Starting phenix.real_space_refine on Thu Mar 14 20:22:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/03_2024/8haf_34587_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/03_2024/8haf_34587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/03_2024/8haf_34587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/03_2024/8haf_34587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/03_2024/8haf_34587_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/03_2024/8haf_34587_updated.pdb" } resolution = 3.25 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= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6258 2.51 5 N 1635 2.21 5 O 1730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "P GLU 4": "OE1" <-> "OE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 113": "OD1" <-> "OD2" Residue "R ASP 137": "OD1" <-> "OD2" Residue "R PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9681 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "P" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 301 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "R" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3395 Unusual residues: {'CLR': 6, 'PLM': 11} Classifications: {'peptide': 369, 'undetermined': 17} Link IDs: {'PTRANS': 11, 'TRANS': 357, None: 17} Not linked: pdbres="LEU R 481 " pdbres="PLM R1501 " Not linked: pdbres="PLM R1501 " pdbres="PLM R1502 " Not linked: pdbres="PLM R1502 " pdbres="PLM R1503 " Not linked: pdbres="PLM R1503 " pdbres="PLM R1504 " Not linked: pdbres="PLM R1504 " pdbres="PLM R1505 " ... (remaining 12 not shown) Chain breaks: 3 Time building chain proxies: 5.54, per 1000 atoms: 0.57 Number of scatterers: 9681 At special positions: 0 Unit cell: (103.824, 130.192, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1730 8.00 N 1635 7.00 C 6258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.6 seconds 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 38.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.267A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 236 through 240 removed outlier: 4.311A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.553A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.539A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.659A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'P' and resid 6 through 31 Processing helix chain 'P' and resid 33 through 35 No H-bonds generated for 'chain 'P' and resid 33 through 35' Processing helix chain 'R' and resid 34 through 52 removed outlier: 3.596A pdb=" N PHE R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 171 removed outlier: 3.576A pdb=" N CYS R 170 " --> pdb=" O TYR R 167 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL R 171 " --> pdb=" O SER R 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 167 through 171' Processing helix chain 'R' and resid 179 through 211 Processing helix chain 'R' and resid 218 through 243 removed outlier: 3.735A pdb=" N ALA R 242 " --> pdb=" O PHE R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 311 removed outlier: 3.653A pdb=" N GLY R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 346 removed outlier: 3.846A pdb=" N LEU R 321 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP R 322 " --> pdb=" O LYS R 319 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY R 330 " --> pdb=" O PHE R 327 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU R 331 " --> pdb=" O GLY R 328 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.951A pdb=" N LEU R 346 " --> pdb=" O ARG R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 392 removed outlier: 3.781A pdb=" N GLN R 364 " --> pdb=" O TRP R 361 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL R 365 " --> pdb=" O ILE R 362 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 3.528A pdb=" N SER R 370 " --> pdb=" O ILE R 367 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR R 392 " --> pdb=" O LEU R 389 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 414 removed outlier: 3.769A pdb=" N ARG R 404 " --> pdb=" O ARG R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 459 removed outlier: 4.088A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 464 through 480 