Starting phenix.real_space_refine on Fri Feb 16 04:42:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbl_27289/02_2024/8dbl_27289_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbl_27289/02_2024/8dbl_27289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbl_27289/02_2024/8dbl_27289.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbl_27289/02_2024/8dbl_27289.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbl_27289/02_2024/8dbl_27289_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbl_27289/02_2024/8dbl_27289_updated.pdb" } resolution = 2.4 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= 0.334 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 12 5.21 5 S 102 5.16 5 C 8922 2.51 5 N 2490 2.21 5 O 2808 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 51": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" 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" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14358 Number of models: 1 Model: "" Number of chains: 18 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: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 318 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 306 not shown) Time building chain proxies: 8.21, per 1000 atoms: 0.57 Number of scatterers: 14358 At special positions: 0 Unit cell: (122.728, 130.134, 77.234, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 24 15.00 Mg 12 11.99 O 2808 8.00 N 2490 7.00 C 8922 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: 6.20 Conformation dependent library (CDL) restraints added in 2.7 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 18 sheets defined 37.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 172 through 185 removed outlier: 5.017A pdb=" N LYS A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 177 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 255 through 263 removed outlier: 4.420A pdb=" N ILE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.667A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 172 through 185 removed outlier: 5.017A pdb=" N LYS B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 177 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 255 through 263 removed outlier: 4.420A pdb=" N ILE B 258 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.666A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 172 through 185 removed outlier: 5.017A pdb=" N LYS C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 177 " --> pdb=" O GLY C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 255 through 263 removed outlier: 4.419A pdb=" N ILE C 258 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.666A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 310 through 314 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 148 through 158 Processing helix chain 'D' and resid 172 through 185 removed outlier: 5.017A pdb=" N LYS D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D 177 " --> pdb=" O GLY D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 255 through 263 removed outlier: 4.420A pdb=" N ILE D 258 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.667A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 148 through 158 Processing helix chain 'E' and resid 172 through 185 removed outlier: 5.016A pdb=" N LYS E 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG E 177 " --> pdb=" O GLY E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 255 through 263 removed outlier: 4.421A pdb=" N ILE E 258 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.666A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 305 Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'F' and resid 13 through 22 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 172 through 185 removed outlier: 5.017A pdb=" N LYS F 176 " --> pdb=" O GLY F 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG F 177 " --> pdb=" O GLY F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 255 through 263 removed outlier: 4.421A pdb=" N ILE F 258 " --> pdb=" O GLY F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.666A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 310 through 314 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.287A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS A 123 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE A 89 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 125 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR A 126 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASP A 143 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 287 through 290 removed outlier: 6.306A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 216 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 218 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 