" O ALA X 150 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'X' and resid 113 through 115 Processing sheet with id=AJ2, first strand: chain 'X' and resid 347 through 349 Processing sheet with id=AJ3, first strand: chain 'X' and resid 455 through 459 Processing sheet with id=AJ4, first strand: chain 'Z' and resid 346 through 347 removed outlier: 3.776A pdb=" N VAL Z 346 " --> pdb=" O TYR Z 364 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Z' and resid 455 through 459 removed outlier: 7.986A pdb=" N ASN a 492 " --> pdb=" O PHE Z 474 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU Z 476 " --> pdb=" O ASN a 492 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'a' and resid 46 through 48 removed outlier: 4.547A pdb=" N VAL a 81 " --> pdb=" O VAL a 48 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE a 28 " --> pdb=" O TYR a 82 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU a 84 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL a 30 " --> pdb=" O LEU a 84 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG a 86 " --> pdb=" O VAL a 30 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY a 32 " --> pdb=" O ARG a 86 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS a 27 " --> pdb=" O VAL a 220 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N VAL a 222 " --> pdb=" O LYS a 27 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU a 29 " --> pdb=" O VAL a 222 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE a 256 " --> pdb=" O LEU a 223 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY a 253 " --> pdb=" O SER a 275 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU a 277 " --> pdb=" O GLY a 253 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL a 255 " --> pdb=" O LEU a 277 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL a 345 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG a 276 " --> pdb=" O VAL a 345 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'a' and resid 347 through 349 Processing sheet with id=AJ8, first strand: chain 'a' and resid 455 through 459 Processing sheet with id=AJ9, first strand: chain 'c' and resid 46 through 47 removed outlier: 3.678A pdb=" N GLY c 32 " --> pdb=" O LEU c 84 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N PHE c 256 " --> pdb=" O LEU c 223 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY c 253 " --> pdb=" O SER c 275 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU c 277 " --> pdb=" O GLY c 253 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL c 255 " --> pdb=" O LEU c 277 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU c 279 " --> pdb=" O VAL c 255 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN c 257 " --> pdb=" O LEU c 279 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N VAL c 345 " --> pdb=" O LEU c 274 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG c 276 " --> pdb=" O VAL c 345 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N SER c 347 " --> pdb=" O ARG c 276 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA c 278 " --> pdb=" O SER c 347 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'c' and resid 96 through 98 Processing sheet with id=AK2, first strand: chain 'c' and resid 323 through 324 Processing sheet with id=AK3, first strand: chain 'c' and resid 455 through 459 removed outlier: 8.309A pdb=" N ASN d 492 " --> pdb=" O PHE c 474 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU c 476 " --> pdb=" O ASN d 492 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'd' and resid 46 through 47 removed outlier: 6.090A pdb=" N ILE d 28 " --> pdb=" O TYR d 82 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU d 84 " --> pdb=" O ILE d 28 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL d 30 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG d 86 " --> pdb=" O VAL d 30 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY d 32 " --> pdb=" O ARG d 86 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU d 29 " --> pdb=" O VAL d 222 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU d 223 " --> pdb=" O TYR d 254 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE d 256 " --> pdb=" O LEU d 223 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL d 255 " --> pdb=" O SER d 275 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'd' and resid 158 through 161 Processing sheet with id=AK6, first strand: chain 'd' and resid 347 through 349 Processing sheet with id=AK7, first strand: chain 'd' and resid 409 through 410 removed outlier: 6.459A pdb=" N ALA d 409 " --> pdb=" O THR d 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK7 Processing sheet with id=AK8, first strand: chain 'd' and resid 455 through 459 Processing sheet with id=AK9, first strand: chain 'f' and resid 46 through 48 removed outlier: 3.703A pdb=" N VAL f 48 " --> pdb=" O VAL f 81 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL f 81 " --> pdb=" O VAL f 48 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE f 256 " --> pdb=" O LEU f 223 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL f 255 " --> pdb=" O SER f 275 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'f' and resid 347 through 349 Processing sheet with id=AL2, first strand: chain 'f' and resid 409 through 410 removed outlier: 6.583A pdb=" N ALA f 409 " --> pdb=" O THR f 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'f' and resid 456 through 459 removed outlier: 8.377A pdb=" N ASN g 492 " --> pdb=" O PHE f 474 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU f 476 " --> pdb=" O ASN g 492 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'g' and resid 13 through 15 removed outlier: 6.094A pdb=" N CYS g 14 " --> pdb=" O MET j 493 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ASN j 492 " --> pdb=" O PHE i 474 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU i 476 " --> pdb=" O ASN j 492 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA j 494 " --> pdb=" O LEU i 476 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N MET i 478 " --> pdb=" O ALA j 494 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'g' and resid 29 through 31 removed outlier: 7.246A pdb=" N VAL g 30 " --> pdb=" O LEU g 84 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'g' and resid 220 through 222 Processing sheet with id=AL7, first strand: chain 'g' and resid 409 through 410 removed outlier: 6.439A pdb=" N ALA g 409 " --> pdb=" O THR g 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL7 Processing sheet with id=AL8, first strand: chain 'g' and resid 455 through 459 Processing sheet with id=AL9, first strand: chain 'i' and resid 46 through 47 removed outlier: 6.037A pdb=" N ILE i 28 " --> pdb=" O TYR i 82 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU i 84 " --> pdb=" O ILE i 28 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL i 30 " --> pdb=" O LEU i 84 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG i 86 " --> pdb=" O VAL i 30 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY i 32 " --> pdb=" O ARG i 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU i 223 " --> pdb=" O TYR i 254 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N PHE i 256 " --> pdb=" O LEU i 223 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY i 253 " --> pdb=" O SER i 275 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU i 277 " --> pdb=" O GLY i 253 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL i 255 " --> pdb=" O LEU i 277 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU i 279 " --> pdb=" O VAL i 255 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASN i 257 " --> pdb=" O LEU i 279 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'j' and resid 46 through 47 removed outlier: 6.163A pdb=" N ILE j 28 " --> pdb=" O TYR j 82 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU j 84 " --> pdb=" O ILE j 28 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL j 30 " --> pdb=" O LEU j 84 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG j 86 " --> pdb=" O VAL j 30 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY j 32 " --> pdb=" O ARG j 86 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR j 221 " --> pdb=" O TYR j 254 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N PHE j 256 " --> pdb=" O TYR j 221 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N LEU j 223 " --> pdb=" O PHE j 256 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N LYS j 258 " --> pdb=" O LEU j 223 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY j 253 " --> pdb=" O SER j 275 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU j 277 " --> pdb=" O GLY j 253 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL j 255 " --> pdb=" O LEU j 277 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU j 279 " --> pdb=" O VAL j 255 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASN j 257 " --> pdb=" O LEU j 279 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'j' and resid 149 through 154 Processing sheet with id=AM3, first strand: chain 'j' and resid 122 through 126 Processing sheet with id=AM4, first strand: chain 'j' and resid 347 through 349 Processing sheet with id=AM5, first strand: chain 'j' and resid 455 through 459 1689 hydrogen bonds defined for protein. 4521 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: 20.52 Time building geometry restraints manager: 17.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18752 1.34 - 1.47: 12526 1.47 - 1.59: 24789 1.59 - 1.71: 0 1.71 - 1.83: 464 Bond restraints: 56531 Sorted by residual: bond pdb=" CB CYS U 300 " pdb=" SG CYS U 300 " ideal model delta sigma weight residual 1.808 1.761 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CA ASN Z 20 " pdb=" CB ASN Z 20 " ideal model delta sigma weight residual 1.523 1.542 -0.019 1.35e-02 5.49e+03 1.97e+00 bond pdb=" CA VAL d 213 " pdb=" CB VAL d 213 " ideal model delta sigma weight residual 1.531 1.546 -0.015 1.11e-02 8.12e+03 1.94e+00 bond pdb=" CB ASN i 207 " pdb=" CG ASN i 207 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.91e+00 bond pdb=" C PRO B 129 " pdb=" N PRO B 130 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.33e+00 ... (remaining 56526 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.60: 1806 106.60 - 113.57: 30994 113.57 - 120.54: 21274 120.54 - 127.51: 22603 127.51 - 134.49: 415 Bond angle restraints: 77092 Sorted by residual: angle pdb=" C GLU Z 24 " pdb=" CA GLU Z 24 " pdb=" CB GLU Z 24 " ideal model delta sigma weight residual 115.79 109.62 6.17 1.19e+00 7.06e-01 2.69e+01 angle pdb=" N PHE g 448 " pdb=" CA PHE g 448 " pdb=" CB PHE g 448 " ideal model delta sigma weight residual 110.49 118.96 -8.47 1.69e+00 3.50e-01 2.51e+01 angle pdb=" C GLU g 447 " pdb=" N PHE g 448 " pdb=" CA PHE g 448 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C GLU U 447 " pdb=" N PHE U 448 " pdb=" CA PHE U 448 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C CYS Q 3 " pdb=" N ASN Q 4 " pdb=" CA ASN Q 4 " ideal model delta sigma weight residual 126.32 134.49 -8.17 1.74e+00 3.30e-01 2.20e+01 ... (remaining 77087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 31013 17.98 - 35.96: 2467 35.96 - 53.95: 393 53.95 - 71.93: 98 71.93 - 89.91: 49 Dihedral angle restraints: 34020 sinusoidal: 13104 harmonic: 20916 Sorted by residual: dihedral pdb=" CB CYS a 26 " pdb=" SG CYS a 26 " pdb=" SG CYS a 303 " pdb=" CB CYS a 303 " ideal model delta sinusoidal sigma weight residual -86.00 -163.40 77.40 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS c 217 " pdb=" SG CYS c 217 " pdb=" SG CYS c 249 " pdb=" CB CYS c 249 " ideal model delta sinusoidal sigma weight residual -86.00 -158.46 72.46 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CA GLU d 447 " pdb=" C GLU d 447 " pdb=" N PHE d 448 " pdb=" CA PHE d 448 " ideal model delta harmonic sigma weight residual 180.00 139.40 40.60 0 5.00e+00 4.00e-02 6.59e+01 ... (remaining 34017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 6635 0.043 - 0.087: 1672 0.087 - 0.130: 627 0.130 - 0.173: 18 0.173 - 0.216: 3 Chirality restraints: 8955 Sorted by residual: chirality pdb=" CB ILE c 473 " pdb=" CA ILE c 473 " pdb=" CG1 ILE c 473 " pdb=" CG2 ILE c 473 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE i 422 " pdb=" CA ILE i 422 " pdb=" CG1 ILE i 422 " pdb=" CG2 ILE i 422 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CB THR g 328 " pdb=" CA THR g 328 " pdb=" OG1 THR g 328 " pdb=" CG2 THR g 328 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 8952 not shown) Planarity restraints: 10182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR U 328 " -0.078 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO U 329 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO U 329 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO U 329 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE U 448 " 0.019 2.00e-02 2.50e+03 2.76e-02 1.33e+01 pdb=" CG PHE U 448 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE U 448 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE U 448 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE U 448 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE U 448 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE U 448 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE W 448 " 0.022 2.00e-02 2.50e+03 2.74e-02 1.31e+01 pdb=" CG PHE W 448 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE W 448 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE W 448 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE W 448 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE W 448 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE W 448 " 0.001 2.00e-02 2.50e+03 ... (remaining 10179 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 753 2.64 - 3.21: 50864 3.21 - 3.77: 81554 3.77 - 4.34: 112448 4.34 - 4.90: 189455 Nonbonded interactions: 435074 Sorted by model distance: nonbonded pdb=" OE1 GLU U 66 " pdb=" OH TYR U 120 " model vdw 2.078 2.440 nonbonded pdb=" OD1 ASP c 373 " pdb=" N GLU c 374 " model vdw 2.093 2.520 nonbonded pdb=" OG SER T 271 " pdb=" OE1 GLU T 273 " model vdw 2.126 2.440 nonbonded pdb=" OG1 THR f 415 " pdb=" OE2 GLU g 447 " model vdw 2.141 2.440 nonbonded pdb=" OG SER g 271 " pdb=" OE1 GLU g 273 " model vdw 2.145 2.440 ... (remaining 435069 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 'B' selection = (chain 'C' and resid 4 through 133) selection = chain 'D' selection = (chain 'E' and resid 4 through 133) selection = chain 'F' selection = (chain 'G' and resid 4 through 133) selection = (chain 'H' and resid 4 through 133) selection = (chain 'I' and resid 4 through 133) selection = (chain 'J' and resid 4 through 133) selection = (chain 'K' and resid 4 through 133) selection = (chain 'L' and resid 4 through 133) selection = (chain 'M' and resid 4 through 133) selection = (chain 'N' and resid 4 through 133) selection = (chain 'O' and resid 4 through 133) selection = (chain 'P' and resid 4 through 133) selection = (chain 'Q' and resid 4 through 133) selection = (chain 'R' and resid 4 through 133) selection = chain 'S' } ncs_group { reference = (chain 'T' and (resid 17 through 90 or resid 161 through 172 or resid 201 throug \ h 350 or resid 359 through 493)) selection = (chain 'U' and (resid 17 through 90 or resid 161 through 172 or resid 201 throug \ h 350 or resid 359 through 493)) selection = (chain 'W' and (resid 17 through 90 or resid 161 through 172 or resid 201 throug \ h 493)) selection = (chain 'X' and (resid 17 through 90 or resid 161 through 172 or resid 201 throug \ h 350 or resid 359 through 493)) selection = (chain 'a' and (resid 17 through 90 or resid 161 through 172 or resid 201 throug \ h 350 or resid 359 through 493)) selection = (chain 'c' and (resid 17 through 90 or resid 161 through 172 or resid 201 throug \ h 350 or resid 359 through 493)) selection = (chain 'd' and (resid 17 through 90 or resid 161 through 172 or resid 201 throug \ h 350 or resid 359 through 493)) selection = (chain 'f' and (resid 17 through 90 or resid 161 through 172 or resid 201 throug \ h 350 or resid 359 through 493)) selection = (chain 'j' and (resid 17 through 90 or resid 161 through 172 or resid 201 throug \ h 350 or resid 359 through 493)) } ncs_group { reference = (chain 'g' and (resid 4 through 351 or resid 357 through 486)) selection = (chain 'i' and (resid 4 through 89 or resid 203 through 486)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 12.810 Check model and map are aligned: 0.590 Set scattering table: 0.380 Process input model: 111.060 Find NCS groups from input model: 3.520 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 56531 Z= 0.169 Angle : 0.564 10.388 77092 Z= 0.301 Chirality : 0.043 0.216 8955 Planarity : 0.004 0.117 10182 Dihedral : 13.335 89.910 20339 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.14 % Favored : 92.29 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.82 (0.10), residues: 7147 helix: 1.29 (0.14), residues: 1459 sheet: -0.25 (0.13), residues: 1833 loop : -1.46 (0.10), residues: 3855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 230 HIS 0.002 0.000 HIS B 30 PHE 0.063 0.001 PHE W 448 TYR 0.030 0.001 TYR G 40 ARG 0.007 0.000 ARG Z 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1103 time to evaluate : 4.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8879 (mp10) cc_final: 0.8505 (mp10) REVERT: C 124 ILE cc_start: 0.9000 (mt) cc_final: 0.7853 (mt) REVERT: D 22 GLN cc_start: 0.8171 (mp10) cc_final: 0.7864 (mp10) REVERT: D 117 MET cc_start: 0.8373 (mtt) cc_final: 0.7648 (mtt) REVERT: F 124 ILE cc_start: 0.9112 (mt) cc_final: 0.8142 (mt) REVERT: J 93 ASP cc_start: 0.7935 (p0) cc_final: 0.7683 (p0) REVERT: K 39 THR cc_start: 0.9157 (m) cc_final: 0.8650 (p) REVERT: K 70 ARG cc_start: 0.8505 (tmm-80) cc_final: 0.8243 (ttt90) REVERT: L 25 ILE cc_start: 0.8133 (mm) cc_final: 0.7894 (mm) REVERT: L 101 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8020 (mt-10) REVERT: M 54 TYR cc_start: 0.8909 (m-80) cc_final: 0.8530 (m-80) REVERT: N 86 ASP cc_start: 0.8328 (m-30) cc_final: 0.8102 (m-30) REVERT: N 97 MET cc_start: 0.8149 (mmt) cc_final: 0.7517 (mmt) REVERT: N 111 ASP cc_start: 0.9060 (p0) cc_final: 0.8706 (p0) REVERT: P 21 THR cc_start: 0.8386 (t) cc_final: 0.8052 (t) REVERT: P 101 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7652 (tm-30) REVERT: Q 31 GLU cc_start: 0.7802 (tt0) cc_final: 0.7371 (tt0) REVERT: S 18 ASP cc_start: 0.8494 (t0) cc_final: 0.8262 (t0) REVERT: S 117 MET cc_start: 0.8260 (mtt) cc_final: 0.8048 (mtt) REVERT: T 242 TRP cc_start: 0.6552 (m-10) cc_final: 0.6336 (m-10) REVERT: T 305 ASN cc_start: 0.7265 (t0) cc_final: 0.6906 (t0) REVERT: T 325 GLU cc_start: 0.6964 (pp20) cc_final: 0.5749 (mp0) REVERT: T 412 THR cc_start: 0.8195 (t) cc_final: 0.7686 (p) REVERT: T 454 ASP cc_start: 0.8009 (m-30) cc_final: 0.7807 (m-30) REVERT: T 488 ARG cc_start: 0.7421 (mmm-85) cc_final: 0.6255 (pmt-80) REVERT: U 16 ASP cc_start: 0.7484 (t70) cc_final: 0.7154 (t70) REVERT: W 229 ASP cc_start: 0.7291 (m-30) cc_final: 0.7081 (t0) REVERT: W 362 TYR cc_start: 0.5847 (t80) cc_final: 0.5622 (t80) REVERT: W 466 LYS cc_start: 0.6726 (tptt) cc_final: 0.6456 (tptp) REVERT: W 479 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7741 (ttm110) REVERT: X 97 TYR cc_start: 0.5804 (m-10) cc_final: 0.5407 (m-10) REVERT: X 365 ASN cc_start: 0.6854 (t0) cc_final: 0.6029 (t0) REVERT: X 452 ASN cc_start: 0.8800 (m110) cc_final: 0.8341 (m-40) REVERT: X 466 LYS cc_start: 0.6032 (tptt) cc_final: 0.5676 (mtpt) REVERT: X 481 ARG cc_start: 0.5047 (tpt170) cc_final: 0.3821 (mmp-170) REVERT: a 31 GLU cc_start: 0.7252 (tt0) cc_final: 0.6589 (tt0) REVERT: a 307 GLU cc_start: 0.7948 (pm20) cc_final: 0.7270 (pm20) REVERT: a 325 GLU cc_start: 0.5615 (pm20) cc_final: 0.5097 (pt0) REVERT: a 429 MET cc_start: 0.8755 (mtp) cc_final: 0.8531 (mtp) REVERT: a 481 ARG cc_start: 0.5659 (tpt170) cc_final: 0.5340 (mmp-170) REVERT: c 52 LEU cc_start: 0.7306 (tp) cc_final: 0.7056 (tt) REVERT: c 82 TYR cc_start: 0.8928 (m-80) cc_final: 0.8348 (m-80) REVERT: c 372 ARG cc_start: 0.7293 (mtt-85) cc_final: 0.6692 (mtm110) REVERT: c 453 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8110 (mm-30) REVERT: d 19 LEU cc_start: 0.8448 (mm) cc_final: 0.8231 (mp) REVERT: d 57 ARG cc_start: 0.7671 (mtt180) cc_final: 0.7304 (mtt180) REVERT: d 481 ARG cc_start: 0.4509 (mmp-170) cc_final: 0.4019 (ptp-110) REVERT: d 497 LEU cc_start: 0.7087 (pt) cc_final: 0.6862 (tp) REVERT: f 176 TYR cc_start: 0.6448 (t80) cc_final: 0.6222 (t80) REVERT: f 454 ASP cc_start: 0.8712 (m-30) cc_final: 0.8410 (m-30) REVERT: g 19 LEU cc_start: 0.8720 (mm) cc_final: 0.8405 (mp) REVERT: g 331 TRP cc_start: 0.3838 (m100) cc_final: 0.3378 (m100) REVERT: g 346 VAL cc_start: 0.8067 (p) cc_final: 0.7784 (m) REVERT: g 479 ARG cc_start: 0.3615 (tpt170) cc_final: 0.3407 (tpt170) REVERT: i 94 LYS cc_start: 0.7701 (mttm) cc_final: 0.7395 (tptt) REVERT: i 446 SER cc_start: 0.7469 (m) cc_final: 0.7267 (m) REVERT: j 12 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7911 (ttm-80) REVERT: j 453 GLU cc_start: 0.7838 (pm20) cc_final: 0.7560 (pm20) REVERT: j 466 LYS cc_start: 0.6974 (tmtt) cc_final: 0.6774 (tptt) outliers start: 3 outliers final: 1 residues processed: 1104 average time/residue: 0.4992 time to fit residues: 937.3874 Evaluate side-chains 820 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 819 time to evaluate : 4.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 60 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 609 optimal weight: 10.0000 chunk 547 optimal weight: 7.9990 chunk 303 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 565 optimal weight: 6.9990 chunk 218 optimal weight: 0.8980 chunk 344 optimal weight: 6.9990 chunk 421 optimal weight: 5.9990 chunk 655 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 ASN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN J 84 GLN K 11 ASN L 88 GLN ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 ASN R 52 ASN ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 291 ASN ** T 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 464 GLN W 214 ASN W 291 ASN W 440 ASN ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 311 GLN a 342 ASN ** a 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 490 ASN c 252 HIS ** c 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 291 ASN c 414 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 477 ASN d 203 ASN ** d 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 170 ASN f 311 GLN ** f 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 342 ASN f 438 GLN f 477 ASN g 263 GLN ** g 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 438 GLN ** i 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 438 GLN ** j 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 56531 Z= 0.415 Angle : 0.644 9.224 77092 Z= 0.339 Chirality : 0.047 0.183 8955 Planarity : 0.005 0.088 10182 Dihedral : 4.930 64.887 7745 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.91 % Favored : 90.56 % Rotamer: Outliers : 1.74 % Allowed : 9.02 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.04 (0.10), residues: 7147 helix: 1.05 (0.14), residues: 1513 sheet: -0.55 (0.12), residues: 1878 loop : -1.52 (0.10), residues: 3756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP X 242 HIS 0.005 0.001 HIS i 252 PHE 0.027 0.002 PHE g 448 TYR 0.041 0.002 TYR S 40 ARG 0.008 0.001 ARG X 388 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 829 time to evaluate : 4.639 Fit side-chains revert: symmetry clash REVERT: D 22 GLN cc_start: 0.8426 (mp10) cc_final: 0.7972 (mp10) REVERT: D 125 ASP cc_start: 0.8144 (t70) cc_final: 0.7769 (t70) REVERT: F 64 MET cc_start: 0.8600 (ttm) cc_final: 0.8386 (ttm) REVERT: G 97 MET cc_start: 0.8742 (mmt) cc_final: 0.8426 (mmt) REVERT: G 101 GLU cc_start: 0.7719 (mp0) cc_final: 0.7472 (mp0) REVERT: J 93 ASP cc_start: 0.8156 (p0) cc_final: 0.7818 (p0) REVERT: K 39 THR cc_start: 0.9166 (m) cc_final: 0.8689 (p) REVERT: K 125 ASP cc_start: 0.8197 (t70) cc_final: 0.7953 (t70) REVERT: L 25 ILE cc_start: 0.8459 (mm) cc_final: 0.8257 (mm) REVERT: L 52 ASN cc_start: 0.8292 (t0) cc_final: 0.8055 (t0) REVERT: L 60 SER cc_start: 0.9299 (t) cc_final: 0.9037 (t) REVERT: L 101 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8056 (mt-10) REVERT: N 97 MET cc_start: 0.8108 (mmt) cc_final: 0.7521 (mmt) REVERT: Q 97 MET cc_start: 0.8447 (mmt) cc_final: 0.8099 (mmt) REVERT: S 18 ASP cc_start: 0.8709 (t0) cc_final: 0.8411 (t0) REVERT: S 97 MET cc_start: 0.8415 (mmt) cc_final: 0.7914 (mmt) REVERT: T 325 GLU cc_start: 0.7052 (pp20) cc_final: 0.5769 (mp0) REVERT: T 412 THR cc_start: 0.8288 (t) cc_final: 0.7862 (p) REVERT: T 454 ASP cc_start: 0.8385 (m-30) cc_final: 0.8179 (m-30) REVERT: T 488 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.6336 (pmt-80) REVERT: U 16 ASP cc_start: 0.7558 (t70) cc_final: 0.7216 (t70) REVERT: W 362 TYR cc_start: 0.6278 (t80) cc_final: 0.5597 (t80) REVERT: W 466 LYS cc_start: 0.6848 (tptt) cc_final: 0.6530 (tptp) REVERT: W 479 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7790 (ttm110) REVERT: X 365 ASN cc_start: 0.7430 (t0) cc_final: 0.6900 (t0) REVERT: X 452 ASN cc_start: 0.8767 (m110) cc_final: 0.8409 (m110) REVERT: X 466 LYS cc_start: 0.5979 (tptt) cc_final: 0.5613 (mtpt) REVERT: X 480 TYR cc_start: 0.4233 (p90) cc_final: 0.3791 (p90) REVERT: X 481 ARG cc_start: 0.5149 (tpt170) cc_final: 0.3810 (mmp-170) REVERT: Z 232 GLU cc_start: 0.5408 (tm-30) cc_final: 0.5087 (tm-30) REVERT: Z 307 GLU cc_start: 0.7988 (pm20) cc_final: 0.7666 (pm20) REVERT: Z 365 ASN cc_start: 0.7406 (t0) cc_final: 0.7120 (t0) REVERT: Z 371 LEU cc_start: 0.5631 (OUTLIER) cc_final: 0.5421 (mt) REVERT: a 69 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.8415 (mtp85) REVERT: a 307 GLU cc_start: 0.8158 (pm20) cc_final: 0.7222 (pm20) REVERT: a 325 GLU cc_start: 0.5857 (pm20) cc_final: 0.5305 (pt0) REVERT: c 82 TYR cc_start: 0.8916 (m-80) cc_final: 0.8149 (m-80) REVERT: c 230 TRP cc_start: 0.7482 (OUTLIER) cc_final: 0.7146 (t60) REVERT: d 51 GLU cc_start: 0.8080 (tt0) cc_final: 0.7591 (tm-30) REVERT: d 481 ARG cc_start: 0.4576 (mmp-170) cc_final: 0.3623 (ptp-110) REVERT: d 497 LEU cc_start: 0.7191 (pt) cc_final: 0.6862 (tp) REVERT: f 27 LYS cc_start: 0.7793 (ptpt) cc_final: 0.7478 (mtmt) REVERT: f 454 ASP cc_start: 0.8710 (m-30) cc_final: 0.8456 (m-30) REVERT: g 256 PHE cc_start: 0.5226 (p90) cc_final: 0.5016 (p90) REVERT: g 331 TRP cc_start: 0.3496 (m100) cc_final: 0.3104 (m100) REVERT: g 479 ARG cc_start: 0.3684 (tpt170) cc_final: 0.3477 (tpt170) REVERT: i 94 LYS cc_start: 0.7734 (mttm) cc_final: 0.7391 (tptt) REVERT: i 439 ASP cc_start: 0.8613 (m-30) cc_final: 0.8252 (m-30) REVERT: i 446 SER cc_start: 0.7583 (m) cc_final: 0.7373 (m) REVERT: j 12 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7855 (ttm-80) REVERT: j 115 MET cc_start: 0.8027 (mpp) cc_final: 0.7685 (mmm) REVERT: j 377 ARG cc_start: 0.7850 (mmp80) cc_final: 0.7636 (mmp-170) REVERT: j 466 LYS cc_start: 0.7026 (tmtt) cc_final: 0.6801 (tptt) outliers start: 107 outliers final: 75 residues processed: 898 average time/residue: 0.5309 time to fit residues: 820.1719 Evaluate side-chains 835 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 758 time to evaluate : 4.