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.635A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 243 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.000A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.548A 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: 6.848A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.714A 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: 6.923A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.566A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.632A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.149A 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: 6.525A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.916A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.526A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 17 through 23 419 hydrogen bonds defined for protein. 1041 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: 2.86 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3073 1.35 - 1.46: 2394 1.46 - 1.58: 4348 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9897 Sorted by residual: bond pdb=" C1 PLM R1507 " pdb=" C2 PLM R1507 " ideal model delta sigma weight residual 1.542 1.573 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 PLM R1501 " pdb=" C2 PLM R1501 " ideal model delta sigma weight residual 1.542 1.572 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 PLM R1511 " pdb=" C2 PLM R1511 " ideal model delta sigma weight residual 1.542 1.571 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 PLM R1504 " pdb=" C2 PLM R1504 " ideal model delta sigma weight residual 1.542 1.571 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 PLM R1503 " pdb=" C2 PLM R1503 " ideal model delta sigma weight residual 1.542 1.571 -0.029 2.00e-02 2.50e+03 2.05e+00 ... (remaining 9892 not shown) Histogram of bond angle deviations from ideal: 77.79 - 89.03: 2 89.03 - 100.28: 6 100.28 - 111.52: 4477 111.52 - 122.77: 7926 122.77 - 134.01: 958 Bond angle restraints: 13369 Sorted by residual: angle pdb=" C17 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C18 CLR R1515 " ideal model delta sigma weight residual 110.18 77.79 32.39 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C12 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C18 CLR R1515 " ideal model delta sigma weight residual 111.01 78.96 32.05 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C4 CLR R1512 " pdb=" C3 CLR R1512 " pdb=" O1 CLR R1512 " ideal model delta sigma weight residual 111.96 130.39 -18.43 3.00e+00 1.11e-01 3.77e+01 angle pdb=" C12 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C17 CLR R1515 " ideal model delta sigma weight residual 116.52 133.93 -17.41 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C14 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C18 CLR R1515 " ideal model delta sigma weight residual 112.24 95.10 17.14 3.00e+00 1.11e-01 3.27e+01 ... (remaining 13364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 5993 35.92 - 71.83: 176 71.83 - 107.75: 2 107.75 - 143.67: 2 143.67 - 179.58: 5 Dihedral angle restraints: 6178 sinusoidal: 2782 harmonic: 3396 Sorted by residual: dihedral pdb=" CB CYS R 131 " pdb=" SG CYS R 131 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 153.39 -60.39 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" C18 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C14 CLR R1515 " pdb=" C8 CLR R1515 " ideal model delta sinusoidal sigma weight residual 62.65 -116.93 179.58 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C15 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C14 CLR R1515 " pdb=" C18 CLR R1515 " ideal model delta sinusoidal sigma weight residual 69.18 -111.99 -178.83 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 6175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 1468 0.349 - 0.699: 1 0.699 - 1.048: 1 1.048 - 1.397: 0 1.397 - 1.746: 1 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C13 CLR R1515 " pdb=" C12 CLR R1515 " pdb=" C14 CLR R1515 " pdb=" C17 CLR R1515 " both_signs ideal model delta sigma weight residual False -2.93 -1.19 -1.75 2.00e-01 2.50e+01 7.62e+01 chirality pdb=" C3 CLR R1512 " pdb=" C2 CLR R1512 " pdb=" C4 CLR R1512 " pdb=" O1 CLR R1512 " both_signs ideal model delta sigma weight residual False -2.46 -1.41 