Starting phenix.real_space_refine on Wed Mar 20 20:54:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbd_27280/03_2024/8dbd_27280.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbd_27280/03_2024/8dbd_27280.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/8dbd_27280/03_2024/8dbd_27280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbd_27280/03_2024/8dbd_27280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbd_27280/03_2024/8dbd_27280.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbd_27280/03_2024/8dbd_27280.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= -0.000 sd= 0.280 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 204 5.16 5 C 17784 2.51 5 N 4980 2.21 5 O 5472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 163": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E ARG 260": "NH1" <-> "NH2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 260": "NH1" <-> "NH2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F ARG 301": "NH1" <-> "NH2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G ARG 104": "NH1" <-> "NH2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 177": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "G ARG 214": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 260": "NH1" <-> "NH2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G ARG 301": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H ARG 104": "NH1" <-> "NH2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H ARG 163": "NH1" <-> "NH2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "H ARG 214": "NH1" <-> "NH2" Residue "H ARG 243": "NH1" <-> "NH2" Residue "H ARG 260": "NH1" <-> "NH2" Residue "H GLU 267": "OE1" <-> "OE2" Residue "H ARG 301": "NH1" <-> "NH2" Residue "H ARG 302": "NH1" <-> "NH2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I ARG 84": "NH1" <-> "NH2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I ARG 163": "NH1" <-> "NH2" Residue "I ARG 177": "NH1" <-> "NH2" Residue "I ARG 184": "NH1" <-> "NH2" Residue "I ARG 204": "NH1" <-> "NH2" Residue "I ARG 214": "NH1" <-> "NH2" Residue "I ARG 243": "NH1" <-> "NH2" Residue "I ARG 260": "NH1" <-> "NH2" Residue "I GLU 267": "OE1" <-> "OE2" Residue "I ARG 301": "NH1" <-> "NH2" Residue "I ARG 302": "NH1" <-> "NH2" Residue "J ARG 22": "NH1" <-> "NH2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J ARG 104": "NH1" <-> "NH2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J ARG 163": "NH1" <-> "NH2" Residue "J ARG 177": "NH1" <-> "NH2" Residue "J ARG 184": "NH1" <-> "NH2" Residue "J ARG 204": "NH1" <-> "NH2" Residue "J ARG 214": "NH1" <-> "NH2" Residue "J ARG 243": "NH1" <-> "NH2" Residue "J ARG 260": "NH1" <-> "NH2" Residue "J GLU 267": "OE1" <-> "OE2" Residue "J ARG 301": "NH1" <-> "NH2" Residue "J ARG 302": "NH1" <-> "NH2" Residue "K ARG 22": "NH1" <-> "NH2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K ARG 84": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "K GLU 148": "OE1" <-> "OE2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K ARG 163": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ARG 184": "NH1" <-> "NH2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "K ARG 214": "NH1" <-> "NH2" Residue "K ARG 243": "NH1" <-> "NH2" Residue "K ARG 260": "NH1" <-> "NH2" Residue "K GLU 267": "OE1" <-> "OE2" Residue "K ARG 301": "NH1" <-> "NH2" Residue "K ARG 302": "NH1" <-> "NH2" Residue "L ARG 22": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 104": "NH1" <-> "NH2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L ARG 156": "NH1" <-> "NH2" Residue "L ARG 163": "NH1" <-> "NH2" Residue "L ARG 177": "NH1" <-> "NH2" Residue "L ARG 184": "NH1" <-> "NH2" Residue "L ARG 204": "NH1" <-> "NH2" Residue "L ARG 214": "NH1" <-> "NH2" Residue "L ARG 243": "NH1" <-> "NH2" Residue "L ARG 260": "NH1" <-> "NH2" Residue "L GLU 267": "OE1" <-> "OE2" Residue "L ARG 301": "NH1" <-> "NH2" Residue "L ARG 302": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28464 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "G" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "H" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "I" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "J" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "K" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "L" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 636 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 624 not shown) Time building chain proxies: 15.27, per 1000 atoms: 0.54 Number of scatterers: 28464 At special positions: 0 Unit cell: (128.24, 138.545, 140.835, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 204 16.00 P 24 15.00 O 5472 8.00 N 4980 7.00 C 17784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.01 Conformation dependent library (CDL) restraints added in 5.1 seconds 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 36 sheets defined 44.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 62 through 80 Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER A 314 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 256 through 264 Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.633A pdb=" N SER B 314 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 62 through 80 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 164 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 226 through 239 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER C 314 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER D 314 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 Processing helix chain 'E' and resid 62 through 80 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 131 through 138 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 174 through 186 Processing helix chain 'E' and resid 226 through 239 Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.665A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 306 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.631A pdb=" N SER E 314 " --> pdb=" O TYR E 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 62 through 80 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 131 through 138 Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 161 through 164 Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 226 through 239 Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER F 314 " --> pdb=" O TYR F 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 62 through 80 Processing helix chain 'G' and resid 107 through 120 Processing helix chain 'G' and resid 131 through 138 Processing helix chain 'G' and resid 147 through 159 Processing helix chain 'G' and resid 161 through 164 Processing helix chain 'G' and resid 174 through 186 Processing helix chain 'G' and resid 226 through 239 Processing helix chain 'G' and resid 256 through 264 Processing helix chain 'G' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 306 Processing helix chain 'G' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER G 314 " --> pdb=" O TYR G 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 24 Processing helix chain 'H' and resid 62 through 80 Processing helix chain 'H' and resid 107 through 120 Processing helix chain 'H' and resid 131 through 138 Processing helix chain 'H' and resid 147 through 159 Processing helix chain 'H' and resid 161 through 