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 314 THR Chi-restraints excluded: chain T residue 347 SER Chi-restraints excluded: chain T residue 387 SER Chi-restraints excluded: chain T residue 439 ASP Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 363 ILE Chi-restraints excluded: chain U residue 459 THR Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 432 LYS Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 288 TYR Chi-restraints excluded: chain X residue 398 LEU Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain a residue 46 THR Chi-restraints excluded: chain a residue 226 ASP Chi-restraints excluded: chain a residue 357 ASN Chi-restraints excluded: chain a residue 359 THR Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 230 TRP Chi-restraints excluded: chain c residue 492 ASN Chi-restraints excluded: chain d residue 26 CYS Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 213 VAL Chi-restraints excluded: chain d residue 285 VAL Chi-restraints excluded: chain d residue 351 THR Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 170 ASN Chi-restraints excluded: chain f residue 326 SER Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 415 THR Chi-restraints excluded: chain g residue 491 VAL Chi-restraints excluded: chain i residue 73 CYS Chi-restraints excluded: chain i residue 229 ASP Chi-restraints excluded: chain i residue 269 ASP Chi-restraints excluded: chain i residue 448 PHE Chi-restraints excluded: chain j residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 364 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 545 optimal weight: 8.9990 chunk 446 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 656 optimal weight: 9.9990 chunk 709 optimal weight: 10.0000 chunk 584 optimal weight: 10.0000 chunk 651 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 526 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN M 22 GLN ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 ASN ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 252 HIS ** c 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 414 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 440 ASN ** d 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 56531 Z= 0.314 Angle : 0.578 9.954 77092 Z= 0.304 Chirality : 0.045 0.177 8955 Planarity : 0.005 0.070 10182 Dihedral : 4.886 67.585 7745 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.24 % Favored : 91.26 % Rotamer: Outliers : 2.39 % Allowed : 11.93 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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 (0.10), residues: 7147 helix: 1.11 (0.14), residues: 1503 sheet: -0.62 (0.12), residues: 1898 loop : -1.53 (0.10), residues: 3746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 237 HIS 0.005 0.001 HIS f 171 PHE 0.025 0.001 PHE c 10 TYR 0.032 0.001 TYR S 40 ARG 0.006 0.000 ARG U 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 813 time to evaluate : 4.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8476 (mt-10) REVERT: D 22 GLN cc_start: 0.8458 (mp10) cc_final: 0.7970 (mp10) REVERT: D 125 ASP cc_start: 0.8196 (t70) cc_final: 0.7868 (t70) REVERT: E 101 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7845 (mm-30) REVERT: G 97 MET cc_start: 0.8758 (mmt) cc_final: 0.8376 (mmt) REVERT: J 52 ASN cc_start: 0.7887 (t0) cc_final: 0.7597 (t0) REVERT: J 93 ASP cc_start: 0.8181 (p0) cc_final: 0.7812 (p0) REVERT: K 52 ASN cc_start: 0.7857 (t0) cc_final: 0.7654 (t0) REVERT: K 125 ASP cc_start: 0.8177 (t70) cc_final: 0.7907 (t70) REVERT: L 25 ILE cc_start: 0.8468 (mm) cc_final: 0.8266 (mm) REVERT: L 52 ASN cc_start: 0.8222 (t0) cc_final: 0.7948 (t0) REVERT: L 60 SER cc_start: 0.9267 (t) cc_final: 0.9003 (t) REVERT: L 101 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8080 (mt-10) REVERT: M 52 ASN cc_start: 0.8589 (t0) cc_final: 0.8311 (t0) REVERT: M 54 TYR cc_start: 0.8895 (m-80) cc_final: 0.8606 (m-80) REVERT: N 86 ASP cc_start: 0.8288 (m-30) cc_final: 0.8050 (m-30) REVERT: N 97 MET cc_start: 0.8130 (mmt) cc_final: 0.7523 (mmt) REVERT: P 101 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7903 (tm-30) REVERT: Q 97 MET cc_start: 0.8533 (mmt) cc_final: 0.8162 (mmt) REVERT: Q 123 GLU cc_start: 0.7239 (pp20) cc_final: 0.6869 (pt0) REVERT: S 18 ASP cc_start: 0.8714 (t0) cc_final: 0.8444 (t0) REVERT: S 97 MET cc_start: 0.8439 (mmt) cc_final: 0.7761 (mmt) REVERT: T 325 GLU cc_start: 0.7096 (pp20) cc_final: 0.5785 (mp0) REVERT: T 412 THR cc_start: 0.8383 (t) cc_final: 0.7986 (p) REVERT: T 454 ASP cc_start: 0.8344 (m-30) cc_final: 0.8129 (m-30) REVERT: T 488 ARG cc_start: 0.7472 (mmm-85) cc_final: 0.6380 (pmt-80) REVERT: U 16 ASP cc_start: 0.7600 (t70) cc_final: 0.7268 (t70) REVERT: U 305 ASN cc_start: 0.7777 (t0) cc_final: 0.7575 (t0) REVERT: W 362 TYR cc_start: 0.6368 (t80) cc_final: 0.5854 (t80) REVERT: W 466 LYS cc_start: 0.6850 (tptt) cc_final: 0.6549 (tptp) REVERT: X 69 ARG cc_start: 0.7090 (ttm-80) cc_final: 0.6844 (ttm-80) REVERT: X 365 ASN cc_start: 0.7402 (t0) cc_final: 0.6878 (t0) REVERT: X 452 ASN cc_start: 0.8752 (m110) cc_final: 0.8418 (m110) REVERT: X 466 LYS cc_start: 0.6040 (tptt) cc_final: 0.5693 (mtpt) REVERT: X 480 TYR cc_start: 0.4237 (p90) cc_final: 0.3828 (p90) REVERT: X 481 ARG cc_start: 0.5092 (tpt170) cc_final: 0.3782 (mmp-170) REVERT: Z 365 ASN cc_start: 0.7011 (t0) cc_final: 0.6659 (t0) REVERT: Z 400 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7695 (mm-30) REVERT: a 69 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8403 (mtp85) REVERT: a 325 GLU cc_start: 0.5613 (pm20) cc_final: 0.5025 (pt0) REVERT: c 69 ARG cc_start: 0.7547 (mmm-85) cc_final: 0.7151 (mtp-110) REVERT: c 82 TYR cc_start: 0.8905 (m-80) cc_final: 0.8143 (m-80) REVERT: c 230 TRP cc_start: 0.7614 (OUTLIER) cc_final: 0.7250 (t60) REVERT: d 51 GLU cc_start: 0.8111 (tt0) cc_final: 0.7626 (tm-30) REVERT: d 481 ARG cc_start: 0.4264 (mmp-170) cc_final: 0.3368 (ptp-110) REVERT: d 497 LEU cc_start: 0.7192 (pt) cc_final: 0.6853 (tp) REVERT: f 27 LYS cc_start: 0.7724 (ptpt) cc_final: 0.7467 (mtmt) REVERT: f 454 ASP cc_start: 0.8718 (m-30) cc_final: 0.8452 (m-30) REVERT: g 34 MET cc_start: 0.5377 (OUTLIER) cc_final: 0.4885 (ttm) REVERT: g 256 PHE cc_start: 0.5229 (p90) cc_final: 0.4875 (p90) REVERT: g 331 TRP cc_start: 0.3268 (m100) cc_final: 0.2945 (m100) REVERT: i 94 LYS cc_start: 0.7732 (mttm) cc_final: 0.7427 (tptt) REVERT: i 439 ASP cc_start: 0.8636 (m-30) cc_final: 0.8407 (m-30) REVERT: i 446 SER cc_start: 0.7594 (m) cc_final: 0.7381 (m) REVERT: j 12 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7896 (ttm-80) REVERT: j 115 MET cc_start: 0.8034 (mpp) cc_final: 0.7725 (mmm) REVERT: j 377 ARG cc_start: 0.7898 (mmp80) cc_final: 0.7670 (mmp-170) outliers start: 147 outliers final: 112 residues processed: 912 average time/residue: 0.4999 time to fit residues: 783.1593 Evaluate side-chains 889 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 775 time to evaluate : 5.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain O residue 31 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 307 GLU Chi-restraints excluded: chain T residue 314 THR Chi-restraints excluded: chain T residue 439 ASP Chi-restraints excluded: chain T residue 459 THR Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 321 ILE Chi-restraints excluded: chain U residue 363 ILE Chi-restraints excluded: chain U residue 384 ASP Chi-restraints excluded: chain U residue 459 THR Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 371 LEU Chi-restraints excluded: chain W residue 415 THR Chi-restraints excluded: chain W residue 432 LYS Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 201 SER Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 288 TYR Chi-restraints excluded: chain X residue 398 LEU Chi-restraints excluded: chain X residue 446 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 484 VAL Chi-restraints excluded: chain a residue 46 THR Chi-restraints excluded: chain a residue 226 ASP Chi-restraints excluded: chain a residue 308 LEU Chi-restraints excluded: chain a residue 357 ASN Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 230 TRP Chi-restraints excluded: chain c residue 300 CYS Chi-restraints excluded: chain c residue 440 ASN Chi-restraints excluded: chain c residue 455 ILE Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 26 CYS Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 213 VAL Chi-restraints excluded: chain d residue 285 VAL Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain f residue 326 SER Chi-restraints excluded: chain f residue 362 TYR Chi-restraints excluded: chain f residue 375 LYS Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 34 MET Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 415 THR Chi-restraints excluded: chain g residue 491 VAL Chi-restraints excluded: chain i residue 205 THR Chi-restraints excluded: chain i residue 229 ASP Chi-restraints excluded: chain i residue 269 ASP Chi-restraints excluded: chain i residue 448 PHE Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 443 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 648 optimal weight: 8.9990 chunk 493 optimal weight: 9.9990 chunk 340 optimal weight: 10.0000 chunk 72 optimal weight: 0.4980 chunk 313 optimal weight: 0.7980 chunk 441 optimal weight: 0.0980 chunk 659 optimal weight: 9.9990 chunk 697 optimal weight: 7.9990 chunk 344 optimal weight: 0.0040 chunk 624 optimal weight: 0.3980 chunk 188 optimal weight: 2.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 GLN J 56 GLN K 22 GLN ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 ASN ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 369 ASN ** U 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 291 ASN ** X 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 311 GLN ** a 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 291 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 170 ASN f 311 GLN ** f 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 56531 Z= 0.137 Angle : 0.502 8.222 77092 Z= 0.265 Chirality : 0.042 0.159 8955 Planarity : 0.004 0.071 10182 Dihedral : 4.499 62.754 7745 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.56 % Favored : 91.97 % Rotamer: Outliers : 1.87 % Allowed : 13.81 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: -0.76 (0.10), residues: 7147 helix: 1.32 (0.14), residues: 1506 sheet: -0.38 (0.12), residues: 1789 loop : -1.32 (0.10), residues: 3852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP g 237 HIS 0.002 0.000 HIS f 171 PHE 0.023 0.001 PHE c 10 TYR 0.019 0.001 TYR d 362 ARG 0.008 0.000 ARG U 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 890 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8846 (mp10) cc_final: 0.8611 (mp10) REVERT: C 52 ASN cc_start: 0.8233 (p0) cc_final: 0.8010 (p0) REVERT: C 101 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8352 (mt-10) REVERT: D 22 GLN cc_start: 0.8347 (mp10) cc_final: 0.7876 (mp10) REVERT: E 101 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7755 (mm-30) REVERT: E 111 ASP cc_start: 0.8185 (p0) cc_final: 0.7945 (p0) REVERT: F 31 GLU cc_start: 0.8052 (tt0) cc_final: 0.7676 (tt0) REVERT: F 101 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8058 (mt-10) REVERT: G 93 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8728 (p0) REVERT: G 97 MET cc_start: 0.8691 (mmt) cc_final: 0.8288 (mmt) REVERT: I 39 THR cc_start: 0.7875 (p) cc_final: 0.7647 (p) REVERT: J 52 ASN cc_start: 0.7907 (t0) cc_final: 0.7539 (t0) REVERT: J 93 ASP cc_start: 0.8145 (p0) cc_final: 0.7743 (p0) REVERT: J 97 MET cc_start: 0.8509 (mmt) cc_final: 0.8184 (mmt) REVERT: K 52 ASN cc_start: 0.7878 (t0) cc_final: 0.7535 (t0) REVERT: K 70 ARG cc_start: 0.8430 (tmm-80) cc_final: 0.7942 (ttt90) REVERT: K 125 ASP cc_start: 0.8224 (t70) cc_final: 0.7866 (t70) REVERT: L 60 SER cc_start: 0.9167 (t) cc_final: 0.8948 (t) REVERT: L 101 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7938 (mt-10) REVERT: L 111 ASP cc_start: 0.8852 (p0) cc_final: 0.8609 (p0) REVERT: M 52 ASN cc_start: 0.8520 (t0) cc_final: 0.8263 (t0) REVERT: N 86 ASP cc_start: 0.8105 (m-30) cc_final: 0.7882 (m-30) REVERT: N 97 MET cc_start: 0.8117 (mmt) cc_final: 0.7526 (mmt) REVERT: P 22 GLN cc_start: 0.8090 (mm110) cc_final: 0.7617 (tp40) REVERT: P 97 MET cc_start: 0.8334 (mmt) cc_final: 0.8113 (mmt) REVERT: Q 40 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: Q 97 MET cc_start: 0.8334 (mmt) cc_final: 0.7941 (mmt) REVERT: Q 123 GLU cc_start: 0.7230 (pp20) cc_final: 0.6899 (pt0) REVERT: S 18 ASP cc_start: 0.8614 (t0) cc_final: 0.8352 (t0) REVERT: S 97 MET cc_start: 0.8474 (mmt) cc_final: 0.7803 (mmt) REVERT: T 325 GLU cc_start: 0.6902 (pp20) cc_final: 0.5658 (mp0) REVERT: T 412 THR cc_start: 0.8249 (t) cc_final: 0.7754 (p) REVERT: T 454 ASP cc_start: 0.8234 (m-30) cc_final: 0.8003 (m-30) REVERT: T 488 ARG cc_start: 0.7502 (mmm-85) cc_final: 0.6335 (pmt-80) REVERT: U 16 ASP cc_start: 0.7482 (t70) cc_final: 0.7184 (t70) REVERT: U 466 LYS cc_start: 0.7733 (tptt) cc_final: 0.7518 (tptt) REVERT: W 362 TYR cc_start: 0.5931 (t80) cc_final: 0.5679 (t80) REVERT: W 466 LYS cc_start: 0.6704 (tptt) cc_final: 0.6410 (tptp) REVERT: W 479 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7717 (ttm110) REVERT: X 24 GLU cc_start: 0.7496 (pm20) cc_final: 0.7228 (pm20) REVERT: X 365 ASN cc_start: 0.6782 (t0) cc_final: 0.5772 (t0) REVERT: X 452 ASN cc_start: 0.8724 (m110) cc_final: 0.8423 (m110) REVERT: X 466 LYS cc_start: 0.6006 (tptt) cc_final: 0.5662 (mtpt) REVERT: X 481 ARG cc_start: 0.5091 (tpt170) cc_final: 0.3795 (mmp-170) REVERT: Z 232 GLU cc_start: 0.5458 (tm-30) cc_final: 0.5121 (tm-30) REVERT: Z 307 GLU cc_start: 0.7789 (pm20) cc_final: 0.7472 (pm20) REVERT: Z 365 ASN cc_start: 0.6998 (t0) cc_final: 0.6579 (t0) REVERT: Z 400 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7624 (mm-30) REVERT: Z 462 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7734 (pt0) REVERT: a 19 LEU cc_start: 0.8449 (tp) cc_final: 0.8164 (mp) REVERT: a 69 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.8435 (mtp85) REVERT: a 283 TYR cc_start: 0.8512 (t80) cc_final: 0.7943 (t80) REVERT: a 325 GLU cc_start: 0.5631 (pm20) cc_final: 0.4910 (pt0) REVERT: c 69 ARG cc_start: 0.7505 (mmm-85) cc_final: 0.7161 (mtp-110) REVERT: c 82 TYR cc_start: 0.8883 (m-80) cc_final: 0.8086 (m-80) REVERT: c 372 ARG cc_start: 0.7306 (mtt-85) cc_final: 0.6741 (mtm110) REVERT: d 19 LEU cc_start: 0.8136 (mm) cc_final: 0.7922 (mp) REVERT: d 51 GLU cc_start: 0.8081 (tt0) cc_final: 0.7619 (tm-30) REVERT: d 481 ARG cc_start: 0.4449 (mmp-170) cc_final: 0.3541 (ptp-110) REVERT: d 497 LEU cc_start: 0.7188 (pt) cc_final: 0.6872 (tp) REVERT: f 27 LYS cc_start: 0.7613 (ptpt) cc_final: 0.7243 (mtmt) REVERT: f 168 ILE cc_start: 0.6859 (tp) cc_final: 0.6627 (tp) REVERT: f 307 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7732 (tm-30) REVERT: f 454 ASP cc_start: 0.8660 (m-30) cc_final: 0.8401 (m-30) REVERT: g 370 TYR cc_start: 0.7204 (t80) cc_final: 0.6920 (t80) REVERT: i 48 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7796 (m) REVERT: i 94 LYS cc_start: 0.7689 (mttm) cc_final: 0.7363 (tptt) REVERT: i 439 ASP cc_start: 0.8473 (m-30) cc_final: 0.8033 (m-30) REVERT: i 446 SER cc_start: 0.7581 (m) cc_final: 0.7363 (m) REVERT: j 12 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7707 (ttm-80) REVERT: j 115 MET cc_start: 0.8002 (mpp) cc_final: 0.7677 (mmm) REVERT: j 377 ARG cc_start: 0.7817 (mmp80) cc_final: 0.7586 (mmp-170) outliers start: 115 outliers final: 67 residues processed: 969 average time/residue: 0.5065 time to fit residues: 841.4306 Evaluate side-chains 877 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 807 time to evaluate : 4.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 40 TYR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 128 LEU Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain Q residue 40 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain T residue 347 SER Chi-restraints excluded: chain T residue 439 ASP Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 384 ASP Chi-restraints excluded: chain U residue 448 PHE Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 371 LEU Chi-restraints excluded: chain W residue 432 LYS Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 288 TYR Chi-restraints excluded: chain X residue 398 LEU Chi-restraints excluded: chain X residue 491 VAL Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 357 ASN Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 230 TRP Chi-restraints excluded: chain c residue 300 CYS Chi-restraints excluded: chain d residue 26 CYS Chi-restraints excluded: chain d residue 213 VAL Chi-restraints excluded: chain d residue 448 PHE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 170 ASN Chi-restraints excluded: chain f residue 319 SER Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 491 VAL Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 229 ASP Chi-restraints excluded: chain i residue 269 ASP Chi-restraints excluded: chain i residue 448 PHE Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 443 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 581 optimal weight: 6.9990 chunk 396 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 519 optimal weight: 8.9990 chunk 287 optimal weight: 20.0000 chunk 595 optimal weight: 7.9990 chunk 482 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 chunk 626 optimal weight: 9.9990 chunk 176 optimal weight: 0.5980 overall best weight: 5.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 GLN K 118 ASN ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 ASN P 11 ASN P 118 ASN R 52 ASN ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 305 ASN ** U 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 291 ASN W 369 ASN ** X 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 452 ASN Z 440 ASN ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 311 GLN ** a 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 440 ASN ** c 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 291 ASN c 414 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 291 ASN ** d 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 170 ASN f 311 GLN ** f 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 438 GLN ** g 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN ** i 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 342 ASN ** j 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 56531 Z= 0.440 Angle : 0.636 9.832 77092 Z= 0.333 Chirality : 0.047 0.210 8955 Planarity : 0.005 0.069 10182 Dihedral : 4.821 29.526 7742 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.28 % Favored : 90.25 % Rotamer: Outliers : 3.50 % Allowed : 14.44 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: -1.03 (0.10), residues: 7147 helix: 1.21 (0.14), residues: 1498 sheet: -0.63 (0.12), residues: 1862 loop : -1.52 (0.10), residues: 3787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP T 242 HIS 0.006 0.001 HIS f 171 PHE 0.027 0.002 PHE c 461 TYR 0.020 0.002 TYR g 362 ARG 0.018 0.001 ARG T 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 787 time to evaluate : 4.768 Fit side-chains REVERT: B 52 ASN cc_start: 0.8061 (t0) cc_final: 0.7822 (t0) REVERT: C 101 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8448 (mt-10) REVERT: D 22 GLN cc_start: 0.8515 (mp10) cc_final: 0.7919 (mp10) REVERT: D 125 ASP cc_start: 0.8186 (t70) cc_final: 0.7844 (t70) REVERT: E 101 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7808 (mm-30) REVERT: G 101 GLU cc_start: 0.7827 (mp0) cc_final: 0.7549 (mp0) REVERT: J 52 ASN cc_start: 0.7993 (t0) cc_final: 0.7775 (t0) REVERT: J 93 ASP cc_start: 0.8253 (p0) cc_final: 0.7883 (p0) REVERT: K 52 ASN cc_start: 0.8018 (t0) cc_final: 0.7732 (t0) REVERT: K 125 ASP cc_start: 0.8203 (t70) cc_final: 0.7936 (t70) REVERT: L 60 SER cc_start: 0.9246 (t) cc_final: 0.8967 (t) REVERT: L 101 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8233 (mt-10) REVERT: M 52 ASN cc_start: 0.8779 (t0) cc_final: 0.8451 (t0) REVERT: M 117 MET cc_start: 0.8912 (mtt) cc_final: 0.8589 (mtt) REVERT: N 97 MET cc_start: 0.8100 (mmt) cc_final: 0.7500 (mmt) REVERT: P 22 GLN cc_start: 0.8155 (mm110) cc_final: 0.7711 (tp40) REVERT: Q 40 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: Q 97 MET cc_start: 0.8527 (mmt) cc_final: 0.7993 (mmt) REVERT: Q 123 GLU cc_start: 0.7263 (pp20) cc_final: 0.6926 (pt0) REVERT: S 18 ASP cc_start: 0.8738 (t0) cc_final: 0.8450 (t0) REVERT: S 97 MET cc_start: 0.8549 (mmt) cc_final: 0.7882 (mmt) REVERT: T 194 PHE cc_start: 0.8422 (t80) cc_final: 0.8219 (t80) REVERT: T 325 GLU cc_start: 0.7123 (pp20) cc_final: 0.5714 (mp0) REVERT: T 365 ASN cc_start: 0.8047 (t0) cc_final: 0.7837 (t0) REVERT: T 454 ASP cc_start: 0.8380 (m-30) cc_final: 0.8162 (m-30) REVERT: U 16 ASP cc_start: 0.7583 (t70) cc_final: 0.7265 (t70) REVERT: U 466 LYS cc_start: 0.7815 (tptt) cc_final: 0.7579 (tptt) REVERT: W 52 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7565 (pp) REVERT: W 362 TYR cc_start: 0.5920 (t80) cc_final: 0.5700 (t80) REVERT: W 440 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8763 (m-40) REVERT: W 466 LYS cc_start: 0.6720 (tptt) cc_final: 0.6438 (tptp) REVERT: W 479 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7706 (ttm110) REVERT: X 12 ARG cc_start: 0.7467 (ptm160) cc_final: 0.7258 (ptm160) REVERT: X 365 ASN cc_start: 0.7605 (t0) cc_final: 0.7007 (t0) REVERT: X 466 LYS cc_start: 0.5858 (tptt) cc_final: 0.5610 (mtpt) REVERT: X 481 ARG cc_start: 0.5113 (tpt170) cc_final: 0.3723 (mmp-170) REVERT: Z 232 GLU cc_start: 0.5468 (tm-30) cc_final: 0.5117 (tm-30) REVERT: Z 307 GLU cc_start: 0.7946 (pm20) cc_final: 0.7623 (pm20) REVERT: Z 362 TYR cc_start: 0.4508 (t80) cc_final: 0.4290 (m-80) REVERT: Z 363 ILE cc_start: 0.5504 (OUTLIER) cc_final: 0.4732 (tp) REVERT: Z 365 ASN cc_start: 0.7176 (t0) cc_final: 0.6757 (t0) REVERT: Z 400 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7570 (mm-30) REVERT: a 215 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7010 (pm20) REVERT: a 307 GLU cc_start: 0.8507 (pm20) cc_final: 0.8274 (pm20) REVERT: a 325 GLU cc_start: 0.5655 (pm20) cc_final: 0.5078 (pt0) REVERT: c 69 ARG cc_start: 0.7555 (mmm-85) cc_final: 0.7179 (mtp-110) REVERT: c 82 TYR cc_start: 0.8993 (m-80) cc_final: 0.8251 (m-80) REVERT: c 88 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: c 230 TRP cc_start: 0.7659 (OUTLIER) cc_final: 0.7246 (t60) REVERT: c 282 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9032 (t) REVERT: c 470 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: d 51 GLU cc_start: 0.8104 (tt0) cc_final: 0.7676 (tm-30) REVERT: d 226 ASP cc_start: 0.8053 (p0) cc_final: 0.7575 (t0) REVERT: d 335 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7106 (pp20) REVERT: d 364 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6792 (m-10) REVERT: d 481 ARG cc_start: 0.4330 (mmp-170) cc_final: 0.3347 (ptp-110) REVERT: d 497 LEU cc_start: 0.7403 (pt) cc_final: 0.7069 (tp) REVERT: f 27 LYS cc_start: 0.7704 (ptpt) cc_final: 0.7339 (mtmt) REVERT: f 226 ASP cc_start: 0.6430 (OUTLIER) cc_final: 0.5863 (t0) REVERT: f 307 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7868 (tm-30) REVERT: f 364 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: f 454 ASP cc_start: 0.8701 (m-30) cc_final: 0.8439 (m-30) REVERT: g 34 MET cc_start: 0.5363 (OUTLIER) cc_final: 0.4891 (ttm) REVERT: i 48 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7815 (m) REVERT: i 94 LYS cc_start: 0.7774 (mttm) cc_final: 0.7422 (tptt) REVERT: i 439 ASP cc_start: 0.8612 (m-30) cc_final: 0.8369 (m-30) REVERT: i 446 SER cc_start: 0.7617 (m) cc_final: 0.7398 (m) REVERT: j 12 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7832 (ttm-80) REVERT: j 115 MET cc_start: 0.8053 (mpp) cc_final: 0.7720 (mmm) REVERT: j 263 GLN cc_start: 0.8150 (mt0) cc_final: 0.7626 (mt0) outliers start: 216 outliers final: 149 residues processed: 943 average time/residue: 0.5047 time to fit residues: 821.4464 Evaluate side-chains 925 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 762 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 40 TYR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain O residue 31 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 128 LEU Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 40 TYR Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain T residue 314 THR Chi-restraints excluded: chain T residue 363 ILE Chi-restraints excluded: chain T residue 387 SER Chi-restraints excluded: chain T residue 421 ILE Chi-restraints excluded: chain T residue 439 ASP Chi-restraints excluded: chain T residue 459 THR Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 363 ILE Chi-restraints excluded: chain U residue 384 ASP Chi-restraints excluded: chain U residue 459 THR Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 371 LEU Chi-restraints excluded: chain W residue 432 LYS Chi-restraints excluded: chain W residue 440 ASN Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 201 SER Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 282 THR Chi-restraints excluded: chain X residue 288 TYR Chi-restraints excluded: chain X residue 387 SER Chi-restraints excluded: chain X