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" C3 CLR R1515 " pdb=" C2 CLR R1515 " pdb=" C4 CLR R1515 " pdb=" O1 CLR R1515 " both_signs ideal model delta sigma weight residual False -2.46 -3.00 0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 1468 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 164 " -0.024 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP R 164 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP R 164 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP R 164 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 164 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 164 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 164 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 164 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 164 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP R 164 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 137 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C ASP R 137 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP R 137 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE R 138 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG P 21 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C ARG P 21 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG P 21 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE P 22 " -0.013 2.00e-02 2.50e+03 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 8 2.32 - 2.96: 4455 2.96 - 3.61: 13900 3.61 - 4.25: 21109 4.25 - 4.90: 36195 Nonbonded interactions: 75667 Sorted by model distance: nonbonded pdb=" O1 CLR R1512 " pdb=" O1 CLR R1515 " model vdw 1.671 2.432 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.043 2.440 nonbonded pdb=" O1 CLR R1512 " pdb=" C2 CLR R1515 " model vdw 2.061 2.752 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.170 2.440 nonbonded pdb=" C4 CLR R1512 " pdb=" O1 CLR R1515 " model vdw 2.236 2.752 ... (remaining 75662 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 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: 1.140 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: 5.880 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.890 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9897 Z= 0.199 Angle : 0.821 32.394 13369 Z= 0.376 Chirality : 0.068 1.746 1471 Planarity : 0.004 0.052 1652 Dihedral : 16.056 179.584 3972 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.40 % Allowed : 17.96 % Favored : 81.64 % 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: 0.83 (0.26), residues: 1147 helix: 2.05 (0.25), residues: 460 sheet: 0.92 (0.42), residues: 175 loop : -1.03 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP R 164 HIS 0.004 0.001 HIS R 420 PHE 0.017 0.001 PHE R 39 TYR 0.032 0.001 TYR R 191 ARG 0.012 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 215 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6267 (tmm) cc_final: 0.5877 (tmm) REVERT: A 208 PHE cc_start: 0.8405 (m-80) cc_final: 0.8202 (m-80) REVERT: A 211 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7885 (mttt) REVERT: A 283 ARG cc_start: 0.7362 (ptt180) cc_final: 0.6982 (ptp-170) REVERT: A 342 ARG cc_start: 0.7316 (ttp-170) cc_final: 0.7096 (ttt-90) REVERT: B 188 MET cc_start: 0.7690 (mmm) cc_final: 0.7372 (mmm) REVERT: B 217 MET cc_start: 0.6992 (ppp) cc_final: 0.6234 (ppp) REVERT: B 289 TYR cc_start: 0.7813 (m-80) cc_final: 0.6921 (m-80) REVERT: B 295 ASN cc_start: 0.8242 (m-40) cc_final: 0.8003 (m-40) REVERT: N 34 MET cc_start: 0.8015 (mmm) cc_final: 0.7501 (mmm) REVERT: N 49 SER cc_start: 0.8222 (p) cc_final: 0.7787 (t) REVERT: R 240 LYS cc_start: 0.7317 (tmmt) cc_final: 0.7086 (ttpt) REVERT: R 342 VAL cc_start: 0.7439 (t) cc_final: 0.7113 (p) REVERT: R 404 ARG cc_start: 0.7230 (mtt90) cc_final: 0.7021 (mtt90) REVERT: R 413 LEU cc_start: 0.7112 (tp) cc_final: 0.6834 (tp) outliers start: 4 outliers final: 3 residues processed: 217 average time/residue: 0.2816 time to fit residues: 78.7329 Evaluate side-chains 192 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 135 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 271 ASN A 362 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 220 GLN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9897 Z= 0.259 Angle : 