164 Processing helix chain 'H' and resid 174 through 186 Processing helix chain 'H' and resid 226 through 239 Processing helix chain 'H' and resid 256 through 264 Processing helix chain 'H' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 306 Processing helix chain 'H' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER H 314 " --> pdb=" O TYR H 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 24 Processing helix chain 'I' and resid 62 through 80 Processing helix chain 'I' and resid 107 through 120 Processing helix chain 'I' and resid 131 through 138 Processing helix chain 'I' and resid 147 through 159 Processing helix chain 'I' and resid 161 through 164 Processing helix chain 'I' and resid 174 through 186 Processing helix chain 'I' and resid 226 through 239 Processing helix chain 'I' and resid 256 through 264 Processing helix chain 'I' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS I 283 " --> pdb=" O ASP I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 306 Processing helix chain 'I' and resid 309 through 314 removed outlier: 3.631A pdb=" N SER I 314 " --> pdb=" O TYR I 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 24 Processing helix chain 'J' and resid 62 through 80 Processing helix chain 'J' and resid 107 through 120 Processing helix chain 'J' and resid 131 through 138 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 161 through 164 Processing helix chain 'J' and resid 174 through 186 Processing helix chain 'J' and resid 226 through 239 Processing helix chain 'J' and resid 256 through 264 Processing helix chain 'J' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS J 283 " --> pdb=" O ASP J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 306 Processing helix chain 'J' and resid 309 through 314 removed outlier: 3.631A pdb=" N SER J 314 " --> pdb=" O TYR J 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 24 Processing helix chain 'K' and resid 62 through 80 Processing helix chain 'K' and resid 107 through 120 Processing helix chain 'K' and resid 131 through 138 Processing helix chain 'K' and resid 147 through 159 Processing helix chain 'K' and resid 161 through 164 Processing helix chain 'K' and resid 174 through 186 Processing helix chain 'K' and resid 226 through 239 Processing helix chain 'K' and resid 256 through 264 Processing helix chain 'K' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS K 283 " --> pdb=" O ASP K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 306 Processing helix chain 'K' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER K 314 " --> pdb=" O TYR K 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 24 Processing helix chain 'L' and resid 62 through 80 Processing helix chain 'L' and resid 107 through 120 Processing helix chain 'L' and resid 131 through 138 Processing helix chain 'L' and resid 147 through 159 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'L' and resid 174 through 186 Processing helix chain 'L' and resid 226 through 239 Processing helix chain 'L' and resid 256 through 264 Processing helix chain 'L' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS L 283 " --> pdb=" O ASP L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 306 Processing helix chain 'L' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER L 314 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR A 126 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS A 250 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR B 126 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS B 250 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS C 250 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.217A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS D 250 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR E 126 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'E' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS E 250 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.215A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS F 123 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR F 126 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 208 removed outlier: 6.746A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS F 250 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS G 5 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL G 56 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE G 7 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL G 53 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL G 88 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE G 55 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS G 123 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET G 127 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE G 124 " --> pdb=" O ASP G 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU G 145 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR G 126 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 30 through 34 Processing sheet with id=AC3, first strand: chain 'G' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET G 222 " --> pdb=" O THR G 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY G 251 " --> pdb=" O MET G 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA G 268 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS G 250 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS H 5 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL H 56 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE H 7 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL H 53 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL H 88 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE H 55 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS H 123 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET H 127 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE H 124 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU H 145 " --> pdb=" O ILE H 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR H 126 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 30 through 34 Processing sheet with id=AC6, first strand: chain 'H' and resid 205 through 208 removed outlier: 6.746A pdb=" N MET H 222 " --> pdb=" O THR H 249 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY H 251 " --> pdb=" O MET H 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA H 268 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS H 250 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS I 5 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL I 56 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE I 7 " --> pdb=" O VAL I 56 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL I 53 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL I 88 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE I 55 " --> pdb=" O VAL I 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS I 123 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET I 127 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE I 124 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU I 145 " --> pdb=" O ILE I 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR I 126 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 30 through 34 Processing sheet with id=AC9, first strand: chain 'I' and resid 205 through 208 