residue 398 LEU Chi-restraints excluded: chain X residue 459 THR Chi-restraints excluded: chain X residue 491 VAL Chi-restraints excluded: chain Z residue 8 ASP Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 363 ILE Chi-restraints excluded: chain Z residue 448 PHE Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 226 ASP Chi-restraints excluded: chain a residue 308 LEU Chi-restraints excluded: chain a residue 357 ASN Chi-restraints excluded: chain a residue 359 THR Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 230 TRP Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 300 CYS Chi-restraints excluded: chain c residue 303 CYS Chi-restraints excluded: chain c residue 455 ILE Chi-restraints excluded: chain c residue 459 THR Chi-restraints excluded: chain c residue 470 GLN Chi-restraints excluded: chain c residue 492 ASN Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 26 CYS Chi-restraints excluded: chain d residue 34 MET Chi-restraints excluded: chain d residue 213 VAL Chi-restraints excluded: chain d residue 285 VAL Chi-restraints excluded: chain d residue 308 LEU Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 364 TYR Chi-restraints excluded: chain d residue 448 PHE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 226 ASP Chi-restraints excluded: chain f residue 269 ASP Chi-restraints excluded: chain f residue 303 CYS Chi-restraints excluded: chain f residue 326 SER Chi-restraints excluded: chain f residue 362 TYR Chi-restraints excluded: chain f residue 364 TYR Chi-restraints excluded: chain g residue 34 MET Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 328 THR Chi-restraints excluded: chain g residue 336 VAL Chi-restraints excluded: chain g residue 337 THR Chi-restraints excluded: chain g residue 491 VAL Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 73 CYS Chi-restraints excluded: chain i residue 229 ASP Chi-restraints excluded: chain i residue 269 ASP Chi-restraints excluded: chain i residue 448 PHE Chi-restraints excluded: chain j residue 185 VAL Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 443 THR Chi-restraints excluded: chain j residue 448 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 234 optimal weight: 0.6980 chunk 628 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 409 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 698 optimal weight: 1.9990 chunk 579 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 366 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN F 11 ASN F 32 GLN ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 ASN P 118 ASN R 52 ASN ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 233 ASN U 305 ASN ** U 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 214 ASN W 291 ASN W 369 ASN X 257 ASN Z 440 ASN a 20 ASN a 311 GLN a 369 ASN ** c 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 291 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 342 ASN ** j 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 56531 Z= 0.153 Angle : 0.518 9.718 77092 Z= 0.272 Chirality : 0.043 0.271 8955 Planarity : 0.004 0.064 10182 Dihedral : 4.549 32.766 7742 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.16 % Favored : 92.37 % Rotamer: Outliers : 2.03 % Allowed : 16.71 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.83 (0.10), residues: 7147 helix: 1.42 (0.14), residues: 1494 sheet: -0.52 (0.12), residues: 1870 loop : -1.40 (0.11), residues: 3783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 237 HIS 0.003 0.000 HIS f 171 PHE 0.032 0.001 PHE c 461 TYR 0.017 0.001 TYR a 362 ARG 0.013 0.000 ARG U 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 842 time to evaluate : 4.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8826 (mp10) cc_final: 0.8603 (mp10) REVERT: B 52 ASN cc_start: 0.7967 (t0) cc_final: 0.7682 (t0) REVERT: C 20 ASP cc_start: 0.8723 (p0) cc_final: 0.8332 (p0) REVERT: C 99 LEU cc_start: 0.9036 (tt) cc_final: 0.8747 (tt) REVERT: D 22 GLN cc_start: 0.8426 (mp10) cc_final: 0.7893 (mp10) REVERT: D 117 MET cc_start: 0.9138 (mtt) cc_final: 0.8716 (mtt) REVERT: E 101 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7721 (mm-30) REVERT: E 111 ASP cc_start: 0.8212 (p0) cc_final: 0.7950 (p0) REVERT: F 64 MET cc_start: 0.8637 (ttm) cc_final: 0.8369 (ttm) REVERT: F 111 ASP cc_start: 0.9057 (p0) cc_final: 0.8851 (p0) REVERT: G 101 GLU cc_start: 0.7803 (mp0) cc_final: 0.7562 (mp0) REVERT: H 108 GLU cc_start: 0.8642 (tp30) cc_final: 0.8434 (tp30) REVERT: I 22 GLN cc_start: 0.8279 (mm-40) cc_final: 0.8031 (mm110) REVERT: J 52 ASN cc_start: 0.7991 (t0) cc_final: 0.7701 (t0) REVERT: J 93 ASP cc_start: 0.8187 (p0) cc_final: 0.7785 (p0) REVERT: J 97 MET cc_start: 0.8551 (mmt) cc_final: 0.8263 (mmt) REVERT: K 52 ASN cc_start: 0.8114 (t0) cc_final: 0.7677 (t0) REVERT: K 125 ASP cc_start: 0.8204 (t70) cc_final: 0.7867 (t70) REVERT: L 60 SER cc_start: 0.9167 (t) cc_final: 0.8935 (t) REVERT: L 101 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8140 (mt-10) REVERT: M 52 ASN cc_start: 0.8669 (t0) cc_final: 0.8345 (t0) REVERT: N 86 ASP cc_start: 0.8137 (m-30) cc_final: 0.7907 (m-30) REVERT: N 97 MET cc_start: 0.8104 (mmt) cc_final: 0.7512 (mmt) REVERT: P 22 GLN cc_start: 0.8160 (mm110) cc_final: 0.7686 (tp40) REVERT: Q 40 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: Q 97 MET cc_start: 0.8399 (mmt) cc_final: 0.7991 (mmt) REVERT: Q 123 GLU cc_start: 0.7188 (pp20) cc_final: 0.6845 (pt0) REVERT: S 18 ASP cc_start: 0.8659 (t0) cc_final: 0.8412 (t0) REVERT: S 97 MET cc_start: 0.8497 (mmt) cc_final: 0.7833 (mmt) REVERT: T 325 GLU cc_start: 0.7074 (pp20) cc_final: 0.5645 (mp0) REVERT: T 365 ASN cc_start: 0.7874 (t0) cc_final: 0.7586 (t0) REVERT: T 454 ASP cc_start: 0.8251 (m-30) cc_final: 0.8002 (m-30) REVERT: T 488 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.6406 (pmt-80) REVERT: U 16 ASP cc_start: 0.7539 (t70) cc_final: 0.7242 (t70) REVERT: U 466 LYS cc_start: 0.7706 (tptt) cc_final: 0.7493 (tptt) REVERT: W 294 TYR cc_start: 0.7895 (t80) cc_final: 0.7692 (t80) REVERT: W 466 LYS cc_start: 0.6735 (tptt) cc_final: 0.6444 (tptp) REVERT: W 479 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7700 (ttm110) REVERT: X 12 ARG cc_start: 0.7299 (ptm160) cc_final: 0.7050 (ptm160) REVERT: X 365 ASN cc_start: 0.7068 (t0) cc_final: 0.6385 (t0) REVERT: X 466 LYS cc_start: 0.6014 (tptt) cc_final: 0.5717 (mtpt) REVERT: X 480 TYR cc_start: 0.4265 (p90) cc_final: 0.3911 (p90) REVERT: X 481 ARG cc_start: 0.5115 (tpt170) cc_final: 0.3812 (mmp-170) REVERT: Z 232 GLU cc_start: 0.5441 (tm-30) cc_final: 0.5080 (tm-30) REVERT: Z 365 ASN cc_start: 0.6840 (t0) cc_final: 0.6466 (t0) REVERT: Z 400 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7617 (mm-30) REVERT: a 19 LEU cc_start: 0.8284 (tp) cc_final: 0.7928 (mp) REVERT: a 69 ARG cc_start: 0.8633 (mmm-85) cc_final: 0.8372 (mtp85) REVERT: a 283 TYR cc_start: 0.8569 (t80) cc_final: 0.8022 (t80) REVERT: a 307 GLU cc_start: 0.8490 (pm20) cc_final: 0.8207 (pm20) REVERT: a 325 GLU cc_start: 0.5521 (pm20) cc_final: 0.4917 (pt0) REVERT: c 69 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.7111 (mtp-110) REVERT: c 82 TYR cc_start: 0.8913 (m-80) cc_final: 0.8018 (m-80) REVERT: c 282 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9061 (t) REVERT: c 372 ARG cc_start: 0.7459 (mtt-85) cc_final: 0.6734 (mtm110) REVERT: c 470 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: d 51 GLU cc_start: 0.8100 (tt0) cc_final: 0.7642 (tm-30) REVERT: d 226 ASP cc_start: 0.8024 (p0) cc_final: 0.7633 (t0) REVERT: d 335 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7005 (pp20) REVERT: d 481 ARG cc_start: 0.4290 (mmp-170) cc_final: 0.3313 (ptp-110) REVERT: d 497 LEU cc_start: 0.7183 (pt) cc_final: 0.6867 (tp) REVERT: f 27 LYS cc_start: 0.7501 (ptpt) cc_final: 0.7074 (mtmt) REVERT: f 307 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7719 (tm-30) REVERT: f 454 ASP cc_start: 0.8686 (m-30) cc_final: 0.8410 (m-30) REVERT: g 370 TYR cc_start: 0.7195 (t80) cc_final: 0.6940 (t80) REVERT: i 48 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7725 (m) REVERT: i 94 LYS cc_start: 0.7786 (mttm) cc_final: 0.7417 (tptt) REVERT: i 439 ASP cc_start: 0.8463 (m-30) cc_final: 0.8005 (m-30) REVERT: i 446 SER cc_start: 0.7617 (m) cc_final: 0.7398 (m) REVERT: j 12 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7845 (mtt-85) REVERT: j 115 MET cc_start: 0.7992 (mpp) cc_final: 0.7660 (mmm) outliers start: 125 outliers final: 96 residues processed: 930 average time/residue: 0.4995 time to fit residues: 801.9933 Evaluate side-chains 894 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 793 time to evaluate : 4.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 40 TYR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 40 TYR Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 128 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 40 TYR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 52 ASN Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 233 ASN Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain T residue 282 THR Chi-restraints excluded: chain T residue 371 LEU Chi-restraints excluded: chain T residue 439 ASP Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 384 ASP Chi-restraints excluded: chain U residue 448 PHE Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 340 GLN Chi-restraints excluded: chain W residue 371 LEU Chi-restraints excluded: chain W residue 415 THR Chi-restraints excluded: chain W residue 432 LYS Chi-restraints excluded: chain W residue 440 ASN Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 201 SER Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 288 TYR Chi-restraints excluded: chain X residue 398 LEU Chi-restraints excluded: chain X residue 491 VAL Chi-restraints excluded: chain Z residue 448 PHE Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 357 ASN Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 230 TRP Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 303 CYS Chi-restraints excluded: chain c residue 455 ILE Chi-restraints excluded: chain c residue 459 THR Chi-restraints excluded: chain c residue 470 GLN Chi-restraints excluded: chain d residue 34 MET Chi-restraints excluded: chain d residue 213 VAL Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 448 PHE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 170 ASN Chi-restraints excluded: chain f residue 269 ASP Chi-restraints excluded: chain f residue 303 CYS Chi-restraints excluded: chain f residue 326 SER Chi-restraints excluded: chain f residue 362 TYR Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 328 THR Chi-restraints excluded: chain g residue 336 VAL Chi-restraints excluded: chain g residue 376 ASN Chi-restraints excluded: chain g residue 491 VAL Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 213 VAL Chi-restraints excluded: chain i residue 229 ASP Chi-restraints excluded: chain i residue 269 ASP Chi-restraints excluded: chain i residue 448 PHE Chi-restraints excluded: chain j residue 185 VAL Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 443 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 673 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 398 optimal weight: 10.0000 chunk 510 optimal weight: 1.9990 chunk 395 optimal weight: 9.9990 chunk 588 optimal weight: 10.0000 chunk 390 optimal weight: 4.9990 chunk 695 optimal weight: 7.9990 chunk 435 optimal weight: 0.6980 chunk 424 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 GLN M 22 GLN N 88 GLN ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 ASN P 118 ASN R 52 ASN ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 305 ASN ** U 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 291 ASN W 369 ASN Z 440 ASN a 311 GLN a 440 ASN ** c 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 291 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 342 ASN ** j 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 56531 Z= 0.390 Angle : 0.609 11.333 77092 Z= 0.319 Chirality : 0.046 0.243 8955 Planarity : 0.005 0.140 10182 Dihedral : 4.797 32.273 7742 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.26 % Favored : 90.28 % Rotamer: Outliers : 3.13 % Allowed : 16.53 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.02 (0.10), residues: 7147 helix: 1.24 (0.14), residues: 1501 sheet: -0.65 (0.12), residues: 1875 loop : -1.50 (0.11), residues: 3771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP g 230 HIS 0.004 0.001 HIS i 252 PHE 0.022 0.002 PHE c 461 TYR 0.019 0.002 TYR a 362 ARG 0.007 0.001 ARG U 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 793 time to evaluate : 5.