Starting phenix.real_space_refine on Wed Feb 14 08:52:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/02_2024/6vms_21243_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/02_2024/6vms_21243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/02_2024/6vms_21243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/02_2024/6vms_21243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/02_2024/6vms_21243_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vms_21243/02_2024/6vms_21243_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 65 5.16 5 C 5705 2.51 5 N 1512 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "R GLU 99": "OE1" <-> "OE2" Residue "R ASP 400": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8953 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1823 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2287 Unusual residues: {'08Y': 1} Classifications: {'peptide': 278, 'undetermined': 1} Link IDs: {'PTRANS': 9, 'TRANS': 268, None: 1} Not linked: pdbres="CYS R 443 " pdbres="08Y R 601 " Time building chain proxies: 5.30, per 1000 atoms: 0.59 Number of scatterers: 8953 At special positions: 0 Unit cell: (103.75, 117.86, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 65 16.00 O 1670 8.00 N 1512 7.00 C 5705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS R 399 " - pdb=" SG CYS R 401 " distance=2.04 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: 3.55 Conformation dependent library (CDL) restraints added in 1.7 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 34.5% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.618A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.194A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.977A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.806A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.224A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 23 removed outlier: 4.114A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'R' and resid 36 through 61 removed outlier: 3.515A pdb=" N LEU R 40 " --> pdb=" O TYR R 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE R 48 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN R 52 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL R 53 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL R 55 " --> pdb=" O ASN R 52 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS R 56 " --> pdb=" O VAL R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 86 Processing helix chain 'R' and resid 88 through 96 Processing helix chain 'R' and resid 106 through 137 Processing helix chain 'R' and resid 145 through 170 removed outlier: 3.670A pdb=" N LYS R 149 " --> pdb=" O ARG R 145 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Proline residue: R 169 - end of helix Processing helix chain 'R' and resid 187 through 197 removed outlier: 4.329A pdb=" N ILE R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL R 196 " --> pdb=" O TYR R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 222 Processing helix chain 'R' and resid 364 through 398 removed outlier: 3.526A pdb=" N LYS R 369 " --> pdb=" O GLN R 365 " (cutoff:3.500A) Proline residue: R 388 - end of helix removed outlier: 3.609A pdb=" N ILE R 397 " --> pdb=" O HIS R 393 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS R 398 " --> pdb=" O ILE R 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 425 removed outlier: 3.872A pdb=" N ALA R 410 " --> pdb=" O VAL R 406 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN R 418 " --> pdb=" O LEU R 414 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 431 through 440 