166 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL A 219 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 168 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER A 169 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA A 190 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.287A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG B 84 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR B 126 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASP B 143 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= F, first strand: chain 'B' and resid 287 through 290 removed outlier: 6.306A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 216 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 218 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B 166 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL B 219 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 168 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N SER B 169 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA B 190 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.287A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG C 84 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS C 123 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE C 89 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE C 125 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASP C 143 " --> pdb=" O THR C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= I, first strand: chain 'C' and resid 287 through 290 removed outlier: 6.306A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA C 216 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE C 247 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 218 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 166 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL C 219 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 168 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP C 188 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER C 169 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA C 190 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.287A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS D 123 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE D 89 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE D 125 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASP D 143 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= L, first strand: chain 'D' and resid 287 through 290 removed outlier: 6.306A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA D 216 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE D 247 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU D 218 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 166 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL D 219 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL D 168 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP D 188 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER D 169 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA D 190 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.287A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG E 84 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS E 123 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE E 89 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE E 125 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR E 126 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASP E 143 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'E' and resid 287 through 290 removed outlier: 6.306A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA E 216 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE E 247 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU E 218 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR E 166 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL E 219 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL E 168 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER E 169 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA E 190 " --> pdb=" O SER E 169 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.287A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG F 84 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS F 123 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASP F 143 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= R, first strand: chain 'F' and resid 287 through 290 removed outlier: 6.306A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA F 216 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE F 247 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU F 218 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR F 166 