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 ASN cc_start: 0.8204 (t0) cc_final: 0.7908 (t0) REVERT: C 20 ASP cc_start: 0.8719 (p0) cc_final: 0.8333 (p0) REVERT: D 22 GLN cc_start: 0.8524 (mp10) cc_final: 0.7875 (mp10) REVERT: G 101 GLU cc_start: 0.7863 (mp0) cc_final: 0.7562 (mp0) REVERT: H 108 GLU cc_start: 0.8668 (tp30) cc_final: 0.8455 (tp30) REVERT: J 93 ASP cc_start: 0.8264 (p0) cc_final: 0.7888 (p0) REVERT: K 50 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8034 (mp) REVERT: K 52 ASN cc_start: 0.8281 (t0) cc_final: 0.7879 (t0) REVERT: K 125 ASP cc_start: 0.8194 (t70) cc_final: 0.7951 (t70) REVERT: L 60 SER cc_start: 0.9190 (t) cc_final: 0.8911 (t) REVERT: L 101 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8196 (mt-10) REVERT: L 111 ASP cc_start: 0.8959 (p0) cc_final: 0.8723 (p0) REVERT: M 52 ASN cc_start: 0.8733 (t0) cc_final: 0.8390 (t0) REVERT: N 97 MET cc_start: 0.8095 (mmt) cc_final: 0.7497 (mmt) REVERT: Q 40 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8498 (m-80) REVERT: Q 97 MET cc_start: 0.8555 (mmt) cc_final: 0.8053 (mmt) REVERT: S 18 ASP cc_start: 0.8739 (t0) cc_final: 0.8435 (t0) REVERT: S 97 MET cc_start: 0.8543 (mmt) cc_final: 0.7900 (mmt) REVERT: T 325 GLU cc_start: 0.7081 (pp20) cc_final: 0.5695 (mp0) REVERT: T 365 ASN cc_start: 0.8053 (t0) cc_final: 0.7815 (t0) REVERT: T 454 ASP cc_start: 0.8366 (m-30) cc_final: 0.8121 (m-30) REVERT: U 16 ASP cc_start: 0.7589 (t70) cc_final: 0.7269 (t70) REVERT: U 466 LYS cc_start: 0.7707 (tptt) cc_final: 0.7477 (tptt) REVERT: W 52 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7580 (pp) REVERT: W 362 TYR cc_start: 0.6145 (t80) cc_final: 0.5590 (t80) REVERT: W 466 LYS cc_start: 0.6809 (tptt) cc_final: 0.6553 (tptp) REVERT: W 479 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7676 (ttm110) REVERT: X 362 TYR cc_start: 0.6414 (OUTLIER) cc_final: 0.5557 (t80) REVERT: X 365 ASN cc_start: 0.7481 (t0) cc_final: 0.6838 (t0) REVERT: X 481 ARG cc_start: 0.5165 (tpt170) cc_final: 0.3617 (mmp-170) REVERT: Z 34 MET cc_start: 0.4604 (ttp) cc_final: 0.4354 (ttp) REVERT: Z 232 GLU cc_start: 0.5454 (tm-30) cc_final: 0.5088 (tm-30) REVERT: Z 307 GLU cc_start: 0.7931 (pm20) cc_final: 0.7599 (pm20) REVERT: Z 365 ASN cc_start: 0.7009 (t0) cc_final: 0.6627 (t0) REVERT: Z 400 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7489 (mm-30) REVERT: a 19 LEU cc_start: 0.8359 (tp) cc_final: 0.8006 (mp) REVERT: a 21 PHE cc_start: 0.7462 (m-80) cc_final: 0.7200 (m-80) REVERT: a 60 GLN cc_start: 0.7399 (tt0) cc_final: 0.7001 (pt0) REVERT: a 307 GLU cc_start: 0.8511 (pm20) cc_final: 0.8220 (pm20) REVERT: a 325 GLU cc_start: 0.5533 (pm20) cc_final: 0.4944 (pt0) REVERT: c 69 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.7169 (mtp-110) REVERT: c 82 TYR cc_start: 0.8934 (m-80) cc_final: 0.8065 (m-80) REVERT: c 230 TRP cc_start: 0.7644 (OUTLIER) cc_final: 0.7245 (t60) REVERT: c 282 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.8982 (t) REVERT: c 413 LYS cc_start: 0.8049 (tmmt) cc_final: 0.7294 (tptt) REVERT: c 470 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: d 51 GLU cc_start: 0.8117 (tt0) cc_final: 0.7679 (tm-30) REVERT: d 226 ASP cc_start: 0.8061 (p0) cc_final: 0.7619 (t0) REVERT: d 308 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8873 (tt) REVERT: d 335 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7299 (pp20) REVERT: d 364 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.7115 (m-10) REVERT: d 481 ARG cc_start: 0.4337 (mmp-170) cc_final: 0.3323 (ptp-110) REVERT: d 497 LEU cc_start: 0.7296 (pt) cc_final: 0.6962 (tp) REVERT: f 27 LYS cc_start: 0.7572 (ptpt) cc_final: 0.7143 (mtmt) REVERT: f 307 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7834 (tm-30) REVERT: f 364 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6654 (m-10) REVERT: f 454 ASP cc_start: 0.8633 (m-30) cc_final: 0.8386 (m-30) REVERT: f 485 ARG cc_start: 0.4900 (OUTLIER) cc_final: 0.4083 (tpt170) REVERT: g 34 MET cc_start: 0.5326 (OUTLIER) cc_final: 0.4882 (ttm) REVERT: i 48 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7719 (m) REVERT: i 94 LYS cc_start: 0.7837 (mttm) cc_final: 0.7468 (tptt) REVERT: i 439 ASP cc_start: 0.8591 (m-30) cc_final: 0.8347 (m-30) REVERT: i 446 SER cc_start: 0.7640 (m) cc_final: 0.7418 (m) REVERT: j 69 ARG cc_start: 0.7579 (tpp-160) cc_final: 0.7303 (tpp-160) REVERT: j 115 MET cc_start: 0.7988 (mpp) cc_final: 0.7653 (mmm) outliers start: 193 outliers final: 139 residues processed: 928 average time/residue: 0.5222 time to fit residues: 841.8661 Evaluate side-chains 920 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 767 time to evaluate : 4.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 40 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain J residue 3 CYS Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 40 TYR Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 128 LEU Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 40 TYR Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain T residue 282 THR Chi-restraints excluded: chain T residue 347 SER Chi-restraints excluded: chain T residue 363 ILE Chi-restraints excluded: chain T residue 371 LEU Chi-restraints excluded: chain T residue 412 THR Chi-restraints excluded: chain T residue 439 ASP Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 364 TYR Chi-restraints excluded: chain U residue 448 PHE Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 174 VAL Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 340 GLN Chi-restraints excluded: chain W residue 371 LEU Chi-restraints excluded: chain W residue 415 THR Chi-restraints excluded: chain W residue 432 LYS Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 15 ILE Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 201 SER Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 288 TYR Chi-restraints excluded: chain X residue 362 TYR Chi-restraints excluded: chain X residue 398 LEU Chi-restraints excluded: chain X residue 491 VAL Chi-restraints excluded: chain Z residue 8 ASP Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 336 VAL Chi-restraints excluded: chain Z residue 448 PHE Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 15 ILE Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 46 THR Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 226 ASP Chi-restraints excluded: chain a residue 357 ASN Chi-restraints excluded: chain a residue 419 THR Chi-restraints excluded: chain a residue 440 ASN Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 230 TRP Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 455 ILE Chi-restraints excluded: chain c residue 459 THR Chi-restraints excluded: chain c residue 470 GLN Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 11 VAL Chi-restraints excluded: chain d residue 26 CYS Chi-restraints excluded: chain d residue 213 VAL Chi-restraints excluded: chain d residue 308 LEU Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 362 TYR Chi-restraints excluded: chain d residue 364 TYR Chi-restraints excluded: chain d residue 448 PHE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 170 ASN Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 269 ASP Chi-restraints excluded: chain f residue 303 CYS Chi-restraints excluded: chain f residue 326 SER Chi-restraints excluded: chain f residue 362 TYR Chi-restraints excluded: chain f residue 364 TYR Chi-restraints excluded: chain f residue 375 LYS Chi-restraints excluded: chain f residue 485 ARG Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 34 MET Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 328 THR Chi-restraints excluded: chain g residue 336 VAL Chi-restraints excluded: chain g residue 376 ASN Chi-restraints excluded: chain g residue 491 VAL Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 213 VAL Chi-restraints excluded: chain i residue 229 ASP Chi-restraints excluded: chain i residue 269 ASP Chi-restraints excluded: chain i residue 368 THR Chi-restraints excluded: chain i residue 448 PHE Chi-restraints excluded: chain j residue 185 VAL Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 217 CYS Chi-restraints excluded: chain j residue 443 THR Chi-restraints excluded: chain j residue 448 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 430 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 415 optimal weight: 20.0000 chunk 209 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 442 optimal weight: 9.9990 chunk 474 optimal weight: 1.9990 chunk 344 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 546 optimal weight: 30.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 GLN ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 ASN P 118 ASN R 52 ASN ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 233 ASN ** U 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 369 ASN Z 440 ASN a 311 GLN ** c 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 291 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 438 GLN ** i 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 342 ASN ** j 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 56531 Z= 0.186 Angle : 0.539 14.509 77092 Z= 0.283 Chirality : 0.043 0.218 8955 Planarity : 0.004 0.062 10182 Dihedral : 4.647 29.462 7742 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.44 % Favored : 92.11 % Rotamer: Outliers : 2.77 % Allowed : 17.18 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: -0.90 (0.10), residues: 7147 helix: 1.40 (0.14), residues: 1492 sheet: -0.58 (0.12), residues: 1876 loop : -1.45 (0.10), residues: 3779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 237 HIS 0.002 0.000 HIS Z 475 PHE 0.024 0.001 PHE c 461 TYR 0.018 0.001 TYR I 40 ARG 0.006 0.000 ARG d 383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 825 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8817 (mp10) cc_final: 0.8615 (mp10) REVERT: B 52 ASN cc_start: 0.8137 (t0) cc_final: 0.7854 (t0) REVERT: C 20 ASP cc_start: 0.8705 (p0) cc_final: 0.8313 (p0) REVERT: C 52 ASN cc_start: 0.8176 (p0) cc_final: 0.7959 (p0) REVERT: C 99 LEU cc_start: 0.9059 (tt) cc_final: 0.8783 (tt) REVERT: D 22 GLN cc_start: 0.8496 (mp10) cc_final: 0.7841 (mp10) REVERT: D 117 MET cc_start: 0.8883 (mtt) cc_final: 0.8364 (mtt) REVERT: E 101 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7877 (mm-30) REVERT: F 111 ASP cc_start: 0.9075 (p0) cc_final: 0.8837 (p0) REVERT: G 101 GLU cc_start: 0.7877 (mp0) cc_final: 0.7601 (mp0) REVERT: H 123 GLU cc_start: 0.7894 (mp0) cc_final: 0.7674 (mp0) REVERT: J 93 ASP cc_start: 0.8173 (p0) cc_final: 0.7778 (p0) REVERT: K 52 ASN cc_start: 0.8183 (t0) cc_final: 0.7798 (t0) REVERT: K 70 ARG cc_start: 0.8449 (tmm-80) cc_final: 0.7884 (ttt90) REVERT: K 125 ASP cc_start: 0.8189 (t70) cc_final: 0.7897 (t70) REVERT: L 60 SER cc_start: 0.9175 (t) cc_final: 0.8944 (t) REVERT: L 101 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8152 (mt-10) REVERT: M 52 ASN cc_start: 0.8658 (t0) cc_final: 0.8339 (t0) REVERT: N 86 ASP cc_start: 0.8189 (m-30) cc_final: 0.7957 (m-30) REVERT: N 97 MET cc_start: 0.8105 (mmt) cc_final: 0.7507 (mmt) REVERT: P 22 GLN cc_start: 0.8218 (mm110) cc_final: 0.7747 (tp40) REVERT: Q 40 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: Q 97 MET cc_start: 0.8375 (mmt) cc_final: 0.7985 (mmt) REVERT: R 111 ASP cc_start: 0.8967 (p0) cc_final: 0.8723 (p0) REVERT: S 18 ASP cc_start: 0.8694 (t0) cc_final: 0.8428 (t0) REVERT: S 88 GLN cc_start: 0.8872 (mt0) cc_final: 0.8390 (tt0) REVERT: S 97 MET cc_start: 0.8517 (mmt) cc_final: 0.7841 (mmt) REVERT: T 325 GLU cc_start: 0.7041 (pp20) cc_final: 0.5617 (mp0) REVERT: T 454 ASP cc_start: 0.8277 (m-30) cc_final: 0.8014 (m-30) REVERT: U 16 ASP cc_start: 0.7545 (t70) cc_final: 0.7165 (t70) REVERT: U 19 LEU cc_start: 0.7869 (mt) cc_final: 0.7593 (mt) REVERT: U 466 LYS cc_start: 0.7722 (tptt) cc_final: 0.7438 (tptt) REVERT: W 362 TYR cc_start: 0.6093 (t80) cc_final: 0.5649 (t80) REVERT: W 466 LYS cc_start: 0.6790 (tptt) cc_final: 0.6502 (tptp) REVERT: W 479 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7660 (ttm110) REVERT: X 362 TYR cc_start: 0.6298 (t80) cc_final: 0.5571 (t80) REVERT: X 365 ASN cc_start: 0.7124 (t0) cc_final: 0.6459 (t0) REVERT: X 481 ARG cc_start: 0.5117 (tpt170) cc_final: 0.3794 (mmp-170) REVERT: Z 34 MET cc_start: 0.4506 (ttp) cc_final: 0.4155 (ttp) REVERT: Z 232 GLU cc_start: 0.5434 (tm-30) cc_final: 0.5069 (tm-30) REVERT: Z 365 ASN cc_start: 0.6849 (t0) cc_final: 0.6518 (t0) REVERT: Z 400 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7564 (mm-30) REVERT: a 19 LEU cc_start: 0.8340 (tp) cc_final: 0.8046 (mp) REVERT: a 60 GLN cc_start: 0.7376 (tt0) cc_final: 0.6979 (pt0) REVERT: a 69 ARG cc_start: 0.8677 (mmm-85) cc_final: 0.8396 (mtp85) REVERT: a 283 TYR cc_start: 0.8606 (t80) cc_final: 0.7973 (t80) REVERT: a 325 GLU cc_start: 0.5494 (pm20) cc_final: 0.4861 (pt0) REVERT: c 69 ARG cc_start: 0.7525 (mmm-85) cc_final: 0.7148 (mtp-110) REVERT: c 82 TYR cc_start: 0.8889 (m-80) cc_final: 0.8035 (m-80) REVERT: c 282 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9014 (t) REVERT: c 372 ARG cc_start: 0.7475 (mtt-85) cc_final: 0.6794 (mtm110) REVERT: c 470 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: d 51 GLU cc_start: 0.8132 (tt0) cc_final: 0.7648 (tm-30) REVERT: d 226 ASP cc_start: 0.8020 (p0) cc_final: 0.7639 (t0) REVERT: d 335 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7177 (pp20) REVERT: d 481 ARG cc_start: 0.4263 (mmp-170) cc_final: 0.3311 (ptp-110) REVERT: d 497 LEU cc_start: 0.7186 (pt) cc_final: 0.6871 (tp) REVERT: f 27 LYS cc_start: 0.7450 (ptpt) cc_final: 0.7069 (mtmt) REVERT: f 307 