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.563A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.985A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.924A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.800A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.070A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.804A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.563A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.440A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.530A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 225 through 231 removed outlier: 6.413A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1095 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: 2.83 Time building geometry restraints manager: 3.84 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: 2875 1.34 - 1.47: 2292 1.47 - 1.60: 3880 1.60 - 1.73: 0 1.73 - 1.86: 94 Bond restraints: 9141 Sorted by residual: bond pdb=" C25 08Y R 601 " pdb=" C29 08Y R 601 " ideal model delta sigma weight residual 1.367 1.403 -0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" C LEU R 407 " pdb=" N TYR R 408 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.25e-02 6.40e+03 1.84e+00 bond pdb=" C2 08Y R 601 " pdb=" O1 08Y R 601 " ideal model delta sigma weight residual 1.398 1.425 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" CB VAL A 342 " pdb=" CG2 VAL A 342 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.36e+00 bond pdb=" CG LEU B 336 " pdb=" CD2 LEU B 336 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.31e+00 ... (remaining 9136 not shown) Histogram of bond angle deviations from ideal: 99.14 - 107.26: 259 107.26 - 115.37: 5631 115.37 - 123.49: 6150 123.49 - 131.61: 340 131.61 - 139.73: 21 Bond angle restraints: 12401 Sorted by residual: angle pdb=" CB LYS C 32 " pdb=" CG LYS C 32 " pdb=" CD LYS C 32 " ideal model delta sigma weight residual 111.30 120.41 -9.11 2.30e+00 1.89e-01 1.57e+01 angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" C MET E 192 " ideal model delta sigma weight residual 110.80 117.44 -6.64 2.13e+00 2.20e-01 9.71e+00 angle pdb=" N ARG R 361 " pdb=" CA ARG R 361 " pdb=" C ARG R 361 " ideal model delta sigma weight residual 110.80 117.11 -6.31 2.13e+00 2.20e-01 8.77e+00 angle pdb=" N GLY E 33 " pdb=" CA GLY E 33 " pdb=" C GLY E 33 " ideal model delta sigma weight residual 112.89 108.41 4.48 1.58e+00 4.01e-01 8.05e+00 angle pdb=" C ILE B 338 " pdb=" N TRP B 339 " pdb=" CA TRP B 339 " ideal model delta sigma weight residual 123.05 126.75 -3.70 1.40e+00 5.10e-01 7.00e+00 ... (remaining 12396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5249 17.47 - 34.94: 195 34.94 - 52.41: 35 52.41 - 69.88: 18 69.88 - 87.35: 6 Dihedral angle restraints: 5503 sinusoidal: 2192 harmonic: 3311 Sorted by residual: dihedral pdb=" CB CYS R 399 " pdb=" SG CYS R 399 " pdb=" SG CYS R 401 " pdb=" CB CYS R 401 " ideal model delta sinusoidal sigma weight residual -86.00 -145.68 59.68 1 1.00e+01 1.00e-02 4.75e+01 dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 149.27 -56.27 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA PRO R 139 " pdb=" C PRO R 139 " pdb=" N MET R 140 " pdb=" CA MET R 140 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 5500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 765 0.029 - 0.058: 431 0.058 - 0.087: 140 0.087 - 0.116: 70 0.116 - 0.145: 13 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CA ILE A 221 " pdb=" N ILE A 221 " pdb=" C ILE A 221 " pdb=" CB ILE A 221 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL B 135 " pdb=" N VAL B 135 " pdb=" C VAL B 135 " pdb=" CB VAL B 135 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1416 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" BR 08Y R 601 " 0.071 2.00e-02 2.50e+03 8.71e-02 2.28e+02 pdb=" C21 08Y R 601 " -0.099 2.00e-02 2.50e+03 pdb=" C23 08Y R 601 " 0.157 2.00e-02 2.50e+03 pdb=" C24 08Y R 601 " -0.063 2.00e-02 