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL F 219 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL F 168 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER F 169 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA F 190 " --> pdb=" O SER F 169 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1152 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: 4.13 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4775 1.34 - 1.46: 2118 1.46 - 1.57: 7471 1.57 - 1.69: 24 1.69 - 1.81: 150 Bond restraints: 14538 Sorted by residual: bond pdb=" C1 PRP B 401 " pdb=" O4 PRP B 401 " ideal model delta sigma weight residual 1.656 1.420 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1 PRP A 401 " pdb=" O4 PRP A 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1 PRP C 401 " pdb=" O4 PRP C 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1 PRP F 401 " pdb=" O4 PRP F 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1 PRP D 401 " pdb=" O4 PRP D 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 ... (remaining 14533 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.18: 373 106.18 - 113.15: 8395 113.15 - 120.12: 4918 120.12 - 127.10: 5886 127.10 - 134.07: 126 Bond angle restraints: 19698 Sorted by residual: angle pdb=" C THR E 272 " pdb=" CA THR E 272 " pdb=" CB THR E 272 " ideal model delta sigma weight residual 109.51 117.38 -7.87 1.71e+00 3.42e-01 2.12e+01 angle pdb=" C THR C 272 " pdb=" CA THR C 272 " pdb=" CB THR C 272 " ideal model delta sigma weight residual 109.51 117.37 -7.86 1.71e+00 3.42e-01 2.11e+01 angle pdb=" C THR A 272 " pdb=" CA THR A 272 " pdb=" CB THR A 272 " ideal model delta sigma weight residual 109.51 117.37 -7.86 1.71e+00 3.42e-01 2.11e+01 angle pdb=" C THR B 272 " pdb=" CA THR B 272 " pdb=" CB THR B 272 " ideal model delta sigma weight residual 109.51 117.36 -7.85 1.71e+00 3.42e-01 2.11e+01 angle pdb=" C THR F 272 " pdb=" CA THR F 272 " pdb=" CB THR F 272 " ideal model delta sigma weight residual 109.51 117.34 -7.83 1.71e+00 3.42e-01 2.10e+01 ... (remaining 19693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 8013 17.71 - 35.41: 660 35.41 - 53.12: 207 53.12 - 70.82: 60 70.82 - 88.53: 36 Dihedral angle restraints: 8976 sinusoidal: 3600 harmonic: 5376 Sorted by residual: dihedral pdb=" CA GLU C 62 " pdb=" C GLU C 62 " pdb=" N ILE C 63 " pdb=" CA ILE C 63 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU E 62 " pdb=" C GLU E 62 " pdb=" N ILE E 63 " pdb=" CA ILE E 63 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU B 62 " pdb=" C GLU B 62 " pdb=" N ILE B 63 " pdb=" CA ILE B 63 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1333 0.041 - 0.082: 659 0.082 - 0.124: 267 0.124 - 0.165: 45 0.165 - 0.206: 30 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CA THR D 272 " pdb=" N THR D 272 " pdb=" C THR D 272 " pdb=" CB THR D 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR E 272 " pdb=" N THR E 272 " pdb=" C THR E 272 " pdb=" CB THR E 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR F 272 " pdb=" N THR F 272 " pdb=" C THR F 272 " pdb=" CB THR F 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2331 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 221 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" CG ASP E 221 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP E 221 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP E 221 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 221 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" CG ASP C 221 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP C 221 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP C 221 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 221 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" CG ASP F 221 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP F 221 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 221 " -0.015 2.00e-02 2.50e+03 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 108 2.49 - 3.09: 10488 3.09 - 3.69: 22519 3.69 - 4.30: 34471 4.30 - 4.90: 55932 Nonbonded interactions: 123518 Sorted by model distance: nonbonded pdb=" O3B PRP E 401 " pdb="MG MG E 403 " model vdw 1.885 2.170 nonbonded pdb=" O3B PRP C 401 " pdb="MG MG C 403 " model vdw 1.886 2.170 nonbonded pdb=" O1B PRP F 401 " pdb="MG MG F 403 " model vdw 1.886 2.170 nonbonded pdb=" O3B PRP A 401 " pdb="MG MG A 403 " model vdw 1.886 2.170 nonbonded pdb=" O1B PRP D 401 " pdb="MG MG D 403 " model vdw 1.886 2.170 ... (remaining 123513 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' } 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=0.91 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: 1.100 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: 0.010 Extract box with map and model: 4.260 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 