removed outlier: 6.746A pdb=" N MET I 222 " --> pdb=" O THR I 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY I 251 " --> pdb=" O MET I 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA I 268 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS I 250 " --> pdb=" O THR I 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS J 5 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL J 56 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE J 7 " --> pdb=" O VAL J 56 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL J 53 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL J 88 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE J 55 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS J 123 " --> pdb=" O VAL J 85 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET J 127 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE J 124 " --> pdb=" O ASP J 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU J 145 " --> pdb=" O ILE J 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR J 126 " --> pdb=" O LEU J 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 30 through 34 Processing sheet with id=AD3, first strand: chain 'J' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET J 222 " --> pdb=" O THR J 249 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY J 251 " --> pdb=" O MET J 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA J 268 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS J 250 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS K 5 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL K 56 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE K 7 " --> pdb=" O VAL K 56 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL K 53 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL K 88 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE K 55 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS K 123 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET K 127 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE K 124 " --> pdb=" O ASP K 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU K 145 " --> pdb=" O ILE K 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR K 126 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 30 through 34 Processing sheet with id=AD6, first strand: chain 'K' and resid 205 through 208 removed outlier: 6.744A pdb=" N MET K 222 " --> pdb=" O THR K 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY K 251 " --> pdb=" O MET K 222 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA K 268 " --> pdb=" O VAL K 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS K 250 " --> pdb=" O THR K 272 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.215A pdb=" N LYS L 5 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL L 56 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE L 7 " --> pdb=" O VAL L 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL L 53 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL L 88 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE L 55 " --> pdb=" O VAL L 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS L 123 " --> pdb=" O VAL L 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET L 127 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE L 124 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU L 145 " --> pdb=" O ILE L 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR L 126 " --> pdb=" O LEU L 145 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 30 through 34 Processing sheet with id=AD9, first strand: chain 'L' and resid 205 through 208 removed outlier: 6.746A pdb=" N MET L 222 " --> pdb=" O THR L 249 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY L 251 " --> pdb=" O MET L 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA L 268 " --> pdb=" O VAL L 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS L 250 " --> pdb=" O THR L 272 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 3996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.45 Time building geometry restraints manager: 11.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9014 1.33 - 1.45: 3429 1.45 - 1.57: 16117 1.57 - 1.69: 0 1.69 - 1.81: 300 Bond restraints: 28860 Sorted by residual: bond pdb=" O4 PO4 I 402 " pdb=" P PO4 I 402 " ideal model delta sigma weight residual 1.568 1.497 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O4 PO4 K 402 " pdb=" P PO4 K 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O4 PO4 A 402 " pdb=" P PO4 A 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 28855 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.73: 705 106.73 - 113.56: 16867 113.56 - 120.39: 10476 120.39 - 127.22: 10760 127.22 - 134.06: 240 Bond angle restraints: 39048 Sorted by residual: angle pdb=" C LEU H 27 " pdb=" N GLY H 28 " pdb=" CA GLY H 28 " ideal model delta sigma weight residual 120.10 115.70 4.40 9.50e-01 1.11e+00 2.14e+01 angle pdb=" C LEU A 27 " pdb=" N GLY A 28 " pdb=" CA GLY A 28 " ideal model delta sigma weight residual 120.10 115.71 4.39 9.50e-01 1.11e+00 2.14e+01 angle pdb=" C LEU C 27 " pdb=" N GLY C 28 " pdb=" CA GLY C 28 " ideal model delta sigma weight residual 120.10 115.72 4.38 9.50e-01 1.11e+00 2.13e+01 angle pdb=" C LEU F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta sigma weight residual 120.10 115.72 4.38 9.50e-01 1.11e+00 2.13e+01 angle pdb=" C LEU E 27 " pdb=" N GLY E 28 " pdb=" CA GLY E 28 " ideal model delta sigma weight residual 120.10 115.72 4.38 9.50e-01 1.11e+00 2.13e+01 ... (remaining 39043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 15588 15.96 - 31.92: 1428 31.92 - 47.88: 432 47.88 - 63.84: 144 63.84 - 79.80: 48 Dihedral angle restraints: 17640 sinusoidal: 6888 harmonic: 10752 Sorted by residual: dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER E 8 " pdb=" C SER E 8 " pdb=" N GLY E 9 " pdb=" CA GLY E 9 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER I 8 " pdb=" C SER I 8 " pdb=" N GLY I 9 " pdb=" CA GLY I 9 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 17637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2891 0.047 - 0.095: 1294 0.095 - 0.142: 326 0.142 - 0.189: 73 0.189 - 0.236: 36 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CA LEU C 27 " pdb=" N LEU C 27 " pdb=" C LEU C 27 " pdb=" CB LEU C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA LEU L 27 " pdb=" N LEU L 27 " pdb=" C LEU L 27 " pdb=" CB LEU L 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA LEU J 27 " pdb=" N LEU J 27 " pdb=" C LEU J 27 " pdb=" CB LEU J 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 4617 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 26 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C GLU I 26 " -0.063 2.00e-02 2.50e+03 pdb=" O GLU I 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU I 27 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 26 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLU G 26 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU G 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU G 27 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 26 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLU D 26 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU D 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU D 27 " 0.021 2.00e-02 2.50e+03 