2.50e+03 pdb=" C25 08Y R 601 " -0.032 2.00e-02 2.50e+03 pdb=" C26 08Y R 601 " -0.107 2.00e-02 2.50e+03 pdb=" C28 08Y R 601 " -0.087 2.00e-02 2.50e+03 pdb=" C29 08Y R 601 " -0.021 2.00e-02 2.50e+03 pdb=" C30 08Y R 601 " 0.092 2.00e-02 2.50e+03 pdb=" C31 08Y R 601 " 0.023 2.00e-02 2.50e+03 pdb=" C32 08Y R 601 " 0.122 2.00e-02 2.50e+03 pdb=" N5 08Y R 601 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 08Y R 601 " 0.060 2.00e-02 2.50e+03 5.54e-02 4.61e+01 pdb=" C3 08Y R 601 " -0.071 2.00e-02 2.50e+03 pdb=" C6 08Y R 601 " -0.074 2.00e-02 2.50e+03 pdb=" C9 08Y R 601 " 0.008 2.00e-02 2.50e+03 pdb=" N2 08Y R 601 " 0.011 2.00e-02 2.50e+03 pdb=" O4 08Y R 601 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 08Y R 601 " -0.067 2.00e-02 2.50e+03 4.51e-02 3.05e+01 pdb=" C3 08Y R 601 " 0.035 2.00e-02 2.50e+03 pdb=" C5 08Y R 601 " 0.055 2.00e-02 2.50e+03 pdb=" C8 08Y R 601 " -0.000 2.00e-02 2.50e+03 pdb=" N1 08Y R 601 " 0.028 2.00e-02 2.50e+03 pdb=" O3 08Y R 601 " -0.051 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 118 2.65 - 3.21: 8357 3.21 - 3.77: 13399 3.77 - 4.34: 19284 4.34 - 4.90: 31092 Nonbonded interactions: 72250 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.082 2.440 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.103 2.440 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.116 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.126 2.440 nonbonded pdb=" OG SER E 106 " pdb=" OH TYR E 190 " model vdw 2.227 2.440 ... (remaining 72245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 5.150 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 28.070 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 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 : 0.005 0.039 9141 Z= 0.314 Angle : 0.704 9.108 12401 Z= 0.393 Chirality : 0.043 0.145 1419 Planarity : 0.005 0.087 1557 Dihedral : 11.035 87.351 3353 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.27 (0.24), residues: 1121 helix: -0.49 (0.24), residues: 380 sheet: 0.63 (0.29), residues: 275 loop : -0.23 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 82 HIS 0.005 0.001 HIS R 106 PHE 0.016 0.002 PHE B 234 TYR 0.012 0.002 TYR R 146 ARG 0.011 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.7739 (t80) cc_final: 0.7508 (t80) REVERT: A 228 SER cc_start: 0.7575 (p) cc_final: 0.6988 (p) REVERT: A 273 LEU cc_start: 0.8501 (mt) cc_final: 0.8101 (tt) REVERT: B 76 ASP cc_start: 0.6632 (t0) cc_final: 0.6373 (t0) REVERT: B 171 ILE cc_start: 0.7446 (tp) cc_final: 0.7173 (tp) REVERT: E 60 TYR cc_start: 0.7906 (m-80) cc_final: 0.7482 (m-80) REVERT: E 68 PHE cc_start: 0.7615 (m-10) cc_final: 0.7041 (m-10) REVERT: E 71 SER cc_start: 0.6618 (t) cc_final: 0.6020 (p) REVERT: E 83 MET cc_start: 0.8704 (mtt) cc_final: 0.8474 (mtm) REVERT: E 234 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7945 (mm-30) REVERT: R 164 PHE cc_start: 0.7718 (t80) cc_final: 0.7498 (t80) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2602 time to fit residues: 105.0350 Evaluate side-chains 175 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 213 HIS A 331 ASN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 44 HIS E 179 GLN E 232 HIS R 106 HIS R 179 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9141 Z= 0.291 Angle : 0.687 6.723 12401 Z= 0.367 Chirality : 0.047 0.198 1419 Planarity : 0.005 0.063 1557 Dihedral : 5.837 65.834 1312 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.67 % Allowed : 11.12 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.56 (0.25), residues: 1121 helix: 0.66 (0.27), residues: 389 sheet: 0.74 (0.29), residues: 277 loop : 0.05 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 100 HIS 0.012 0.002 HIS R 393 PHE 0.028 0.002 PHE R 390 TYR 0.021 0.002 TYR B 59 ARG 0.006 