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7798 (tm-30) REVERT: f 454 ASP cc_start: 0.8630 (m-30) cc_final: 0.8337 (m-30) REVERT: f 485 ARG cc_start: 0.4738 (OUTLIER) cc_final: 0.3673 (mmp-170) REVERT: g 27 LYS cc_start: 0.6759 (OUTLIER) cc_final: 0.6287 (ttmt) REVERT: g 34 MET cc_start: 0.5323 (OUTLIER) cc_final: 0.4908 (ttm) REVERT: i 48 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7689 (m) REVERT: i 94 LYS cc_start: 0.7774 (mttm) cc_final: 0.7418 (tptt) REVERT: i 446 SER cc_start: 0.7612 (m) cc_final: 0.7386 (m) REVERT: j 69 ARG cc_start: 0.7547 (tpp-160) cc_final: 0.7273 (tpp-160) outliers start: 171 outliers final: 136 residues processed: 947 average time/residue: 0.4861 time to fit residues: 796.9940 Evaluate side-chains 941 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 797 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 40 TYR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain J residue 3 CYS Chi-restraints excluded: chain J residue 40 TYR Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 40 TYR Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 128 LEU Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 40 TYR Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain Q residue 40 TYR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 233 ASN Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain T residue 282 THR Chi-restraints excluded: chain T residue 347 SER Chi-restraints excluded: chain T residue 371 LEU Chi-restraints excluded: chain T residue 387 SER Chi-restraints excluded: chain T residue 439 ASP Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 364 TYR Chi-restraints excluded: chain U residue 384 ASP Chi-restraints excluded: chain U residue 448 PHE Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 174 VAL Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 340 GLN Chi-restraints excluded: chain W residue 371 LEU Chi-restraints excluded: chain W residue 415 THR Chi-restraints excluded: chain W residue 432 LYS Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 201 SER Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 288 TYR Chi-restraints excluded: chain X residue 398 LEU Chi-restraints excluded: chain X residue 491 VAL Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 414 ASN Chi-restraints excluded: chain Z residue 448 PHE Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 357 ASN Chi-restraints excluded: chain a residue 419 THR Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 230 TRP Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 285 VAL Chi-restraints excluded: chain c residue 303 CYS Chi-restraints excluded: chain c residue 455 ILE Chi-restraints excluded: chain c residue 459 THR Chi-restraints excluded: chain c residue 470 GLN Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 11 VAL Chi-restraints excluded: chain d residue 26 CYS Chi-restraints excluded: chain d residue 213 VAL Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 362 TYR Chi-restraints excluded: chain d residue 448 PHE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 170 ASN Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 269 ASP Chi-restraints excluded: chain f residue 303 CYS Chi-restraints excluded: chain f residue 326 SER Chi-restraints excluded: chain f residue 362 TYR Chi-restraints excluded: chain f residue 485 ARG Chi-restraints excluded: chain f residue 491 VAL Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain g residue 34 MET Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 328 THR Chi-restraints excluded: chain g residue 336 VAL Chi-restraints excluded: chain g residue 376 ASN Chi-restraints excluded: chain g residue 438 GLN Chi-restraints excluded: chain g residue 491 VAL Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 213 VAL Chi-restraints excluded: chain i residue 229 ASP Chi-restraints excluded: chain i residue 269 ASP Chi-restraints excluded: chain i residue 368 THR Chi-restraints excluded: chain i residue 448 PHE Chi-restraints excluded: chain j residue 117 GLU Chi-restraints excluded: chain j residue 185 VAL Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 217 CYS Chi-restraints excluded: chain j residue 443 THR Chi-restraints excluded: chain j residue 448 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 633 optimal weight: 9.9990 chunk 666 optimal weight: 7.9990 chunk 608 optimal weight: 4.9990 chunk 648 optimal weight: 9.9990 chunk 390 optimal weight: 10.0000 chunk 282 optimal weight: 6.9990 chunk 509 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 585 optimal weight: 5.9990 chunk 613 optimal weight: 0.9980 chunk 646 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN J 22 GLN N 80 GLN N 88 GLN ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 ASN P 118 ASN R 52 ASN ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 233 ASN ** U 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 305 ASN ** U 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 369 ASN Z 440 ASN a 311 GLN a 440 ASN ** c 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 291 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 342 ASN ** j 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 56531 Z= 0.397 Angle : 0.621 14.296 77092 Z= 0.326 Chirality : 0.046 0.253 8955 Planarity : 0.005 0.063 10182 Dihedral : 4.871 30.220 7742 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.44 % Favored : 90.11 % Rotamer: Outliers : 2.99 % Allowed : 17.56 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.07 (0.10), residues: 7147 helix: 1.19 (0.14), residues: 1502 sheet: -0.58 (0.12), residues: 1818 loop : -1.59 (0.10), residues: 3827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP i 331 HIS 0.004 0.001 HIS Q 30 PHE 0.022 0.002 PHE c 10 TYR 0.020 0.002 TYR I 40 ARG 0.008 0.001 ARG d 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 792 time to evaluate : 4.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8890 (mp10) cc_final: 0.8673 (mp10) REVERT: B 52 ASN cc_start: 0.8251 (t0) cc_final: 0.7974 (t0) REVERT: C 20 ASP cc_start: 0.8717 (p0) cc_final: 0.8342 (p0) REVERT: D 22 GLN cc_start: 0.8562 (mp10) cc_final: 0.7857 (mp10) REVERT: E 101 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7949 (mm-30) REVERT: H 40 TYR cc_start: 0.8844 (m-80) cc_final: 0.8342 (m-80) REVERT: J 93 ASP cc_start: 0.8270 (p0) cc_final: 0.7888 (p0) REVERT: K 50 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8010 (mp) REVERT: K 52 ASN cc_start: 0.8378 (t0) cc_final: 0.7986 (t0) REVERT: K 70 ARG cc_start: 0.8597 (tmm-80) cc_final: 0.7921 (ttt180) REVERT: K 125 ASP cc_start: 0.8192 (t70) cc_final: 0.7939 (t70) REVERT: L 60 SER cc_start: 0.9190 (t) cc_final: 0.8911 (t) REVERT: L 101 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8198 (mt-10) REVERT: N 97 MET cc_start: 0.8093 (mmt) cc_final: 0.7490 (mmt) REVERT: P 22 GLN cc_start: 0.8206 (mm110) cc_final: 0.7780 (tp40) REVERT: Q 40 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: Q 97 MET cc_start: 0.8555 (mmt) cc_final: 0.8035 (mmt) REVERT: S 18 ASP cc_start: 0.8743 (t0) cc_final: 0.8463 (t0) REVERT: S 88 GLN cc_start: 0.8930 (mt0) cc_final: 0.8480 (tt0) REVERT: S 97 MET cc_start: 0.8546 (mmt) cc_final: 0.7896 (mmt) REVERT: T 325 GLU cc_start: 0.7122 (pp20) cc_final: 0.5709 (mp0) REVERT: T 365 ASN cc_start: 0.8155 (t0) cc_final: 0.7953 (t0) REVERT: U 16 ASP cc_start: 0.7542 (t70) cc_final: 0.7209 (t70) REVERT: U 466 LYS cc_start: 0.7707 (tptt) cc_final: 0.7497 (tptt) REVERT: W 52 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7620 (pp) REVERT: W 362 TYR cc_start: 0.6149 (t80) cc_final: 0.5659 (t80) REVERT: W 466 LYS cc_start: 0.6831 (tptt) cc_final: 0.6569 (tptp) REVERT: W 479 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7664 (ttm110) REVERT: X 362 TYR cc_start: 0.6417 (OUTLIER) cc_final: 0.5529 (t80) REVERT: X 365 ASN cc_start: 0.7494 (t0) cc_final: 0.6837 (t0) REVERT: X 481 ARG cc_start: 0.5141 (tpt170) cc_final: 0.3563 (mmp-170) REVERT: Z 34 MET cc_start: 0.4593 (ttp) cc_final: 0.4297 (ttp) REVERT: Z 232 GLU cc_start: 0.5381 (tm-30) cc_final: 0.5007 (tm-30) REVERT: Z 307 GLU cc_start: 0.7938 (pm20) cc_final: 0.7599 (pm20) REVERT: Z 365 ASN cc_start: 0.6968 (t0) cc_final: 0.6621 (t0) REVERT: Z 400 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7537 (mm-30) REVERT: a 19 LEU cc_start: 0.8326 (tp) cc_final: 0.8025 (mp) REVERT: a 60 GLN cc_start: 0.7424 (tt0) cc_final: 0.7037 (pt0) REVERT: a 215 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7048 (pm20) REVERT: a 283 TYR cc_start: 0.8628 (t80) cc_final: 0.7814 (t80) REVERT: a 325 GLU cc_start: 0.5505 (pm20) cc_final: 0.4948 (pt0) REVERT: c 69 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.7180 (mtp-110) REVERT: c 82 TYR cc_start: 0.8949 (m-80) cc_final: 0.8101 (m-80) REVERT: c 88 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7346 (m-30) REVERT: c 230 TRP cc_start: 0.7573 (OUTLIER) cc_final: 0.7112 (t60) REVERT: c 282 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.8990 (t) REVERT: c 413 LYS cc_start: 0.8011 (tmmt) cc_final: 0.7309 (tptt) REVERT: c 470 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: d 51 GLU cc_start: 0.8125 (tt0) cc_final: 0.7687 (tm-30) REVERT: d 226 ASP cc_start: 0.8034 (p0) cc_final: 0.7591 (t0) REVERT: d 308 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8841 (tt) REVERT: d 335 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7382 (pp20) REVERT: d 481 ARG cc_start: 0.4432 (mmp-170) cc_final: 0.3339 (ptp-110) REVERT: d 497 LEU cc_start: 0.7286 (pt) cc_final: 0.6958 (tp) REVERT: f 27 LYS cc_start: 0.7511 (ptpt) cc_final: 0.7110 (mtmt) REVERT: f 307 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7844 (tm-30) REVERT: f 364 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.6719 (m-10) REVERT: f 454 ASP cc_start: 0.8684 (m-30) cc_final: 0.8419 (m-30) REVERT: f 485 ARG cc_start: 0.4902 (OUTLIER) cc_final: 0.4062 (tpt170) REVERT: g 27 LYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6302 (ttmt) REVERT: g 34 MET cc_start: 0.5390 (OUTLIER) cc_final: 0.4947 (ttm) REVERT: g 256 PHE cc_start: 0.5386 (p90) cc_final: 0.4612 (p90) REVERT: i 48 VAL cc_start: 0.8007 (OUTLIER) cc_final: 0.7664 (m) REVERT: i 94 LYS cc_start: 0.7788 (mttm) cc_final: 0.7423 (tptt) REVERT: i 439 ASP cc_start: 0.8511 (m-30) cc_final: 0.8235 (m-30) REVERT: i 446 SER cc_start: 0.7637 (m) cc_final: 0.7411 (m) outliers start: 184 outliers final: 148 residues processed: 923 average time/residue: 0.4908 time to fit residues: 781.6942 Evaluate side-chains 930 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 767 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 40 TYR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain J residue 3 CYS Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 40 TYR Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 128 LEU Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 40 TYR Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 40 TYR Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 233 ASN Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain T residue 282 THR Chi-restraints excluded: chain T residue 347 SER Chi-restraints excluded: chain T residue 363 ILE Chi-restraints excluded: chain T residue 371 LEU Chi-restraints excluded: chain T residue 387 SER Chi-restraints excluded: chain T residue 421 ILE Chi-restraints excluded: chain T residue 439 ASP Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 364 TYR Chi-restraints excluded: chain U residue 448 PHE Chi-restraints excluded: chain U residue 459 THR Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 340 GLN Chi-restraints excluded: chain W residue 371 LEU Chi-restraints excluded: chain W residue 432 LYS Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 201 SER Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 288 TYR Chi-restraints excluded: chain X residue 362 TYR Chi-restraints excluded: chain X residue 398 LEU Chi-restraints excluded: chain X residue 491 VAL Chi-restraints excluded: chain Z residue 8 ASP Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 238 ILE Chi-restraints excluded: chain Z residue 448 PHE Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 15 ILE Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 46 THR Chi-restraints excluded: chain a residue 308 LEU Chi-restraints excluded: chain a residue 357 ASN Chi-restraints excluded: chain a residue 419 THR Chi-restraints excluded: chain a residue 440 ASN Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 230 TRP Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 285 VAL Chi-restraints excluded: chain c residue 303 CYS Chi-restraints excluded: chain c residue 455 ILE Chi-restraints excluded: chain c residue 470 GLN Chi-restraints excluded: chain c residue 491 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 11 VAL Chi-restraints excluded: chain d residue 26 CYS Chi-restraints excluded: chain d residue 213 VAL Chi-restraints excluded: chain d residue 285 VAL Chi-restraints excluded: chain d residue 308 LEU Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 362 TYR Chi-restraints excluded: chain d residue 448 PHE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 170 ASN Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 269 ASP Chi-restraints excluded: chain f residue 303 CYS Chi-restraints excluded: chain f residue 326 SER Chi-restraints excluded: chain f residue 362 TYR Chi-restraints excluded: chain f residue 364 TYR Chi-restraints excluded: chain f residue 485 ARG Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain g residue 34 MET Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 328 THR Chi-restraints excluded: chain g residue 336 VAL Chi-restraints excluded: chain g residue 376 ASN Chi-restraints excluded: chain g residue 491 VAL Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 213 VAL Chi-restraints excluded: chain i residue 229 ASP Chi-restraints excluded: chain i residue 269 ASP Chi-restraints excluded: chain i residue 368 THR Chi-restraints excluded: chain i residue 448 PHE Chi-restraints excluded: chain j residue 117 GLU Chi-restraints excluded: chain j residue 185 VAL Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 217 CYS Chi-restraints excluded: chain j residue 271 SER Chi-restraints excluded: chain j residue 443 THR Chi-restraints excluded: chain j residue 448 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 425 optimal weight: 9.9990 chunk 685 optimal weight: 20.0000 chunk 418 optimal weight: 10.0000 chunk 325 optimal weight: 10.0000 chunk 476 optimal weight: 9.9990 chunk 719 optimal weight: 0.4980 chunk 662 optimal weight: 8.9990 chunk 572 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 442 optimal weight: 10.0000 chunk 351 optimal weight: 9.9990 overall best weight: 5.