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 496 2.68 - 3.23: 27371 3.23 - 3.79: 47180 3.79 - 4.34: 64031 4.34 - 4.90: 104172 Nonbonded interactions: 243250 Sorted by model distance: nonbonded pdb=" NZ LYS K 176 " pdb=" OD2 ASP L 101 " model vdw 2.119 2.520 nonbonded pdb=" NZ LYS E 176 " pdb=" OD2 ASP F 101 " model vdw 2.120 2.520 nonbonded pdb=" O ILE G 6 " pdb=" N GLY G 28 " model vdw 2.217 2.520 nonbonded pdb=" O ILE A 6 " pdb=" N GLY A 28 " model vdw 2.218 2.520 nonbonded pdb=" O ILE H 6 " pdb=" N GLY H 28 " model vdw 2.218 2.520 ... (remaining 243245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.90 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: 1.430 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: 0.020 Extract box with map and model: 6.720 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 77.410 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.240 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 : 0.007 0.071 28860 Z= 0.476 Angle : 0.768 5.827 39048 Z= 0.485 Chirality : 0.059 0.236 4620 Planarity : 0.004 0.036 4992 Dihedral : 15.086 79.805 10632 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.74 % Allowed : 13.30 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3660 helix: 1.21 (0.15), residues: 1488 sheet: 0.04 (0.18), residues: 948 loop : -0.47 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP I 162 HIS 0.006 0.002 HIS C 130 PHE 0.011 0.002 PHE I 189 TYR 0.023 0.004 TYR B 146 ARG 0.004 0.001 ARG H 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 783 time to evaluate : 3.005 Fit side-chains revert: symmetry clash REVERT: A 8 SER cc_start: 0.8101 (t) cc_final: 0.7762 (p) REVERT: A 66 ASN cc_start: 0.9156 (m-40) cc_final: 0.8731 (m-40) REVERT: A 79 ILE cc_start: 0.8977 (pt) cc_final: 0.8645 (mm) REVERT: A 291 ASP cc_start: 0.7994 (t70) cc_final: 0.7634 (t70) REVERT: A 307 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 73 MET cc_start: 0.8569 (mtp) cc_final: 0.8158 (mtp) REVERT: B 273 ASN cc_start: 0.8857 (p0) cc_final: 0.8470 (p0) REVERT: C 5 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8095 (mmtp) REVERT: C 65 ASP cc_start: 0.7693 (m-30) cc_final: 0.7462 (m-30) REVERT: C 79 ILE cc_start: 0.9052 (pt) cc_final: 0.8655 (mm) REVERT: C 114 ASN cc_start: 0.8412 (m-40) cc_final: 0.8176 (m-40) REVERT: C 220 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7617 (t0) REVERT: C 263 ASN cc_start: 0.8210 (m-40) cc_final: 0.7910 (m-40) REVERT: C 291 ASP cc_start: 0.7999 (t70) cc_final: 0.7632 (t70) REVERT: D 37 ASN cc_start: 0.7751 (p0) cc_final: 0.7453 (p0) REVERT: D 57 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7928 (tp40) REVERT: E 5 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8288 (mmtp) REVERT: E 68 MET cc_start: 0.8211 (tpp) cc_final: 0.8009 (tpt) REVERT: E 79 ILE cc_start: 0.9003 (pt) cc_final: 0.8587 (mm) REVERT: E 143 ASP cc_start: 0.8068 (m-30) cc_final: 0.7821 (m-30) REVERT: F 57 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7826 (tp-100) REVERT: G 46 GLU cc_start: 0.7623 (pt0) cc_final: 0.7395 (pt0) REVERT: G 68 MET cc_start: 0.7818 (tpp) cc_final: 0.7577 (tpt) REVERT: G 294 MET cc_start: 0.7992 (pmm) cc_final: 0.7703 (pmm) REVERT: H 5 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8210 (mmtp) REVERT: H 68 MET cc_start: 0.8213 (tpp) cc_final: 0.8010 (tpt) REVERT: H 79 ILE cc_start: 0.8964 (pt) cc_final: 0.8546 (mm) REVERT: H 99 LYS cc_start: 0.7386 (pttp) cc_final: 0.7160 (pttp) REVERT: H 143 ASP cc_start: 0.7878 (m-30) cc_final: 0.7571 (m-30) REVERT: I 21 ASP cc_start: 0.5804 (m-30) cc_final: 0.5579 (m-30) REVERT: J 5 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7796 (mmmm) REVERT: J 65 ASP cc_start: 0.7719 (m-30) cc_final: 0.7494 (m-30) REVERT: J 78 LYS cc_start: 0.8370 (tptm) cc_final: 0.8169 (tmtm) REVERT: J 79 ILE cc_start: 0.9008 (pt) cc_final: 0.8682 (mm) REVERT: J 114 ASN cc_start: 0.8490 (m-40) cc_final: 0.8235 (m-40) REVERT: J 220 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7541 (t0) REVERT: J 263 ASN cc_start: 0.8338 (m-40) cc_final: 0.8022 (m-40) REVERT: J 291 ASP cc_start: 0.8052 (t70) cc_final: 0.7348 (t0) REVERT: K 73 MET cc_start: 0.8575 (mtp) cc_final: 0.8185 (mtp) REVERT: L 291 ASP cc_start: 0.8043 (t70) cc_final: 0.7767 (t70) outliers start: 86 outliers final: 29 residues processed: 851 average time/residue: 0.4533 time to fit residues: 581.0613 Evaluate side-chains 642 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 611 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 220 ASP Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 220 ASP Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 326 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 193 HIS A 305 ASN B 305 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN E 305 ASN F 305 ASN G 37 ASN G 305 ASN H 193 HIS H 305 ASN I 305 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 305 ASN L 66 ASN L 123 HIS L 305 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 : 0.004 0.038 28860 Z= 0.237 Angle : 0.521 12.673 39048 Z= 0.285 Chirality : 0.048 0.166 4620 Planarity : 0.003 0.024 4992 Dihedral : 5.158 46.200 3975 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.78 % Allowed : 13.58 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3660 helix: 1.45 (0.14), residues: 1512 sheet: -0.16 (0.16), residues: 1008 loop : -0.37 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 162 HIS 0.004 0.001 HIS J 12 PHE 0.010 0.002 PHE B 138 TYR 0.010 0.001 TYR L 146 ARG 0.004 0.000 ARG I 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 695 time to evaluate : 3.317 Fit side-chains REVERT: A 22 ARG cc_start: 0.8702 (mtt90) cc_final: 0.8460 (ttm170) REVERT: A 96 ARG cc_start: 0.6956 (mtp85) cc_final: 0.6730 (mtp85) REVERT: A 99 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7248 (pttt) REVERT: A 307 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7993 (mt-10) REVERT: B 115 MET cc_start: 0.8695 (mtm) cc_final: 0.8438 (mtp) REVERT: C 263 ASN cc_start: 0.8266 (m-40) cc_final: 0.7805 (m-40) REVERT: C 291 ASP cc_start: 0.8252 (t70) cc_final: 0.7919 (t70) REVERT: D 17 GLN cc_start: 0.7995 (tp40) cc_final: 0.7567 (tp40) REVERT: D 286 LYS cc_start: 0.8439 (ptpp) cc_final: 0.8236 (mtmm) REVERT: D 305 ASN cc_start: 0.8441 (m110) cc_final: 0.8130 (m-40) REVERT: E 22 ARG cc_start: 0.8631 (mtt90) cc_final: 0.8282 (mtt90) REVERT: E 66 ASN cc_start: 0.9230 (m-40) cc_final: 0.8782 (m110) REVERT: E 96 ARG cc_start: 0.6543 (mtp85) cc_final: 0.6267 (mtp85) REVERT: E 143 ASP cc_start: 0.8053 (m-30) cc_final: 0.7682 (m-30) REVERT: E 274 THR cc_start: 0.9026 (p) cc_final: 0.8822 (p) REVERT: E 307 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8121 (mt-10) REVERT: F 294 MET cc_start: 0.7798 (pmm) cc_final: 0.7390 (pmm) REVERT: G 38 GLN cc_start: 0.7629 (mt0) cc_final: 0.7415 (mt0) REVERT: G 263 ASN cc_start: 0.8376 (m-40) cc_final: 0.8131 (m110) REVERT: H 96 ARG cc_start: 0.6524 (mtp85) cc_final: 0.6198 (mtp85) REVERT: H 143 ASP cc_start: 0.8047 (m-30) cc_final: 0.7685 (m-30) REVERT: H 220 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7335 (t0) REVERT: H 291 ASP cc_start: 0.8108 (t70) cc_final: 0.7860 (t0) REVERT: I 37 ASN cc_start: 0.7350 (p0) cc_final: 0.7147 (p0) REVERT: I 305 ASN cc_start: 0.8431 (m110) cc_final: 0.8106 (m-40) REVERT: J 5 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8237 (mmtp) REVERT: J 143 ASP cc_start: 0.8002 (m-30) cc_final: 0.7707 (m-30) REVERT: J 217 ILE cc_start: 0.8461 (mt) cc_final: 0.8249 (mt) REVERT: J 263 ASN cc_start: 0.8266 (m-40) cc_final: 0.7815 (m-40) REVERT: K 115 MET cc_start: 0.8667 (mtm) cc_final: 0.8449 (mtp) outliers start: 119 outliers final: 61 residues processed: 772 average time/residue: 0.4079 time to fit residues: 488.5799 Evaluate side-chains 708 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 645 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 3 ASN Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 220 ASP Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain L residue 12 HIS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 327 optimal weight: 3.9990 chunk 353 optimal weight: 8.9990 chunk 291 optimal weight: 3.9990 chunk 324 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 262 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN B 17 GLN C 66 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN E 158 ASN ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN G 37 ASN H 158 ASN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 123 HIS L 304 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 28860 Z= 0.302 Angle : 0.523 10.076 39048 Z= 0.284 Chirality : 0.048 0.172 4620 Planarity : 0.003 0.024 4992 Dihedral : 4.841 47.591 3948 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.15 % Allowed : 16.19 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3660 helix: 1.68 (0.14), residues: 1512 sheet: -0.37 (0.16), residues: 1020 loop : -0.99 (0.16), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.005 0.001 HIS I 12 PHE 0.015 0.001 PHE F 35 TYR 0.012 0.002 TYR E 146 ARG 0.004 0.000 ARG E 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 703 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8762 (mmtp) cc_final: 0.8347 (mmtp) REVERT: A 96 ARG cc_start: 0.6780 (mtp85) cc_final: 0.6234 (mtp85) REVERT: A 291 ASP cc_start: 0.8616 (t70) cc_final: 0.8411 (t70) REVERT: A 292 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8893 (pp) REVERT: A 307 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7900 (mt-10) REVERT: B 96 ARG cc_start: 0.6694 (mtp85) cc_final: 0.6346 (mtp85) REVERT: B 115 MET cc_start: 0.8723 (mtm) cc_final: 0.8466 (mtp) REVERT: C 39 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7575 (mt-10) REVERT: C 263 ASN cc_start: 0.8223 (m-40) cc_final: 0.7986 (m-40) REVERT: D 17 GLN cc_start: 0.8253 (tp40) cc_final: 0.7755 (tp40) REVERT: E 13 GLN cc_start: 0.7657 (tp40) cc_final: 0.7422 (tp40) REVERT: E 96 ARG cc_start: 0.6572 (mtp85) cc_final: 0.6181 (mtp85) REVERT: E 143 ASP cc_start: 0.8053 (m-30) cc_final: 0.7676 (m-30) REVERT: E 307 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8173 (mt-10) REVERT: F 38 GLN cc_start: 0.7736 (mt0) cc_final: 0.7526 (mm-40) REVERT: G 17 GLN cc_start: 0.7610 (tp40) cc_final: 0.7387 (tp40) REVERT: G 263 ASN cc_start: 0.8385 (m-40) cc_final: 0.8174 (m-40) REVERT: H 96 ARG cc_start: 0.6500 (mtp85) cc_final: 0.6126 (mtp85) REVERT: H 143 ASP cc_start: 0.8012 (m-30) cc_final: 0.7645 (m-30) REVERT: I 144 ASN cc_start: 0.8625 (t0) cc_final: 0.8419 (t0) REVERT: J 39 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7588 (mt-10) REVERT: J 78 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8409 (tttm) REVERT: J 143 ASP cc_start: 0.8077 (m-30) cc_final: 0.7820 (m-30) REVERT: J 263 ASN cc_start: 0.8248 (m-40) cc_final: 0.7755 (m-40) REVERT: J 291 ASP cc_start: 0.8385 (t70) cc_final: 0.7966 (t70) REVERT: L 5 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8461 (mmtp) REVERT: L 34 LYS cc_start: 0.5714 (mttt) cc_final: 0.5419 (mttt) REVERT: L 78 LYS cc_start: 0.8627 (tppt) cc_final: 0.8220 (tmtm) REVERT: L 291 ASP cc_start: 0.8383 (t70) cc_final: 0.8179 (t0) REVERT: L 292 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8824 (pp) outliers start: 99 outliers final: 61 residues processed: 768 average time/residue: 0.4441 time to fit residues: 532.3248 Evaluate side-chains 731 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 668 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 220 ASP Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 292 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 4.9990 chunk 246 optimal weight: 0.6980 chunk 169 optimal weight: 0.1980 chunk 36 optimal weight: 0.5980 chunk 156 optimal weight: 0.6980 chunk 219 optimal weight: 0.7980 chunk 328 optimal weight: 0.8980 chunk 347 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 311 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN B 158 ASN C 13 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN J 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28860 Z= 0.157 Angle : 0.448 9.874 39048 Z= 0.244 Chirality : 0.046 0.164 4620 Planarity : 0.003 0.023 4992 Dihedral : 4.340 46.272 3940 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.67 % Allowed : 17.53 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3660 helix: 2.01 (0.14), residues: 1512 sheet: -0.43 (0.16), residues: 996 loop : -0.41 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 162 HIS 0.004 0.001 HIS J 12 PHE 0.008 0.001 PHE D 266 TYR 0.008 0.001 TYR H 146 ARG 0.005 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 698 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8706 (mmtp) cc_final: 0.8321 (mmtp) REVERT: A 34 LYS cc_start: 0.5823 (mttt) cc_final: 0.5510 (mttt) REVERT: A 292 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8826 (pp) REVERT: A 307 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7851 (mt-10) REVERT: B 115 MET cc_start: 0.8669 (mtm) cc_final: 0.8415 (mtp) REVERT: C 39 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7527 (mt-10) REVERT: C 263 ASN cc_start: 0.8191 (m-40) cc_final: 0.7926 (m-40) REVERT: C 291 ASP cc_start: 0.8423 (t70) cc_final: 0.8153 (t70) REVERT: C 292 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8764 (pp) REVERT: D 17 GLN cc_start: 0.8135 (tp40) cc_final: 0.7906 (tp40) REVERT: E 143 ASP cc_start: 0.7951 (m-30) cc_final: 0.7659 (m-30) REVERT: E 291 ASP cc_start: 0.8104 (t70) cc_final: 0.7895 (t0) REVERT: E 307 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8107 (mt-10) REVERT: F 17 GLN cc_start: 0.7878 (tp40) cc_final: 0.7436 (tp-100) REVERT: F 21 ASP cc_start: 0.6183 (m-30) cc_final: 0.5812 (m-30) REVERT: F 114 ASN cc_start: 0.9066 (m-40) cc_final: 0.8790 (m-40) REVERT: F 305 ASN cc_start: 0.8419 (m110) cc_final: 0.8197 (m-40) REVERT: G 17 GLN cc_start: 0.7628 (tp40) cc_final: 0.7167 (tp40) REVERT: G 21 ASP cc_start: 0.6050 (m-30) cc_final: 0.5693 (m-30) REVERT: G 114 ASN cc_start: 0.9039 (m-40) cc_final: 0.8721 (m-40) REVERT: G 305 ASN cc_start: 0.8573 (m110) cc_final: 0.8330 (m-40) REVERT: H 13 GLN cc_start: 0.7709 (tp40) cc_final: 0.7471 (tp40) REVERT: H 143 ASP cc_start: 0.7970 (m-30) cc_final: 0.7745 (m-30) REVERT: J 39 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7604 (mt-10) REVERT: J 263 ASN cc_start: 0.8256 (m-40) cc_final: 0.7769 (m-40) REVERT: J 292 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8722 (pp) REVERT: L 5 LYS cc_start: 0.8737 (mmtp) cc_final: 0.8468 (mmtm) REVERT: L 78 LYS cc_start: 0.8540 (tppt) cc_final: 0.8078 (tmtm) REVERT: L 286 LYS cc_start: 