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 214 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7515 (mt-10) REVERT: A 232 LEU cc_start: 0.7349 (tp) cc_final: 0.7078 (tp) REVERT: A 240 MET cc_start: 0.6526 (tpp) cc_final: 0.6160 (ppp) REVERT: A 273 LEU cc_start: 0.8583 (mt) cc_final: 0.8124 (tt) REVERT: A 287 TYR cc_start: 0.7862 (m-80) cc_final: 0.7553 (m-80) REVERT: B 76 ASP cc_start: 0.6928 (t0) cc_final: 0.6700 (t0) REVERT: B 88 ASN cc_start: 0.8286 (m110) cc_final: 0.7872 (m110) REVERT: B 191 SER cc_start: 0.8296 (t) cc_final: 0.8086 (t) REVERT: B 201 SER cc_start: 0.9266 (t) cc_final: 0.9007 (p) REVERT: B 215 GLU cc_start: 0.6430 (tp30) cc_final: 0.5477 (tp30) REVERT: B 259 GLN cc_start: 0.8224 (mt0) cc_final: 0.7800 (mt0) REVERT: B 266 HIS cc_start: 0.6817 (t-170) cc_final: 0.6409 (t70) REVERT: C 47 GLU cc_start: 0.6433 (mp0) cc_final: 0.6075 (mp0) REVERT: E 14 PRO cc_start: 0.7343 (Cg_endo) cc_final: 0.7129 (Cg_exo) REVERT: E 18 ARG cc_start: 0.7648 (tpp-160) cc_final: 0.7385 (tpp-160) REVERT: E 71 SER cc_start: 0.6754 (t) cc_final: 0.6523 (p) REVERT: E 197 SER cc_start: 0.9195 (m) cc_final: 0.8832 (p) REVERT: R 47 VAL cc_start: 0.7910 (m) cc_final: 0.7655 (p) REVERT: R 387 LEU cc_start: 0.8866 (tp) cc_final: 0.8665 (tt) outliers start: 36 outliers final: 17 residues processed: 235 average time/residue: 0.2345 time to fit residues: 73.8771 Evaluate side-chains 192 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 176 GLN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9141 Z= 0.224 Angle : 0.602 12.175 12401 Z= 0.316 Chirality : 0.044 0.157 1419 Planarity : 0.004 0.038 1557 Dihedral : 5.586 64.408 1312 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.06 % Allowed : 14.39 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.62 (0.25), residues: 1121 helix: 0.99 (0.27), residues: 390 sheet: 0.54 (0.29), residues: 279 loop : -0.04 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 100 HIS 0.008 0.001 HIS R 393 PHE 0.015 0.002 PHE B 199 TYR 0.016 0.001 TYR R 34 ARG 0.010 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 202 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8269 (m-30) cc_final: 0.7916 (m-30) REVERT: A 240 MET cc_start: 0.6538 (tpp) cc_final: 0.6201 (ppp) REVERT: A 273 LEU cc_start: 0.8590 (mt) cc_final: 0.8152 (tt) REVERT: A 313 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7388 (mtm-85) REVERT: B 10 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6973 (tp30) REVERT: B 76 ASP cc_start: 0.6913 (t0) cc_final: 0.6682 (t0) REVERT: B 88 ASN cc_start: 0.8423 (m110) cc_final: 0.8025 (m110) REVERT: B 111 TYR cc_start: 0.9027 (m-80) cc_final: 0.8817 (m-80) REVERT: B 175 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7466 (mm110) REVERT: B 201 SER cc_start: 0.9364 (t) cc_final: 0.9126 (p) REVERT: E 14 PRO cc_start: 0.7024 (Cg_endo) cc_final: 0.6725 (Cg_exo) REVERT: E 18 ARG cc_start: 0.7574 (tpp-160) cc_final: 0.7203 (tpp-160) REVERT: E 71 SER cc_start: 0.6804 (t) cc_final: 0.6539 (p) REVERT: E 197 SER cc_start: 0.9241 (m) cc_final: 0.8871 (p) REVERT: R 47 VAL cc_start: 0.8152 (m) cc_final: 0.7899 (p) REVERT: R 108 ASP cc_start: 0.6749 (m-30) cc_final: 0.6347 (m-30) REVERT: R 180 ASN cc_start: 0.6003 (p0) cc_final: 0.5363 (p0) REVERT: R 387 LEU cc_start: 0.8822 (tp) cc_final: 0.8617 (tt) outliers start: 30 outliers final: 20 residues processed: 222 average time/residue: 0.2133 time to fit residues: 64.1392 Evaluate side-chains 197 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 213 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9141 Z= 0.255 Angle : 0.597 9.957 12401 Z= 0.314 Chirality : 0.044 0.167 1419 Planarity : 0.004 0.035 1557 Dihedral : 5.437 59.281 1312 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.08 % Allowed : 15.10 