41.450 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.011 0.236 14538 Z= 0.727 Angle : 0.823 9.765 19698 Z= 0.454 Chirality : 0.057 0.206 2334 Planarity : 0.003 0.024 2496 Dihedral : 16.538 88.531 5472 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.67 % Allowed : 15.27 % Favored : 82.06 % 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: 0.14 (0.21), residues: 1830 helix: 1.25 (0.20), residues: 738 sheet: -0.62 (0.24), residues: 522 loop : -0.54 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 162 HIS 0.003 0.001 HIS E 193 PHE 0.017 0.002 PHE E 138 TYR 0.027 0.004 TYR B 245 ARG 0.004 0.001 ARG E 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 322 time to evaluate : 1.792 Fit side-chains REVERT: A 5 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8431 (mmpt) REVERT: A 115 MET cc_start: 0.8598 (mtp) cc_final: 0.8244 (mtp) REVERT: A 127 MET cc_start: 0.8545 (ttm) cc_final: 0.8273 (ttm) REVERT: A 220 ASP cc_start: 0.8493 (t0) cc_final: 0.8267 (t70) REVERT: A 222 MET cc_start: 0.7806 (ptp) cc_final: 0.7530 (ptp) REVERT: A 267 GLU cc_start: 0.7586 (tp30) cc_final: 0.7162 (tp30) REVERT: B 122 ASP cc_start: 0.8460 (m-30) cc_final: 0.8248 (m-30) REVERT: B 220 ASP cc_start: 0.8601 (t0) cc_final: 0.8173 (t0) REVERT: C 38 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7382 (mp-120) REVERT: C 122 ASP cc_start: 0.8624 (m-30) cc_final: 0.8372 (m-30) REVERT: C 220 ASP cc_start: 0.8648 (t0) cc_final: 0.8328 (t70) REVERT: D 38 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7383 (mp-120) REVERT: D 220 ASP cc_start: 0.8649 (t0) cc_final: 0.8391 (t70) REVERT: E 5 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8457 (mmpt) REVERT: E 122 ASP cc_start: 0.8447 (m-30) cc_final: 0.8239 (m-30) REVERT: E 220 ASP cc_start: 0.8597 (t0) cc_final: 0.8164 (t0) REVERT: F 5 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8429 (mmpt) REVERT: F 115 MET cc_start: 0.8588 (mtp) cc_final: 0.8224 (mtp) REVERT: F 127 MET cc_start: 0.8570 (ttm) cc_final: 0.8294 (ttm) REVERT: F 220 ASP cc_start: 0.8510 (t0) cc_final: 0.8270 (t70) REVERT: F 267 GLU cc_start: 0.7575 (tp30) cc_final: 0.7133 (tp30) outliers start: 42 outliers final: 26 residues processed: 353 average time/residue: 1.3375 time to fit residues: 514.7987 Evaluate side-chains 315 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 284 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 285 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 85 optimal weight: 0.0570 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 HIS B 288 GLN C 277 GLN C 288 GLN D 37 ASN D 277 GLN D 288 GLN E 288 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14538 Z= 0.136 Angle : 0.437 4.159 19698 Z= 0.242 Chirality : 0.046 0.164 2334 Planarity : 0.003 0.021 2496 Dihedral : 8.493 66.033 2166 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.01 % Allowed : 14.19 % Favored : 81.81 % 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: 0.31 (0.20), residues: 1830 helix: 1.10 (0.20), residues: 738 sheet: -0.23 (0.26), residues: 414 loop : -0.36 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 162 HIS 0.004 0.001 HIS B 283 PHE 0.008 0.001 PHE E 35 TYR 0.017 0.002 TYR D 311 ARG 0.002 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 321 time to evaluate : 1.687 Fit side-chains REVERT: A 5 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8246 (mmpt) REVERT: A 97 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6578 (mp10) REVERT: A 115 MET cc_start: 0.8704 (mtp) cc_final: 0.8447 (mtp) REVERT: A 178 VAL cc_start: 0.8291 (m) cc_final: 0.8081 (m) REVERT: A 180 SER cc_start: 0.8088 (t) cc_final: 0.7829 (t) REVERT: A 220 ASP cc_start: 0.8416 (t0) cc_final: 0.8182 (t70) REVERT: B 97 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6747 (mm110) REVERT: B 122 ASP cc_start: 0.8330 (m-30) cc_final: 0.8073 (m-30) REVERT: B 220 ASP cc_start: 0.8387 (t0) cc_final: 0.8160 (t70) REVERT: B 267 GLU cc_start: 0.7481 (tp30) cc_final: 0.7083 (tp30) REVERT: C 68 MET cc_start: 0.8345 (tpp) cc_final: 0.8088 (tpt) REVERT: C 122 ASP cc_start: 0.8540 (m-30) cc_final: 0.8327 (m-30) REVERT: D 68 MET cc_start: 0.8343 (tpp) cc_final: 0.8083 (tpt) REVERT: D 220 ASP cc_start: 0.8388 (t0) cc_final: 0.8116 (t0) REVERT: E 97 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6733 (mm110) REVERT: E 122 ASP cc_start: 0.8343 (m-30) cc_final: 0.8104 (m-30) REVERT: E 220 ASP cc_start: 0.8390 (t0) cc_final: 0.8155 (t70) REVERT: E 267 GLU cc_start: 0.7474 (tp30) cc_final: 0.7075 (tp30) REVERT: F 5 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8234 (mmpt) REVERT: F 97 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6551 (mp10) REVERT: F 115 MET cc_start: 0.8711 (mtp) cc_final: 0.8440 (mtp) REVERT: F 220 ASP cc_start: 0.8264 (t0) cc_final: 0.8053 (t70) outliers start: 63 outliers final: 23 residues processed: 360 average time/residue: 1.2581 time to fit residues: 495.9438 Evaluate side-chains 320 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 291 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 97 GLN A 283 HIS B 12 HIS B 97 GLN B 263 ASN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 HIS E 12 HIS E 97 GLN E 263 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14538 Z= 0.387 Angle : 0.584 5.776 19698 Z= 0.316 Chirality : 0.051 0.176 2334 Planarity : 0.004 0.024 2496 Dihedral : 7.546 59.704 2144 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.26 % Allowed : 13.74 % Favored : 82.00 % 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: 0.10 (0.20), residues: 1830 helix: 0.77 (0.20), residues: 738 sheet: -0.31 (0.24), residues: 480 loop : -0.26 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP E 162 HIS 0.004 0.001 HIS D 193 PHE 0.014 0.002 PHE D 138 TYR 0.017 0.003 TYR E 245 ARG 0.003 0.000 ARG F 301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 278 time to evaluate : 1.643 Fit side-chains REVERT: A 5 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8429 (mmpt) REVERT: A 97 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6452 (mp10) REVERT: A 115 MET cc_start: 0.8570 (mtp) cc_final: 0.8266 (mtp) REVERT: A 127 MET cc_start: 0.8536 (ttm) cc_final: 0.8323 (ttm) REVERT: A 220 ASP cc_start: 0.8554 (t0) cc_final: 0.8285 (t70) REVERT: B 97 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6858 (mm-40) REVERT: B 191 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7297 (mt) REVERT: B 220 ASP cc_start: 0.8611 (t0) cc_final: 0.8401 (t70) REVERT: B 267 GLU cc_start: 0.7639 (tp30) cc_final: 0.7219 (tp30) REVERT: C 68 MET cc_start: 0.8403 (tpp) cc_final: 0.8135 (tpt) REVERT: C 122 ASP cc_start: 0.8529 (m-30) cc_final: 0.8282 (m-30) REVERT: C 314 SER cc_start: 0.6155 (OUTLIER) cc_final: 0.5734 (p) REVERT: D 68 MET cc_start: 0.8401 (tpp) cc_final: 0.8129 (tpt) REVERT: D 220 ASP cc_start: 0.8572 (t0) cc_final: 0.8274 (t0) REVERT: E 191 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7279 (mt) REVERT: E 220 ASP cc_start: 0.8617 (t0) cc_final: 0.8388 (t70) REVERT: E 267 GLU cc_start: 0.7626 (tp30) cc_final: 0.7205 (tp30) REVERT: F 5 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8391 (mmpt) REVERT: F 68 MET cc_start: 0.8484 (tpp) cc_final: 0.8270 (mmm) REVERT: F 97 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6376 (mp10) REVERT: F 115 MET cc_start: 0.8556 (mtp) cc_final: 0.8252 (mtp) REVERT: F 127 MET cc_start: 0.8533 (ttm) cc_final: 0.8310 (ttm) REVERT: F 220 ASP cc_start: 0.8534 (t0) cc_final: 0.8271 (t70) outliers start: 67 outliers final: 33 residues processed: 321 average time/residue: 1.2982 time to fit residues: 455.5319 Evaluate side-chains 310 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 269 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.8980 chunk 123 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 78 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 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 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 283 HIS D 37 ASN D 283 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN E 283 HIS F 12 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14538 Z= 0.153 Angle : 0.444 4.316 19698 Z= 0.244 Chirality : 0.046 0.165 2334 Planarity : 0.003 0.020 2496 Dihedral : 6.363 57.487 2144 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.75 % Allowed : 13.80 % Favored : 82.44 % 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 (0.20), residues: 1830 helix: 1.30 (0.20), residues: 696 sheet: -0.05 (0.25), residues: 408 loop : -0.11 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 162 HIS 0.003 0.001 HIS D 193 PHE 0.011 0.001 PHE C 138 TYR 0.020 0.002 TYR D 311 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 302 time to evaluate : 1.668 Fit side-chains REVERT: A 5 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8267 (mmpt) REVERT: A 115 MET cc_start: 0.8679 (mtp) cc_final: 0.8418 (mtp) REVERT: A 180 SER cc_start: 0.8002 (t) cc_final: 0.7725 (t) REVERT: A 220 ASP cc_start: 0.8480 (t0) cc_final: 0.8212 (t70) REVERT: B 22 ARG cc_start: 0.8756 (mtp85) cc_final: 0.8543 (mtp85) REVERT: B 115 MET cc_start: 0.8727 (mtp) cc_final: 0.8501 (mtp) REVERT: B 127 MET cc_start: 0.8518 (ttm) cc_final: 0.8165 (tpp) REVERT: B 191 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7085 (mt) REVERT: B 267 GLU cc_start: 0.7614 (tp30) cc_final: 0.7266 (tp30) REVERT: C 38 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6680 (mp-120) REVERT: C 68 MET cc_start: 0.8360 (tpp) cc_final: 0.8050 (tpt) REVERT: D 68 MET cc_start: 0.8360 (tpp) cc_final: 0.8040 (tpt) REVERT: D 