0.8003 (ptpt) cc_final: 0.7751 (mtmt) REVERT: L 292 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8818 (pp) REVERT: L 307 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7860 (mt-10) outliers start: 84 outliers final: 50 residues processed: 744 average time/residue: 0.4288 time to fit residues: 490.1429 Evaluate side-chains 699 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 645 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 292 ILE Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 220 ASP Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 HIS E 158 ASN ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN H 158 ASN H 305 ASN I 123 HIS J 13 GLN J 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** L 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 28860 Z= 0.507 Angle : 0.588 9.330 39048 Z= 0.319 Chirality : 0.051 0.180 4620 Planarity : 0.004 0.029 4992 Dihedral : 4.810 47.792 3940 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.28 % Allowed : 17.21 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3660 helix: 1.67 (0.14), residues: 1512 sheet: -0.60 (0.16), residues: 972 loop : -0.79 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 162 HIS 0.011 0.002 HIS L 12 PHE 0.022 0.002 PHE F 35 TYR 0.012 0.002 TYR E 146 ARG 0.007 0.001 ARG L 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 697 time to evaluate : 3.567 Fit side-chains REVERT: A 292 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8838 (pp) REVERT: A 307 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7913 (mt-10) REVERT: B 115 MET cc_start: 0.8766 (mtm) cc_final: 0.8551 (mtm) REVERT: C 39 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7629 (mt-10) REVERT: C 263 ASN cc_start: 0.8185 (m-40) cc_final: 0.7934 (m-40) REVERT: C 292 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8767 (pp) REVERT: D 17 GLN cc_start: 0.8378 (tp40) cc_final: 0.8084 (tp40) REVERT: D 139 ASP cc_start: 0.7310 (m-30) cc_final: 0.6994 (m-30) REVERT: E 143 ASP cc_start: 0.8179 (m-30) cc_final: 0.7905 (m-30) REVERT: E 307 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8203 (mt-10) REVERT: F 21 ASP cc_start: 0.6433 (m-30) cc_final: 0.6135 (m-30) REVERT: G 17 GLN cc_start: 0.7685 (tp40) cc_final: 0.7278 (tp40) REVERT: G 21 ASP cc_start: 0.6216 (m-30) cc_final: 0.5992 (m-30) REVERT: H 65 ASP cc_start: 0.7679 (m-30) cc_final: 0.7436 (m-30) REVERT: H 143 ASP cc_start: 0.8058 (m-30) cc_final: 0.7788 (m-30) REVERT: I 139 ASP cc_start: 0.7243 (m-30) cc_final: 0.7007 (m-30) REVERT: J 5 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8303 (mmmt) REVERT: J 39 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7651 (mt-10) REVERT: J 143 ASP cc_start: 0.8086 (m-30) cc_final: 0.7844 (m-30) REVERT: J 263 ASN cc_start: 0.8241 (m-40) cc_final: 0.7985 (m-40) REVERT: K 307 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6399 (mt-10) REVERT: L 162 TRP cc_start: 0.8239 (p-90) cc_final: 0.7843 (p-90) REVERT: L 307 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7873 (mt-10) outliers start: 103 outliers final: 81 residues processed: 758 average time/residue: 0.4129 time to fit residues: 492.6141 Evaluate side-chains 764 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 681 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 220 ASP Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 285 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 6.9990 chunk 313 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 204 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 348 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN C 13 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS G 193 HIS H 17 GLN I 37 ASN I 193 HIS J 13 GLN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28860 Z= 0.188 Angle : 0.460 9.164 39048 Z= 0.252 Chirality : 0.046 0.173 4620 Planarity : 0.003 0.032 4992 Dihedral : 4.504 46.472 3940 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.09 % Allowed : 18.45 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3660 helix: 2.01 (0.14), residues: 1512 sheet: -0.68 (0.16), residues: 1044 loop : -0.88 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 162 HIS 0.009 0.001 HIS L 12 PHE 0.008 0.001 PHE J 7 TYR 0.010 0.001 TYR K 311 ARG 0.006 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 680 time to evaluate : 4.092 Fit side-chains REVERT: A 96 ARG cc_start: 0.7024 (mtp85) cc_final: 0.6729 (mtp85) REVERT: A 292 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8821 (pp) REVERT: A 307 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7888 (mt-10) REVERT: B 114 ASN cc_start: 0.9245 (m-40) cc_final: 0.9038 (m-40) REVERT: B 115 MET cc_start: 0.8699 (mtm) cc_final: 0.8467 (mtp) REVERT: C 13 GLN cc_start: 0.7784 (tp-100) cc_final: 0.7458 (mm110) REVERT: C 39 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7609 (mt-10) REVERT: C 263 ASN cc_start: 0.8135 (m-40) cc_final: 0.7861 (m-40) REVERT: C 291 ASP cc_start: 0.8547 (t70) cc_final: 0.8249 (t70) REVERT: C 294 MET cc_start: 0.8336 (pmm) cc_final: 0.7853 (pmm) REVERT: D 3 ASN cc_start: 0.7698 (m-40) cc_final: 0.7475 (m-40) REVERT: D 17 GLN cc_start: 0.8297 (tp40) cc_final: 0.8046 (tp40) REVERT: D 139 ASP cc_start: 0.7220 (m-30) cc_final: 0.6983 (m-30) REVERT: E 143 ASP cc_start: 0.8072 (m-30) cc_final: 0.7770 (m-30) REVERT: E 307 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8108 (mt-10) REVERT: F 17 GLN cc_start: 0.7932 (tp40) cc_final: 0.7587 (tp40) REVERT: F 21 ASP cc_start: 0.6426 (m-30) cc_final: 0.6165 (m-30) REVERT: F 305 ASN cc_start: 0.8481 (m110) cc_final: 0.8241 (m-40) REVERT: H 65 ASP cc_start: 0.7574 (m-30) cc_final: 0.7365 (m-30) REVERT: H 96 ARG cc_start: 0.6998 (mtp85) cc_final: 0.6692 (mtp85) REVERT: H 143 ASP cc_start: 0.8036 (m-30) cc_final: 0.7705 (m-30) REVERT: H 286 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7867 (mtmt) REVERT: I 51 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7032 (mm-30) REVERT: I 139 ASP cc_start: 0.7169 (m-30) cc_final: 0.6938 (m-30) REVERT: I 286 LYS cc_start: 0.8447 (ptpp) cc_final: 0.8247 (mtmm) REVERT: J 5 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8150 (mmmm) REVERT: J 39 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7592 (mt-10) REVERT: J 143 ASP cc_start: 0.8051 (m-30) cc_final: 0.7829 (m-30) REVERT: J 263 ASN cc_start: 0.8201 (m-40) cc_final: 0.7962 (m-40) REVERT: J 292 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8778 (pp) REVERT: K 114 ASN cc_start: 0.9254 (m-40) cc_final: 0.9041 (m-40) REVERT: L 307 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7850 (mt-10) outliers start: 97 outliers final: 77 residues processed: 739 average time/residue: 0.4054 time to fit residues: 469.0021 Evaluate side-chains 738 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 658 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 292 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 220 ASP Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 208 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 293 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 346 optimal weight: 0.4980 chunk 217 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN C 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN ** I 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28860 