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 GLN N 88 GLN ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 ASN O 118 ASN P 118 ASN R 52 ASN ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 233 ASN ** U 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 305 ASN ** U 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 369 ASN ** c 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 369 ASN ** j 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 56531 Z= 0.493 Angle : 0.678 15.690 77092 Z= 0.357 Chirality : 0.048 0.206 8955 Planarity : 0.005 0.068 10182 Dihedral : 5.235 31.579 7742 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.74 % Favored : 89.84 % Rotamer: Outliers : 3.05 % Allowed : 17.86 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.37 (0.10), residues: 7147 helix: 0.92 (0.14), residues: 1504 sheet: -0.78 (0.12), residues: 1805 loop : -1.77 (0.10), residues: 3838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP T 242 HIS 0.005 0.001 HIS Q 30 PHE 0.024 0.002 PHE c 10 TYR 0.029 0.002 TYR I 40 ARG 0.007 0.001 ARG U 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14294 Ramachandran restraints generated. 7147 Oldfield, 0 Emsley, 7147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 757 time to evaluate : 5.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8935 (mp10) cc_final: 0.8725 (mp10) REVERT: B 52 ASN cc_start: 0.8325 (t0) cc_final: 0.8020 (t0) REVERT: B 125 ASP cc_start: 0.8354 (t0) cc_final: 0.8116 (t0) REVERT: C 20 ASP cc_start: 0.8746 (p0) cc_final: 0.8323 (p0) REVERT: C 52 ASN cc_start: 0.8266 (p0) cc_final: 0.8006 (p0) REVERT: D 22 GLN cc_start: 0.8613 (mp10) cc_final: 0.7924 (mp10) REVERT: E 101 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7967 (mm-30) REVERT: H 40 TYR cc_start: 0.8841 (m-80) cc_final: 0.8349 (m-80) REVERT: H 123 GLU cc_start: 0.7962 (mp0) cc_final: 0.7747 (mp0) REVERT: K 50 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8000 (mp) REVERT: K 52 ASN cc_start: 0.8500 (t0) cc_final: 0.8154 (t0) REVERT: K 125 ASP cc_start: 0.8098 (t70) cc_final: 0.7862 (t70) REVERT: L 60 SER cc_start: 0.9251 (t) cc_final: 0.8982 (t) REVERT: L 101 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8196 (mt-10) REVERT: N 97 MET cc_start: 0.8099 (mmt) cc_final: 0.7504 (mmt) REVERT: P 22 GLN cc_start: 0.8236 (mm110) cc_final: 0.7836 (tp40) REVERT: Q 40 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8564 (m-80) REVERT: Q 97 MET cc_start: 0.8573 (mmt) cc_final: 0.8040 (mmt) REVERT: S 18 ASP cc_start: 0.8757 (t0) cc_final: 0.8505 (t0) REVERT: S 97 MET cc_start: 0.8561 (mmt) cc_final: 0.7916 (mmt) REVERT: T 325 GLU cc_start: 0.7047 (pp20) cc_final: 0.5620 (mp0) REVERT: T 454 ASP cc_start: 0.8513 (m-30) cc_final: 0.8110 (m-30) REVERT: U 16 ASP cc_start: 0.7539 (t70) cc_final: 0.7186 (t70) REVERT: U 493 MET cc_start: 0.8243 (mtp) cc_final: 0.8035 (ttm) REVERT: W 52 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7622 (pp) REVERT: W 362 TYR cc_start: 0.6221 (t80) cc_final: 0.5919 (t80) REVERT: W 479 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7704 (ttm110) REVERT: X 362 TYR cc_start: 0.6688 (OUTLIER) cc_final: 0.5630 (t80) REVERT: X 365 ASN cc_start: 0.7638 (t0) cc_final: 0.6991 (t0) REVERT: X 481 ARG cc_start: 0.5285 (tpt170) cc_final: 0.3663 (mmp-170) REVERT: Z 34 MET cc_start: 0.4513 (ttp) cc_final: 0.4235 (ttp) REVERT: Z 365 ASN cc_start: 0.6978 (t0) cc_final: 0.6597 (t0) REVERT: Z 400 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7526 (mm-30) REVERT: a 19 LEU cc_start: 0.8293 (tp) cc_final: 0.7960 (mp) REVERT: a 60 GLN cc_start: 0.7384 (tt0) cc_final: 0.7030 (pt0) REVERT: a 325 GLU cc_start: 0.5623 (pm20) cc_final: 0.5058 (pt0) REVERT: a 440 ASN cc_start: 0.9100 (m-40) cc_final: 0.8877 (t0) REVERT: c 69 ARG cc_start: 0.7609 (mmm-85) cc_final: 0.7231 (mtp-110) REVERT: c 82 TYR cc_start: 0.8973 (m-80) cc_final: 0.8117 (m-80) REVERT: c 88 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: c 230 TRP cc_start: 0.7590 (OUTLIER) cc_final: 0.7159 (t60) REVERT: c 282 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.8956 (t) REVERT: c 470 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: d 19 LEU cc_start: 0.8056 (mm) cc_final: 0.7784 (mp) REVERT: d 51 GLU cc_start: 0.8193 (tt0) cc_final: 0.7744 (tm-30) REVERT: d 226 ASP cc_start: 0.8059 (p0) cc_final: 0.7593 (t0) REVERT: d 308 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8799 (tt) REVERT: d 335 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7310 (pp20) REVERT: d 481 ARG cc_start: 0.4281 (mmp-170) cc_final: 0.3130 (ptp-110) REVERT: d 485 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7080 (ttm110) REVERT: d 497 LEU cc_start: 0.7314 (pt) cc_final: 0.6996 (tp) REVERT: f 21 PHE cc_start: 0.2684 (OUTLIER) cc_final: 0.1620 (m-80) REVERT: f 27 LYS cc_start: 0.7596 (ptpt) cc_final: 0.7165 (mtmt) REVERT: f 97 TYR cc_start: 0.3827 (OUTLIER) cc_final: 0.3169 (t80) REVERT: f 307 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7925 (tm-30) REVERT: f 364 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.6962 (m-10) REVERT: f 454 ASP cc_start: 0.8645 (m-30) cc_final: 0.8384 (m-30) REVERT: f 485 ARG cc_start: 0.5033 (OUTLIER) cc_final: 0.4009 (tpm170) REVERT: g 27 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.5742 (ttpt) REVERT: g 34 MET cc_start: 0.5496 (OUTLIER) cc_final: 0.5052 (ttm) REVERT: g 256 PHE cc_start: 0.5410 (p90) cc_final: 0.4691 (p90) REVERT: g 438 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8228 (mt0) REVERT: i 48 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7818 (m) REVERT: i 94 LYS cc_start: 0.7808 (mttm) cc_final: 0.7429 (tptt) REVERT: i 446 SER cc_start: 0.7627 (m) cc_final: 0.7399 (m) outliers start: 188 outliers final: 159 residues processed: 895 average time/residue: 0.5001 time to fit residues: 773.5516 Evaluate side-chains 917 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 741 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 40 TYR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain J residue 3 CYS Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain N residue 35 ASP Chi-restraints excluded: chain N residue 40 TYR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 52 ASN Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 40 TYR Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 40 TYR Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain T residue 347 SER Chi-restraints excluded: chain T residue 363 ILE Chi-restraints excluded: chain T residue 371 LEU Chi-restraints excluded: chain T residue 387 SER Chi-restraints excluded: chain T residue 439 ASP Chi-restraints excluded: chain T residue 449 ASP Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 305 ASN Chi-restraints excluded: chain U residue 364 TYR Chi-restraints excluded: chain U residue 448 PHE Chi-restraints excluded: chain U residue 459 THR Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 340 GLN Chi-restraints excluded: chain W residue 371 LEU Chi-restraints excluded: chain W residue 432 LYS Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 98 THR Chi-restraints excluded: chain X residue 201 SER Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 288 TYR Chi-restraints excluded: chain X residue 362 TYR Chi-restraints excluded: chain X residue 398 LEU Chi-restraints excluded: chain X residue 491 VAL Chi-restraints excluded: chain Z residue 8 ASP Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 238 ILE Chi-restraints excluded: chain Z residue 414 ASN Chi-restraints excluded: chain Z residue 448 PHE Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 15 ILE Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 46 THR Chi-restraints excluded: chain a residue 226 ASP Chi-restraints excluded: chain a residue 308 LEU Chi-restraints excluded: chain a residue 357 ASN Chi-restraints excluded: chain a residue 419 THR Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 51 GLU Chi-restraints excluded: chain c residue 52 LEU Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 230 TRP Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 285 VAL Chi-restraints excluded: chain c residue 303 CYS Chi-restraints excluded: chain c residue 455 ILE Chi-restraints excluded: chain c residue 470 GLN Chi-restraints excluded: chain c residue 491 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 11 VAL Chi-restraints excluded: chain d residue 26 CYS Chi-restraints excluded: chain d residue 213 VAL Chi-restraints excluded: chain d residue 285 VAL Chi-restraints excluded: chain d residue 308 LEU Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 362 TYR Chi-restraints excluded: chain f residue 21 PHE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 97 TYR Chi-restraints excluded: chain f residue 170 ASN Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 269 ASP Chi-restraints excluded: chain f residue 303 CYS Chi-restraints excluded: chain f residue 326 SER Chi-restraints excluded: chain f residue 362 TYR Chi-restraints excluded: chain f residue 364 TYR Chi-restraints excluded: chain f residue 375 LYS Chi-restraints excluded: chain f residue 485 ARG Chi-restraints excluded: chain g residue 20 ASN Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain g residue 34 MET Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 328 THR Chi-restraints excluded: chain g residue 336 VAL Chi-restraints excluded: chain g residue 376 ASN Chi-restraints excluded: chain g residue 491 VAL Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 213 VAL Chi-restraints excluded: chain i residue 229 ASP Chi-restraints excluded: chain i residue 269 ASP Chi-restraints excluded: chain i residue 368 THR Chi-restraints excluded: chain i residue 448 PHE Chi-restraints excluded: chain j residue 117 GLU Chi-restraints excluded: chain j residue 185 VAL Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 217 CYS Chi-restraints excluded: chain j residue 443 THR Chi-restraints excluded: chain j residue 448 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 454 optimal weight: 8.9990 chunk 610 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 528 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 573 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 589 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 GLN ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 ASN P 118 ASN R 52 ASN ** S 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 305 ASN ** U 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 440 ASN ** c 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099756 restraints weight = 92961.963| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.54 r_work: 0.3134 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.241 56531 Z= 0.398 Angle : 0.796 59.199 77092 Z= 0.438 Chirality : 0.046 0.337 8955 Planarity : 0.005 0.067 10182 Dihedral : 5.259 39.115 7742 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.78 % Favored : 89.79 % Rotamer: Outliers : 3.20 % Allowed : 17.85 % Favored : 78.96 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.39 (0.10), residues: 7147 helix: 0.92 (0.14), residues: 1504 sheet: -0.80 (0.12), residues: 1805 loop : -1.78 (0.10), residues: 3838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP g 237 HIS 0.004 0.001 HIS Q 30 PHE 0.024 0.002 PHE c 10 TYR 0.043 0.002 TYR X 149 ARG 0.009 0.001 ARG T 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13552.51 seconds wall clock time: 237 minutes 56.23 seconds (14276.23 seconds total)