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.62 (0.25), residues: 1121 helix: 1.01 (0.27), residues: 387 sheet: 0.56 (0.28), residues: 296 loop : -0.08 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 100 HIS 0.005 0.001 HIS E 232 PHE 0.019 0.002 PHE R 389 TYR 0.019 0.001 TYR E 190 ARG 0.005 0.001 ARG R 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 187 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8287 (m-30) cc_final: 0.8027 (m-30) REVERT: A 240 MET cc_start: 0.6740 (tpp) cc_final: 0.6319 (ppp) REVERT: A 248 LYS cc_start: 0.8769 (mttt) cc_final: 0.8358 (tmtt) REVERT: A 273 LEU cc_start: 0.8620 (mt) cc_final: 0.8194 (tt) REVERT: A 313 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7442 (mtm-85) REVERT: B 76 ASP cc_start: 0.7049 (t0) cc_final: 0.6751 (t0) REVERT: B 175 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7587 (mm110) REVERT: B 201 SER cc_start: 0.9460 (t) cc_final: 0.9218 (p) REVERT: B 209 LYS cc_start: 0.8376 (mttt) cc_final: 0.8130 (mtpp) REVERT: B 215 GLU cc_start: 0.6908 (tp30) cc_final: 0.6664 (tp30) REVERT: C 28 ILE cc_start: 0.7671 (pt) cc_final: 0.7261 (pt) REVERT: C 32 LYS cc_start: 0.7322 (ptmt) cc_final: 0.7045 (ttpp) REVERT: E 18 ARG cc_start: 0.7648 (tpp-160) cc_final: 0.7179 (tpp-160) REVERT: E 71 SER cc_start: 0.6913 (t) cc_final: 0.6635 (p) REVERT: E 139 VAL cc_start: 0.8625 (t) cc_final: 0.8311 (m) REVERT: E 197 SER cc_start: 0.9273 (m) cc_final: 0.8895 (p) REVERT: R 47 VAL cc_start: 0.8181 (m) cc_final: 0.7953 (p) REVERT: R 108 ASP cc_start: 0.6996 (m-30) cc_final: 0.6675 (m-30) REVERT: R 387 LEU cc_start: 0.8840 (tp) cc_final: 0.8615 (tt) outliers start: 40 outliers final: 24 residues processed: 210 average time/residue: 0.2320 time to fit residues: 64.9229 Evaluate side-chains 196 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 171 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 138 MET Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN R 393 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9141 Z= 0.208 Angle : 0.571 9.259 12401 Z= 0.298 Chirality : 0.043 0.186 1419 Planarity : 0.004 0.056 1557 Dihedral : 5.322 57.956 1312 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.98 % Allowed : 15.41 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.59 (0.25), residues: 1121 helix: 1.05 (0.27), residues: 389 sheet: 0.49 (0.27), residues: 301 loop : -0.15 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 100 HIS 0.005 0.001 HIS R 393 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.022 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8206 (m-30) cc_final: 0.7997 (m-30) REVERT: A 240 MET cc_start: 0.6792 (tpp) cc_final: 0.6234 (ppp) REVERT: A 248 LYS cc_start: 0.8792 (mttt) cc_final: 0.8405 (tmtt) REVERT: A 273 LEU cc_start: 0.8622 (mt) cc_final: 0.8195 (tt) REVERT: A 313 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7383 (mtm-85) REVERT: B 76 ASP cc_start: 0.6987 (t0) cc_final: 0.6690 (t0) REVERT: B 175 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7665 (mm110) REVERT: B 209 LYS cc_start: 0.8568 (mttt) cc_final: 0.8335 (mttp) REVERT: C 28 ILE cc_start: 0.7747 (pt) cc_final: 0.7355 (pt) REVERT: C 32 LYS cc_start: 0.7421 (ptmt) cc_final: 0.7152 (ttpp) REVERT: E 18 ARG cc_start: 0.7691 (tpp-160) cc_final: 0.7424 (tpp-160) REVERT: E 197 SER cc_start: 0.9281 (m) cc_final: 0.8876 (p) REVERT: R 47 VAL cc_start: 0.8268 (m) cc_final: 0.8053 (p) REVERT: R 108 ASP cc_start: 0.7119 (m-30) cc_final: 0.6828 (m-30) REVERT: R 117 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7071 (mmt) REVERT: R 387 LEU cc_start: 0.8872 (tp) cc_final: 0.8646 (tt) outliers start: 39 outliers final: 24 residues processed: 215 average time/residue: 0.2340 time to fit residues: 66.9561 Evaluate side-chains 196 