Z= 0.181 Angle : 0.451 8.998 39048 Z= 0.245 Chirality : 0.046 0.173 4620 Planarity : 0.003 0.026 4992 Dihedral : 4.314 47.279 3938 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.99 % Allowed : 18.83 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3660 helix: 2.16 (0.14), residues: 1512 sheet: -0.63 (0.16), residues: 1044 loop : -0.82 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 162 HIS 0.013 0.001 HIS L 12 PHE 0.015 0.001 PHE F 35 TYR 0.009 0.001 TYR K 311 ARG 0.004 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 694 time to evaluate : 3.156 Fit side-chains revert: symmetry clash REVERT: A 307 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7856 (mt-10) REVERT: B 114 ASN cc_start: 0.9249 (m-40) cc_final: 0.9045 (m-40) REVERT: B 115 MET cc_start: 0.8724 (mtm) cc_final: 0.8492 (mtp) REVERT: C 39 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7611 (mt-10) REVERT: C 263 ASN cc_start: 0.8134 (m-40) cc_final: 0.7859 (m-40) REVERT: C 291 ASP cc_start: 0.8553 (t70) cc_final: 0.8170 (t70) REVERT: C 294 MET cc_start: 0.8310 (pmm) cc_final: 0.7782 (pmm) REVERT: D 3 ASN cc_start: 0.7734 (m-40) cc_final: 0.7509 (m-40) REVERT: D 17 GLN cc_start: 0.8291 (tp40) cc_final: 0.8057 (tp40) REVERT: D 139 ASP cc_start: 0.7177 (m-30) cc_final: 0.6944 (m-30) REVERT: D 305 ASN cc_start: 0.8432 (m110) cc_final: 0.8065 (m-40) REVERT: E 143 ASP cc_start: 0.7948 (m-30) cc_final: 0.7668 (m-30) REVERT: E 307 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8116 (mt-10) REVERT: F 17 GLN cc_start: 0.7941 (tp40) cc_final: 0.7544 (tp40) REVERT: F 21 ASP cc_start: 0.6431 (m-30) cc_final: 0.6130 (m-30) REVERT: G 158 ASN cc_start: 0.7596 (m-40) cc_final: 0.7314 (m-40) REVERT: H 65 ASP cc_start: 0.7568 (m-30) cc_final: 0.7339 (m-30) REVERT: H 143 ASP cc_start: 0.7937 (m-30) cc_final: 0.7657 (m-30) REVERT: H 286 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7891 (mtmt) REVERT: I 51 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6993 (mm-30) REVERT: I 139 ASP cc_start: 0.7154 (m-30) cc_final: 0.6930 (m-30) REVERT: I 305 ASN cc_start: 0.8426 (m110) cc_final: 0.8049 (m-40) REVERT: J 5 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8154 (mmmm) REVERT: J 39 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7619 (mt-10) REVERT: J 143 ASP cc_start: 0.8028 (m-30) cc_final: 0.7792 (m-30) REVERT: J 263 ASN cc_start: 0.8133 (m-40) cc_final: 0.7881 (m-40) REVERT: K 114 ASN cc_start: 0.9253 (m-40) cc_final: 0.9045 (m-40) REVERT: K 294 MET cc_start: 0.7582 (pmm) cc_final: 0.7286 (pmm) REVERT: L 307 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7835 (mt-10) outliers start: 94 outliers final: 82 residues processed: 751 average time/residue: 0.3972 time to fit residues: 469.9872 Evaluate side-chains 764 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 681 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 128 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 220 optimal weight: 0.0060 chunk 236 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 272 optimal weight: 0.0040 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 158 ASN B 263 ASN C 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN E 12 HIS ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 263 ASN L 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 28860 Z= 0.152 Angle : 0.442 8.917 39048 Z= 0.240 Chirality : 0.046 0.167 4620 Planarity : 0.003 0.036 4992 Dihedral : 4.155 47.267 3936 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.05 % Allowed : 18.73 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3660 helix: 2.29 (0.14), residues: 1512 sheet: -0.57 (0.16), residues: 1068 loop : -0.71 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 162 HIS 0.013 0.001 HIS L 12 PHE 0.008 0.001 PHE H 266 TYR 0.009 0.001 TYR K 311 ARG 0.007 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 687 time to evaluate : 4.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7847 (mt-10) REVERT: B 115 MET cc_start: 0.8695 (mtm) cc_final: 0.8467 (mtp) REVERT: B 294 MET cc_start: 0.7648 (pmm) cc_final: 0.7443 (pmm) REVERT: C 13 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7604 (mm110) REVERT: C 39 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7570 (mt-10) REVERT: C 263 ASN cc_start: 0.8080 (m-40) cc_final: 0.7804 (m-40) REVERT: C 291 ASP cc_start: 0.8473 (t70) cc_final: 0.8207 (t70) REVERT: C 294 MET cc_start: 0.8275 (pmm) cc_final: 0.7712 (pmm) REVERT: D 3 ASN cc_start: 0.7743 (m-40) cc_final: 0.7513 (m-40) REVERT: D 17 GLN cc_start: 0.8238 (tp40) cc_final: 0.7941 (tp40) REVERT: D 139 ASP cc_start: 0.7159 (m-30) cc_final: 0.6928 (m-30) REVERT: E 143 ASP cc_start: 0.7987 (m-30) cc_final: 0.7742 (m-30) REVERT: E 291 ASP cc_start: 0.8087 (t70) cc_final: 0.7840 (t0) REVERT: F 17 GLN cc_start: 0.7924 (tp40) cc_final: 0.7527 (tp40) REVERT: F 21 ASP cc_start: 0.6426 (m-30) cc_final: 0.6113 (m-30) REVERT: F 294 MET cc_start: 0.7627 (pmm) cc_final: 0.7161 (pmm) REVERT: G 158 ASN cc_start: 0.7621 (m-40) cc_final: 0.7345 (m-40) REVERT: H 139 ASP cc_start: 0.6470 (m-30) cc_final: 0.6212 (m-30) REVERT: H 143 ASP cc_start: 0.7931 (m-30) cc_final: 0.7681 (m-30) REVERT: H 286 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7875 (mtmt) REVERT: I 3 ASN cc_start: 0.7519 (m110) cc_final: 0.7234 (m-40) REVERT: I 51 GLU cc_start: 0.7265 (mm-30) cc_final: 0.7059 (mm-30) REVERT: I 139 ASP cc_start: 0.7131 (m-30) cc_final: 0.6917 (m-30) REVERT: J 39 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7587 (mt-10) REVERT: J 143 ASP cc_start: 0.7951 (m-30) cc_final: 0.7731 (m-30) REVERT: J 263 ASN cc_start: 0.7989 (m-40) cc_final: 0.7724 (m-40) REVERT: J 305 ASN cc_start: 0.8682 (m110) cc_final: 0.8208 (m110) REVERT: L 307 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7827 (mt-10) outliers start: 96 outliers final: 74 residues processed: 743 average time/residue: 0.3938 time to fit residues: 463.1072 Evaluate side-chains 747 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 672 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 208 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 3.9990 chunk 332 optimal weight: 0.0970 chunk 303 optimal weight: 1.9990 chunk 323 optimal weight: 9.9990 chunk 194 optimal weight: 0.0870 chunk 140 optimal weight: 8.9990 chunk 253 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 292 optimal weight: 2.9990 chunk 305 optimal weight: 0.7980 chunk 322 optimal weight: 2.