220 ASP cc_start: 0.8477 (t0) cc_final: 0.8187 (t0) REVERT: D 222 MET cc_start: 0.8011 (ptp) cc_final: 0.7728 (ptm) REVERT: D 314 SER cc_start: 0.6010 (OUTLIER) cc_final: 0.5636 (p) REVERT: E 97 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6009 (mp10) REVERT: E 115 MET cc_start: 0.8750 (mtp) cc_final: 0.8518 (mtp) REVERT: E 127 MET cc_start: 0.8517 (ttm) cc_final: 0.8165 (tpp) REVERT: F 115 MET cc_start: 0.8674 (mtp) cc_final: 0.8414 (mtp) REVERT: F 220 ASP cc_start: 0.8445 (t0) cc_final: 0.8171 (t70) outliers start: 59 outliers final: 23 residues processed: 336 average time/residue: 1.3040 time to fit residues: 479.2415 Evaluate side-chains 302 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 274 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 283 HIS B 12 HIS B 263 ASN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 283 HIS ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 283 HIS E 12 HIS E 263 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14538 Z= 0.176 Angle : 0.448 4.357 19698 Z= 0.245 Chirality : 0.046 0.166 2334 Planarity : 0.003 0.022 2496 Dihedral : 6.089 59.951 2136 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.63 % Allowed : 14.25 % Favored : 82.12 % 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: 0.61 (0.20), residues: 1830 helix: 1.30 (0.20), residues: 696 sheet: -0.00 (0.25), residues: 408 loop : -0.09 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 162 HIS 0.004 0.001 HIS E 193 PHE 0.011 0.001 PHE C 138 TYR 0.023 0.002 TYR D 311 ARG 0.002 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 275 time to evaluate : 1.710 Fit side-chains REVERT: A 115 MET cc_start: 0.8698 (mtp) cc_final: 0.8494 (mtp) REVERT: A 220 ASP cc_start: 0.8522 (t0) cc_final: 0.8229 (t70) REVERT: B 22 ARG cc_start: 0.8742 (mtp85) cc_final: 0.8529 (mtp85) REVERT: B 97 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6177 (mp-120) REVERT: B 115 MET cc_start: 0.8693 (mtp) cc_final: 0.8468 (mtp) REVERT: B 191 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7117 (mt) REVERT: C 68 MET cc_start: 0.8387 (tpp) cc_final: 0.8096 (tpt) REVERT: D 68 MET cc_start: 0.8387 (tpp) cc_final: 0.8057 (tpt) REVERT: D 314 SER cc_start: 0.6039 (OUTLIER) cc_final: 0.5660 (p) REVERT: E 22 ARG cc_start: 0.8716 (mtp85) cc_final: 0.8508 (mtp85) REVERT: E 97 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6043 (mp10) REVERT: F 115 MET cc_start: 0.8680 (mtp) cc_final: 0.8473 (mtp) REVERT: F 220 ASP cc_start: 0.8492 (t0) cc_final: 0.8172 (t70) outliers start: 57 outliers final: 25 residues processed: 318 average time/residue: 1.2850 time to fit residues: 447.3009 Evaluate side-chains 315 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 286 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 174 optimal weight: 0.0170 chunk 144 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- 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 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 283 HIS ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14538 Z= 0.223 Angle : 0.475 4.406 19698 Z= 0.260 Chirality : 0.047 0.169 2334 Planarity : 0.003 0.022 2496 Dihedral : 5.849 53.158 2132 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.37 % Allowed : 14.12 % Favored : 82.51 % 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 (0.20), residues: 1830 helix: 1.24 (0.20), residues: 696 sheet: 0.01 (0.25), residues: 408 loop : -0.08 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 162 HIS 0.004 0.001 HIS D 193 PHE 0.012 0.002 PHE C 138 TYR 0.025 0.002 TYR D 311 ARG 0.002 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 281 time to evaluate : 1.762 Fit side-chains REVERT: A 97 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.6064 (mp10) REVERT: A 115 MET cc_start: 0.8624 (mtp) cc_final: 0.8342 (mtp) REVERT: A 220 ASP cc_start: 0.8576 (t0) cc_final: 0.8257 (t70) REVERT: B 22 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8531 (mtp85) REVERT: B 97 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6210 (mp-120) REVERT: B 127 MET cc_start: 0.8544 (ttm) cc_final: 0.8254 (tpp) REVERT: B 191 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7151 (mt) REVERT: C 68 MET cc_start: 0.8383 (tpp) cc_final: 0.8048 (tpt) REVERT: D 38 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6863 (mp-120) REVERT: D 68 MET cc_start: 0.8407 (tpp) cc_final: 0.8058 (tpt) REVERT: D 220 ASP cc_start: 0.8598 (t0) cc_final: 0.8286 (t70) REVERT: D 314 SER cc_start: 0.6045 (OUTLIER) cc_final: 0.5665 (p) REVERT: E 22 ARG cc_start: 0.8740 (mtp85) cc_final: 0.8520 (mtp85) REVERT: E 97 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6046 (mp10) REVERT: E 127 MET cc_start: 0.8544 (ttm) cc_final: 0.8254 (tpp) REVERT: E 267 GLU cc_start: 0.7653 (tp30) cc_final: 0.7152 (tp30) REVERT: F 97 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.6000 (mp10) REVERT: F 220 ASP cc_start: 0.8592 (t0) cc_final: 0.8240 (t70) outliers start: 53 outliers final: 31 residues processed: 315 average time/residue: 1.3089 time to fit residues: 451.4286 Evaluate side-chains 311 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 273 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14538 Z= 0.281 Angle : 0.504 4.486 19698 Z= 0.277 Chirality : 0.048 0.172 2334 Planarity : 0.003 0.022 2496 Dihedral : 5.870 41.004 2130 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.88 % Allowed : 13.87 % Favored : 82.25 % 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: 0.49 (0.20), residues: 1830 helix: 1.14 (0.20), residues: 696 sheet: -0.01 (0.25), residues: 408 loop : -0.13 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP B 162 HIS 0.004 0.001 HIS D 193 PHE 0.013 0.002 PHE E 138 TYR 0.026 0.003 TYR D 311 ARG 0.003 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 271 time to evaluate : 1.635 Fit side-chains REVERT: A 97 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.6202 (mp-120) REVERT: A 115 MET cc_start: 0.8605 (mtp) cc_final: 0.8350 (mtp) REVERT: A 220 ASP cc_start: 0.8608 (t0) cc_final: 0.8268 (t70) REVERT: B 97 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6223 (mp-120) REVERT: B 191 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7185 (mt) REVERT: C 38 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6550 (mp-120) REVERT: C 68 MET cc_start: 0.8384 (tpp) cc_final: 0.8054 (tpt) REVERT: C 314 SER cc_start: 0.6145 (OUTLIER) cc_final: 0.5739 (p) REVERT: D 68 MET cc_start: 0.8434 (tpp) cc_final: 0.8081 (tpt) REVERT: D 220 ASP cc_start: 0.8606 (t0) cc_final: 0.8313 (t0) REVERT: D 314 SER cc_start: 0.6061 (OUTLIER) cc_final: 0.5679 (p) REVERT: E 22 ARG cc_start: 0.8740 (mtp85) cc_final: 0.8501 (mtp85) REVERT: E 97 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6044 (mp10) REVERT: F 97 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.6183 (mp-120) REVERT: F 220 ASP cc_start: 0.8619 (t0) cc_final: 0.8270 (t70) outliers start: 61 outliers final: 36 residues processed: 311 average time/residue: 1.2599 time to fit residues: 429.1305 Evaluate side-chains 305 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 261 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14538 Z= 0.306 Angle : 0.522 4.499 19698 Z= 0.286 Chirality : 0.049 0.173 2334 Planarity : 0.003 0.023 2496 Dihedral : 5.891 41.451 2130 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.50 % Allowed : 13.93 % Favored : 82.57 % 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: 0.42 (0.20), residues: 1830 helix: 1.09 (0.20), residues: 696 sheet: -0.07 (0.25), residues: 408 loop : -0.14 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 162 HIS 0.005 0.001 HIS D 193 PHE 0.014 0.002 PHE C 138 TYR 0.027 0.003 TYR D 311 ARG 0.003 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 258 time to evaluate : 1.663 Fit side-chains REVERT: A 97 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.6227 (mp-120) REVERT: A 115 MET cc_start: 0.8613 (mtp) cc_final: 0.8338 (mtp) REVERT: A 220 ASP cc_start: 0.8616 (t0) cc_final: 0.8270 (t70) REVERT: B 97 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6225 (mp-120) REVERT: B 127 MET cc_start: 0.8554 (ttm) cc_final: 0.8173 (tpp) REVERT: B 191 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7225 (mt) REVERT: C 68 MET cc_start: 0.8391 (tpp) cc_final: 0.8056 (tpt) REVERT: C 314 SER cc_start: 0.6130 (OUTLIER) cc_final: 0.5724 (p) REVERT: D 68 MET cc_start: 0.8404 (tpp) cc_final: 0.8074 (tpt) REVERT: D 220 ASP cc_start: 0.8610 (t0) cc_final: 0.8347 (t70) REVERT: D 314 SER cc_start: 0.6071 (OUTLIER) cc_final: 0.5688 (p) REVERT: E 97 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6274 (mp-120) REVERT: E 127 MET cc_start: 0.8550 (ttm) cc_final: 0.8170 (tpp) REVERT: E 191 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7136 (mt) REVERT: F 97 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.6195 (mp-120) REVERT: F 220 ASP cc_start: 0.8631 (t0) cc_final: 0.8272 (t70) outliers start: 55 outliers final: 37 residues processed: 294 average time/residue: 1.2142 time to fit residues: 392.5913 Evaluate side-chains 314 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 269 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 151 optimal weight: 0.3980 chunk 161 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS B 12 HIS B 263 ASN B 283 HIS C 12 HIS E 12 HIS E 263 ASN E 283 HIS F 12 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14538 Z= 0.148 Angle : 0.434 4.928 19698 Z= 0.238 Chirality : 0.045 0.165 2334 Planarity : 0.003 0.021 2496 Dihedral : 5.236 36.307 2130 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.99 % Allowed : 14.95 % Favored : 82.06 % 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: 0.65 (0.20), residues: 1830 helix: 1.33 (0.21), residues: 696 sheet: 0.06 (0.25), residues: 408 loop : -0.09 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 162 HIS 0.004 0.001 HIS D 193 PHE 0.010 0.001 PHE E 138 TYR 0.028 0.002 TYR D 311 ARG 0.002 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 291 time to evaluate : 1.574 Fit side-chains REVERT: A 220 ASP cc_start: 0.8574 (t0) cc_final: 0.8213 (t70) REVERT: B 97 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.6156 (mp-120) REVERT: B 127 MET cc_start: 0.8503 (ttm) cc_final: 0.8103 (tpp) REVERT: B 191 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7134 (mt) REVERT: C 68 MET cc_start: 0.8381 (tpp) cc_final: 0.8034 (tpt) REVERT: D 68 MET cc_start: 0.8431 (tpp) cc_final: 0.8134 (tpt) REVERT: D 220 ASP cc_start: 0.8507 (t0) cc_final: 0.8239 (t70) REVERT: D 222 MET cc_start: 0.7933 (ptp) cc_final: 0.7651 (ptm) REVERT: E 97 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6039 (mp10) REVERT: E 127 MET cc_start: 0.8502 (ttm) cc_final: 0.8101 (tpp) REVERT: E 220 ASP cc_start: 0.8549 (t0) cc_final: 0.8182 (t0) REVERT: F 220 ASP cc_start: 0.8581 (t0) cc_final: 0.8188 (t70) outliers start: 47 outliers final: 26 residues processed: 323 average time/residue: 1.2136 time to fit residues: 430.5552 Evaluate side-chains 300 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 271 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.1980 chunk 104 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS B 12 HIS B 283 HIS C 12 HIS ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS E 263 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14538 Z= 0.169 Angle : 0.451 4.689 19698 Z= 0.245 Chirality : 0.046 0.166 2334 Planarity : 0.003 0.021 2496 Dihedral : 5.265 36.994 2130 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.74 % Allowed : 15.84 % Favored : 81.42 % 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: 0.64 (0.20), residues: 1830 helix: 1.27 (0.20), residues: 696 sheet: 0.14 (0.25), residues: 408 loop : -0.09 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 162 HIS 0.004 0.001 HIS D 193 PHE 0.011 0.001 PHE C 138 TYR 0.027 0.002 TYR C 311 ARG 0.002 0.000 ARG B 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 273 time to evaluate : 1.642 Fit side-chains REVERT: A 97 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6005 (mp10) REVERT: A 220 ASP cc_start: 0.8593 (t0) cc_final: 0.8222 (t70) REVERT: B 97 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6206 (mp-120) REVERT: B 127 MET cc_start: 0.8539 (ttm) cc_final: 0.8193 (tpp) REVERT: B 191 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7124 (mt) REVERT: C 68 MET cc_start: 0.8421 (tpp) cc_final: 0.8083 (tpt) REVERT: D 68 MET cc_start: 0.8376 (tpp) cc_final: 0.8097 (tpt) REVERT: D 220 ASP cc_start: 0.8520 (t0) cc_final: 0.8237 (t70) REVERT: D 222 MET cc_start: 0.8019 (ptp) cc_final: 0.7702 (ptm) REVERT: E 97 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6081 (mp10) REVERT: E 127 MET cc_start: 0.8538 (ttm) cc_final: 0.8189 (tpp) REVERT: E 191 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7135 (mp) REVERT: F 97 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.6061 (mp10) REVERT: F 220 ASP cc_start: 0.8598 (t0) cc_final: 0.8218 (t70) outliers start: 43 outliers final: 27 residues processed: 302 average time/residue: 1.3567 time to fit residues: 447.6886 Evaluate side-chains 286 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 253 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 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 12 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS E 263 ASN E 283 HIS F 12 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.161276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122570 restraints weight = 13580.043| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.43 r_work: 0.3233 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 324 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14538 Z= 0.175 Angle : 0.450 4.483 19698 Z= 0.246 Chirality : 0.046 0.167 2334 Planarity : 0.003 0.022 2496 Dihedral : 5.268 36.710 2130 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.67 % Allowed : 16.09 % Favored : 81.23 % 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: 0.67 (0.20), residues: 1830 helix: 1.28 (0.20), residues: 696 sheet: 0.20 (0.25), residues: 408 loop : -0.09 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 162 HIS 0.004 0.001 HIS D 193 PHE 0.011 0.001 PHE C 138 TYR 0.028 0.002 TYR C 311 ARG 0.002 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6869.71 seconds wall clock time: 121 minutes 48.25 seconds (7308.25 seconds total)