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 117 MET Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 219 ARG Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Chi-restraints excluded: chain R residue 433 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 40.0000 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9141 Z= 0.186 Angle : 0.574 9.887 12401 Z= 0.297 Chirality : 0.043 0.214 1419 Planarity : 0.003 0.039 1557 Dihedral : 5.191 55.180 1312 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.57 % Allowed : 17.45 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.69 (0.26), residues: 1121 helix: 1.20 (0.28), residues: 380 sheet: 0.47 (0.27), residues: 297 loop : -0.07 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 100 HIS 0.004 0.001 HIS E 232 PHE 0.025 0.001 PHE R 390 TYR 0.015 0.001 TYR R 209 ARG 0.009 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8239 (m-30) cc_final: 0.8021 (m-30) REVERT: A 17 LYS cc_start: 0.8043 (mttt) cc_final: 0.7807 (mtpt) REVERT: A 228 SER cc_start: 0.8193 (p) cc_final: 0.7760 (t) REVERT: A 240 MET cc_start: 0.6822 (tpp) cc_final: 0.6221 (ppp) REVERT: A 248 LYS cc_start: 0.8753 (mttt) cc_final: 0.8410 (tmtt) REVERT: A 313 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7382 (mtm-85) REVERT: B 76 ASP cc_start: 0.7017 (t0) cc_final: 0.6694 (t0) REVERT: C 28 ILE cc_start: 0.7872 (pt) cc_final: 0.7656 (pt) REVERT: C 32 LYS cc_start: 0.7556 (ptmt) cc_final: 0.7165 (ttpp) REVERT: C 58 GLU cc_start: 0.6788 (tm-30) cc_final: 0.6278 (tt0) REVERT: E 18 ARG cc_start: 0.7649 (tpp-160) cc_final: 0.7353 (tpp-160) REVERT: E 162 SER cc_start: 0.8669 (m) cc_final: 0.8426 (p) REVERT: E 197 SER cc_start: 0.9296 (m) cc_final: 0.8873 (p) REVERT: E 234 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7341 (mm-30) REVERT: R 47 VAL cc_start: 0.8294 (m) cc_final: 0.8059 (p) REVERT: R 108 ASP cc_start: 0.7098 (m-30) cc_final: 0.6811 (m-30) REVERT: R 116 MET cc_start: 0.7814 (ttt) cc_final: 0.7525 (ttt) REVERT: R 140 MET cc_start: 0.8112 (mmm) cc_final: 0.7690 (mmm) REVERT: R 387 LEU cc_start: 0.8926 (tp) cc_final: 0.8667 (tt) outliers start: 35 outliers final: 25 residues processed: 205 average time/residue: 0.2486 time to fit residues: 67.9152 Evaluate side-chains 198 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 219 ARG Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 0.0970 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9141 Z= 0.161 Angle : 0.564 9.974 12401 Z= 0.291 Chirality : 0.043 0.192 1419 Planarity : 0.003 0.034 1557 Dihedral : 5.051 53.439 1312 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.86 % Allowed : 18.98 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.74 (0.26), residues: 1121 helix: 1.30 (0.28), residues: 381 sheet: 0.46 (0.28), residues: 295 loop : -0.08 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.001 PHE R 390 TYR 0.011 0.001 TYR R 209 ARG 0.008 0.000 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8047 (mttt) cc_final: 0.7814 (mtpt) REVERT: A 228 SER cc_start: 0.8199 (p) cc_final: 0.7786 (t) REVERT: A 240 MET cc_start: 0.6728 (tpp) cc_final: 0.6248 (ppp) REVERT: A 248 LYS cc_start: 0.8751 (mttt) cc_final: 0.8406 (tmtt) REVERT: A 273 LEU cc_start: 0.8669 (mp) cc_final: 0.8067 (tt) REVERT: B 76 ASP cc_start: 0.6939 (t0) cc_final: 0.6612 (t0) REVERT: B 215 GLU cc_start: 0.7244 (mp0) cc_final: 0.6850 (pm20) REVERT: C 15 LEU cc_start: 0.7647 (mp) cc_final: 0.7251 (tp) REVERT: C 32 LYS cc_start: 0.7544 (ptmt) cc_final: 0.7171 (ttpp) REVERT: E 18 ARG cc_start: 0.7588 (tpp-160) cc_final: 0.7356 (tpp-160) REVERT: E 162 SER cc_start: 0.8682 (m) cc_final: 0.8464 (p) REVERT: E 197 SER cc_start: 0.9297 (m) cc_final: 0.8844 (p) REVERT: E 220 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6656 (mp0) REVERT: E 234 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7306 (mm-30) REVERT: R 108 ASP cc_start: 0.7033 (m-30) cc_final: 0.6801 (m-30) REVERT: R 140 MET cc_start: 0.8116 (mmm) cc_final: 0.7564 (mmm) REVERT: R 369 LYS cc_start: 0.6115 (mmmt) cc_final: 0.5418 (tptt) outliers start: 28 outliers final: 20 residues processed: 210 average time/residue: 0.2448 time to fit residues: 68.1373 Evaluate side-chains 193 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 219 ARG Chi-restraints excluded: chain R residue 399 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 0.0050 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.6672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9141 Z= 0.175 Angle : 0.577 9.939 12401 Z= 0.299 Chirality : 0.043 0.241 1419 Planarity : 0.003 0.029 1557 Dihedral : 5.045 53.874 1312 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.24 % Allowed : 20.41 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.70 (0.25), residues: 1121 helix: 1.30 (0.28), residues: 381 sheet: 0.62 (0.28), residues: 281 loop : -0.26 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 100 HIS 0.002 0.001 HIS E 232 PHE 0.011 0.001 PHE E 212 TYR 0.009 0.001 TYR B 59 ARG 0.008 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 2.164 Fit side-chains revert: symmetry clash REVERT: A 228 SER cc_start: 0.8215 (p) cc_final: 0.7795 (t) REVERT: A 240 MET cc_start: 0.6778 (tpp) cc_final: 0.6267 (ppp) REVERT: A 248 LYS cc_start: 0.8757 (mttt) cc_final: 0.8402 (tmtt) REVERT: B 76 ASP cc_start: 0.6933 (t0) cc_final: 0.6609 (t0) REVERT: C 15 LEU cc_start: 0.7662 (mp) cc_final: 0.7322 (tp) REVERT: C 32 LYS cc_start: 0.7567 (ptmt) cc_final: 0.7260 (ttpp) REVERT: E 18 ARG cc_start: 0.7610 (tpp-160) cc_final: 0.7268 (tpp-160) REVERT: E 39 GLN cc_start: 0.8125 (tp40) cc_final: 0.7777 (tp40) REVERT: E 162 SER cc_start: 0.8654 (m) cc_final: 0.8405 (p) REVERT: E 197 SER cc_start: 0.9310 (m) cc_final: 0.8859 (p) REVERT: E 234 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7336 (mm-30) REVERT: R 52 ASN cc_start: 0.7297 (m-40) cc_final: 0.6994 (m-40) REVERT: R 140 MET cc_start: 0.8116 (mmm) cc_final: 0.7565 (mmm) REVERT: R 369 LYS cc_start: 0.6193 (mmmt) cc_final: 0.5489 (tptt) outliers start: 22 outliers final: 16 residues processed: 192 average time/residue: 0.2575 time to fit residues: 65.2918 Evaluate side-chains 187 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 219 ARG Chi-restraints excluded: chain R residue 399 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9141 Z= 0.192 Angle : 0.577 9.859 12401 Z= 0.301 Chirality : 0.043 0.216 1419 Planarity : 0.003 0.029 1557 Dihedral : 5.035 53.685 1312 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.04 % Allowed : 20.82 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.70 (0.26), residues: 1121 helix: 1.23 (0.27), residues: 381 sheet: 0.50 (0.29), residues: 290 loop : -0.11 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.022 0.001 PHE E 212 TYR 0.011 0.001 TYR B 59 ARG 0.009 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 228 SER cc_start: 0.8302 (p) cc_final: 0.7953 (t) REVERT: A 248 LYS cc_start: 0.8790 (mttt) cc_final: 0.8457 (tmtt) REVERT: B 67 SER cc_start: 0.9328 (OUTLIER) cc_final: 0.8696 (t) REVERT: B 76 ASP cc_start: 0.6995 (t0) cc_final: 0.6683 (t0) REVERT: C 11 GLN cc_start: 0.6333 (mp10) cc_final: 0.5220 (mt0) REVERT: C 15 LEU cc_start: 0.7656 (mp) cc_final: 0.7328 (tp) REVERT: C 32 LYS cc_start: 0.7853 (ptmt) cc_final: 0.7531 (ttpp) REVERT: E 18 ARG cc_start: 0.7527 (tpp-160) cc_final: 0.7221 (tpp-160) REVERT: E 39 GLN cc_start: 0.8093 (tp40) cc_final: 0.7735 (tp40) REVERT: E 73 ASP cc_start: 0.7168 (t0) cc_final: 0.6940 (t0) REVERT: E 83 MET cc_start: 0.8234 (mtm) cc_final: 0.7830 (ttm) REVERT: E 162 SER cc_start: 0.8659 (m) cc_final: 0.8386 (p) REVERT: E 197 SER cc_start: 0.9299 (m) cc_final: 0.8842 (p) REVERT: E 220 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6240 (mp0) REVERT: E 234 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7327 (mm-30) REVERT: R 52 ASN cc_start: 0.7404 (m-40) cc_final: 0.7201 (m-40) REVERT: R 140 MET cc_start: 0.8146 (mmm) cc_final: 0.7608 (mmm) REVERT: R 369 LYS cc_start: 0.6275 (mmmt) cc_final: 0.5563 (tptt) outliers start: 20 outliers final: 17 residues processed: 188 average time/residue: 0.2608 time to fit residues: 64.6870 Evaluate side-chains 189 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 219 ARG Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 0.0470 chunk 109 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9141 Z= 0.174 Angle : 0.583 11.066 12401 Z= 0.303 Chirality : 0.043 0.215 1419 Planarity : 0.003 0.029 1557 Dihedral : 4.999 54.745 1312 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.94 % Allowed : 21.02 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1121 helix: 1.15 (0.27), residues: 382 sheet: 0.51 (0.29), residues: 292 loop : -0.10 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.003 0.001 HIS R 393 PHE 0.028 0.001 PHE R 390 TYR 0.035 0.001 TYR A 230 ARG 0.010 0.000 ARG C 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7964 (tt0) cc_final: 0.7656 (tt0) REVERT: A 197 LYS cc_start: 0.8558 (mttt) cc_final: 0.8215 (mttp) REVERT: A 228 SER cc_start: 0.8266 (p) cc_final: 0.7937 (t) REVERT: A 248 LYS cc_start: 0.8805 (mttt) cc_final: 0.8581 (tttm) REVERT: B 67 SER cc_start: 0.9323 (OUTLIER) cc_final: 0.8698 (t) REVERT: B 76 ASP cc_start: 0.6937 (t0) cc_final: 0.6627 (t0) REVERT: B 254 ASP cc_start: 0.7818 (m-30) cc_final: 0.7290 (m-30) REVERT: C 11 GLN cc_start: 0.6365 (mp10) cc_final: 0.5330 (mt0) REVERT: C 13 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.6929 (ptp90) REVERT: C 15 LEU cc_start: 0.7651 (mp) cc_final: 0.7384 (tp) REVERT: E 18 ARG cc_start: 0.7497 (tpp-160) cc_final: 0.7096 (tpp-160) REVERT: E 39 GLN cc_start: 0.8065 (tp40) cc_final: 0.7699 (tp40) REVERT: E 73 ASP cc_start: 0.7175 (t0) cc_final: 0.6959 (t0) REVERT: E 162 SER cc_start: 0.8645 (m) cc_final: 0.8370 (p) REVERT: E 197 SER cc_start: 0.9257 (m) cc_final: 0.8807 (p) REVERT: E 220 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6249 (mp0) REVERT: R 217 ARG cc_start: 0.7008 (mmp-170) cc_final: 0.6714 (ttp-170) REVERT: R 369 LYS cc_start: 0.6288 (mmmt) cc_final: 0.5704 (tptt) outliers start: 19 outliers final: 16 residues processed: 189 average time/residue: 0.2536 time to fit residues: 63.1669 Evaluate side-chains 187 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 219 ARG Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 408 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.153135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.120216 restraints weight = 11988.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121756 restraints weight = 10542.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122748 restraints weight = 8616.033| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9141 Z= 0.200 Angle : 0.597 10.774 12401 Z= 0.310 Chirality : 0.044 0.206 1419 Planarity : 0.003 0.031 1557 Dihedral : 5.023 54.759 1312 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.35 % Allowed : 20.71 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.60 (0.26), residues: 1121 helix: 1.11 (0.27), residues: 384 sheet: 0.46 (0.29), residues: 290 loop : -0.15 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.017 0.001 PHE R 390 TYR 0.021 0.001 TYR A 230 ARG 0.009 0.000 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2244.57 seconds wall clock time: 42 minutes 31.72 seconds (2551.72 seconds total)