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN C 13 GLN C 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN E 13 GLN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN H 13 GLN H 158 ASN I 37 ASN I 158 ASN I 263 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 263 ASN L 13 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 28860 Z= 0.151 Angle : 0.442 8.885 39048 Z= 0.241 Chirality : 0.046 0.165 4620 Planarity : 0.003 0.029 4992 Dihedral : 4.117 48.296 3936 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.80 % Allowed : 19.15 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 3660 helix: 2.33 (0.14), residues: 1512 sheet: -0.51 (0.16), residues: 1068 loop : -0.66 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 162 HIS 0.012 0.001 HIS L 12 PHE 0.015 0.001 PHE F 35 TYR 0.009 0.001 TYR K 311 ARG 0.007 0.000 ARG L 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 677 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7836 (mt-10) REVERT: B 115 MET cc_start: 0.8699 (mtm) cc_final: 0.8478 (mtp) REVERT: B 294 MET cc_start: 0.7616 (pmm) cc_final: 0.7400 (pmm) REVERT: C 13 GLN cc_start: 0.7909 (mm110) cc_final: 0.7496 (tp40) REVERT: C 39 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7541 (mt-10) REVERT: C 263 ASN cc_start: 0.7979 (m-40) cc_final: 0.7709 (m-40) REVERT: C 291 ASP cc_start: 0.8452 (t70) cc_final: 0.8188 (t70) REVERT: C 294 MET cc_start: 0.8279 (pmm) cc_final: 0.7709 (pmm) REVERT: C 305 ASN cc_start: 0.8653 (m110) cc_final: 0.8187 (m110) REVERT: D 17 GLN cc_start: 0.8236 (tp40) cc_final: 0.7954 (tp40) REVERT: D 139 ASP cc_start: 0.7182 (m-30) cc_final: 0.6904 (m-30) REVERT: D 263 ASN cc_start: 0.8283 (m-40) cc_final: 0.8062 (m-40) REVERT: E 66 ASN cc_start: 0.9223 (m-40) cc_final: 0.8825 (m-40) REVERT: E 143 ASP cc_start: 0.8010 (m-30) cc_final: 0.7797 (m-30) REVERT: E 237 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6683 (mt) REVERT: E 291 ASP cc_start: 0.8083 (t70) cc_final: 0.7815 (t0) REVERT: F 17 GLN cc_start: 0.7887 (tp40) cc_final: 0.7197 (tp40) REVERT: F 21 ASP cc_start: 0.6397 (m-30) cc_final: 0.5895 (m-30) REVERT: F 294 MET cc_start: 0.7594 (pmm) cc_final: 0.7182 (pmm) REVERT: G 158 ASN cc_start: 0.7669 (m-40) cc_final: 0.7395 (m-40) REVERT: G 286 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8130 (ptpt) REVERT: G 305 ASN cc_start: 0.8522 (m110) cc_final: 0.8272 (m-40) REVERT: H 139 ASP cc_start: 0.6461 (m-30) cc_final: 0.6224 (m-30) REVERT: H 143 ASP cc_start: 0.7982 (m-30) cc_final: 0.7751 (m-30) REVERT: I 51 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6889 (mm-30) REVERT: I 139 ASP cc_start: 0.7160 (m-30) cc_final: 0.6939 (m-30) REVERT: J 39 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7565 (mt-10) REVERT: J 143 ASP cc_start: 0.7942 (m-30) cc_final: 0.7710 (m-30) REVERT: J 263 ASN cc_start: 0.7972 (m-40) cc_final: 0.7692 (m-40) REVERT: J 305 ASN cc_start: 0.8677 (m110) cc_final: 0.8236 (m110) REVERT: K 39 GLU cc_start: 0.8123 (tt0) cc_final: 0.7914 (mt-10) REVERT: L 307 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7811 (mt-10) outliers start: 88 outliers final: 74 residues processed: 736 average time/residue: 0.4049 time to fit residues: 472.8835 Evaluate side-chains 733 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 657 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 1.9990 chunk 341 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 358 optimal weight: 0.7980 chunk 330 optimal weight: 0.7980 chunk 285 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 220 optimal weight: 0.0070 chunk 175 optimal weight: 3.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 GLN A 57 GLN B 263 ASN C 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 263 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN K 263 ASN L 13 GLN L 57 GLN L 263 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 28860 Z= 0.178 Angle : 0.455 8.797 39048 Z= 0.248 Chirality : 0.046 0.168 4620 Planarity : 0.003 0.036 4992 Dihedral : 4.146 48.732 3936 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.51 % Allowed : 19.72 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.15), residues: 3660 helix: 2.32 (0.14), residues: 1512 sheet: -0.44 (0.16), residues: 1044 loop : -0.73 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 162 HIS 0.012 0.001 HIS L 12 PHE 0.018 0.001 PHE E 35 TYR 0.017 0.001 TYR H 54 ARG 0.007 0.000 ARG F 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 673 time to evaluate : 3.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7837 (mt-10) REVERT: B 115 MET cc_start: 0.8710 (mtm) cc_final: 0.8478 (mtp) REVERT: C 13 GLN cc_start: 0.7963 (mm110) cc_final: 0.7551 (tp40) REVERT: C 39 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7584 (mt-10) REVERT: C 263 ASN cc_start: 0.7949 (m-40) cc_final: 0.7662 (m-40) REVERT: C 294 MET cc_start: 0.8280 (pmm) cc_final: 0.7734 (pmm) REVERT: D 17 GLN cc_start: 0.8252 (tp40) cc_final: 0.7959 (tp40) REVERT: D 139 ASP cc_start: 0.7193 (m-30) cc_final: 0.6917 (m-30) REVERT: D 263 ASN cc_start: 0.8289 (m-40) cc_final: 0.8054 (m-40) REVERT: E 143 ASP cc_start: 0.8038 (m-30) cc_final: 0.7810 (m-30) REVERT: E 237 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6649 (mt) REVERT: E 286 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7894 (mtmt) REVERT: E 291 ASP cc_start: 0.8076 (t70) cc_final: 0.7828 (t0) REVERT: F 17 GLN cc_start: 0.7883 (tp40) cc_final: 0.7317 (tp40) REVERT: F 21 ASP cc_start: 0.6195 (m-30) cc_final: 0.5775 (m-30) REVERT: G 158 ASN cc_start: 0.7662 (m-40) cc_final: 0.7369 (m-40) REVERT: G 305 ASN cc_start: 0.8575 (m110) cc_final: 0.8251 (m-40) REVERT: H 139 ASP cc_start: 0.6487 (m-30) cc_final: 0.6206 (m-30) REVERT: H 143 ASP cc_start: 0.8032 (m-30) cc_final: 0.7807 (m-30) REVERT: I 51 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6930 (mm-30) REVERT: I 139 ASP cc_start: 0.7201 (m-30) cc_final: 0.6943 (m-30) REVERT: I 305 ASN cc_start: 0.8438 (m110) cc_final: 0.8046 (m-40) REVERT: J 39 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7597 (mt-10) REVERT: J 143 ASP cc_start: 0.7872 (m-30) cc_final: 0.7596 (m-30) REVERT: J 263 ASN cc_start: 0.7945 (m-40) cc_final: 0.7660 (m-40) REVERT: J 305 ASN cc_start: 0.8686 (m110) cc_final: 0.8198 (m110) REVERT: K 307 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6314 (mt-10) REVERT: L 12 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.7505 (t70) REVERT: L 307 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7839 (mt-10) outliers start: 79 outliers final: 72 residues processed: 727 average time/residue: 0.3854 time to fit residues: 445.8554 Evaluate side-chains 734 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 659 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain L residue 12 HIS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 263 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 286 optimal weight: 0.1980 chunk 119 optimal weight: 0.9980 chunk 293 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 GLN A 57 GLN B 263 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN H 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN K 263 ASN L 13 GLN L 57 GLN L 263 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.181616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.138063 restraints weight = 29538.527| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.59 r_work: 0.3163 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 648 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 28860 Z= 0.169 Angle : 0.450 8.717 39048 Z= 0.245 Chirality : 0.046 0.166 4620 Planarity : 0.003 0.031 4992 Dihedral : 4.127 49.226 3936 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.61 % Allowed : 19.50 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3660 helix: 2.33 (0.14), residues: 1512 sheet: -0.45 (0.16), residues: 1068 loop : -0.62 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 162 HIS 0.012 0.001 HIS L 12 PHE 0.016 0.001 PHE F 35 TYR 0.009 0.001 TYR E 54 ARG 0.007 0.000 ARG F 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8402.91 seconds wall clock time: 150 minutes 39.91 seconds (9039.91 seconds total)