0.789 32.636 13369 Z= 0.346 Chirality : 0.068 1.661 1471 Planarity : 0.005 0.043 1652 Dihedral : 12.687 179.827 1833 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.10 % Allowed : 16.77 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1147 helix: 2.01 (0.25), residues: 452 sheet: 0.64 (0.37), residues: 206 loop : -1.01 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 164 HIS 0.005 0.001 HIS A 220 PHE 0.020 0.002 PHE R 335 TYR 0.025 0.002 TYR R 191 ARG 0.007 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6342 (tmm) cc_final: 0.5947 (tmm) REVERT: A 51 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7282 (mtmm) REVERT: A 314 GLU cc_start: 0.7087 (mp0) cc_final: 0.6814 (mp0) REVERT: B 55 LEU cc_start: 0.8325 (mt) cc_final: 0.8122 (mp) REVERT: B 78 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8049 (mtmm) REVERT: B 111 TYR cc_start: 0.8336 (m-80) cc_final: 0.7975 (m-80) REVERT: B 188 MET cc_start: 0.7941 (mmm) cc_final: 0.7656 (mmm) REVERT: B 217 MET cc_start: 0.7275 (ppp) cc_final: 0.6472 (ppp) REVERT: B 262 MET cc_start: 0.7512 (pmm) cc_final: 0.6835 (pmm) REVERT: B 289 TYR cc_start: 0.8188 (m-80) cc_final: 0.7742 (m-80) REVERT: B 316 SER cc_start: 0.8022 (t) cc_final: 0.7784 (p) REVERT: B 317 CYS cc_start: 0.8117 (p) cc_final: 0.7841 (p) REVERT: N 38 ARG cc_start: 0.8428 (ptt90) cc_final: 0.8105 (ptt180) REVERT: N 108 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: R 36 GLU cc_start: 0.7046 (tp30) cc_final: 0.6837 (tp30) REVERT: R 181 ARG cc_start: 0.7089 (mmm-85) cc_final: 0.6664 (mmm-85) REVERT: R 295 ASN cc_start: 0.8199 (t0) cc_final: 0.7998 (t0) REVERT: R 309 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7408 (tp) REVERT: R 360 LYS cc_start: 0.7773 (ttpp) cc_final: 0.7572 (ptpp) REVERT: R 404 ARG cc_start: 0.7232 (mtt90) cc_final: 0.7028 (mtt90) REVERT: R 431 GLU cc_start: 0.6783 (mp0) cc_final: 0.6537 (mp0) outliers start: 21 outliers final: 11 residues processed: 200 average time/residue: 0.2684 time to fit residues: 70.1544 Evaluate side-chains 201 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 186 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 362 HIS N 84 ASN R 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9897 Z= 0.199 Angle : 0.740 32.521 13369 Z= 0.319 Chirality : 0.068 1.685 1471 Planarity : 0.004 0.037 1652 Dihedral : 12.207 178.449 1824 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.79 % Allowed : 18.26 % Favored : 78.94 % 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 (0.25), residues: 1147 helix: 1.79 (0.25), residues: 449 sheet: 0.65 (0.36), residues: 207 loop : -0.94 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 362 PHE 0.015 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.006 0.000 ARG R 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6303 (tmm) cc_final: 0.5894 (tmm) REVERT: A 280 ARG cc_start: 0.7174 (ttm-80) cc_final: 0.6959 (ttm-80) REVERT: A 314 GLU cc_start: 0.7090 (mp0) cc_final: 0.6742 (mp0) REVERT: A 346 LEU cc_start: 0.6644 (mt) cc_final: 0.6326 (mt) REVERT: B 78 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7981 (mtmm) REVERT: B 84 SER cc_start: 0.7961 (m) cc_final: 0.7682 (p) REVERT: B 111 TYR cc_start: 0.8432 (m-80) cc_final: 0.8098 (m-80) REVERT: B 188 MET cc_start: 0.7972 (mmm) cc_final: 0.7762 (mmm) REVERT: B 200 VAL cc_start: 0.8412 (m) cc_final: 0.8056 (p) REVERT: B 217 MET cc_start: 0.7401 (ppp) cc_final: 0.6610 (ppp) REVERT: B 275 SER cc_start: 0.7995 (t) cc_final: 0.7695 (t) REVERT: B 289 TYR cc_start: 0.8367 (m-80) cc_final: 0.7960 (m-80) REVERT: B 316 SER cc_start: 0.8073 (t) cc_final: 0.7746 (p) REVERT: B 317 CYS cc_start: 0.8015 (p) cc_final: 0.7737 (p) REVERT: N 13 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: N 87 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8069 (mttp) REVERT: N 108 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: R 36 GLU cc_start: 0.7114 (tp30) cc_final: 0.6910 (tp30) REVERT: R 181 ARG cc_start: 0.7033 (mmm-85) cc_final: 0.6610 (mmm-85) REVERT: R 312 MET cc_start: 0.6664 (tmm) cc_final: 0.6429 (tmm) REVERT: R 360 LYS cc_start: 0.7787 (ttpp) cc_final: 0.7350 (pttp) outliers start: 28 outliers final: 11 residues processed: 218 average time/residue: 0.2818 time to fit residues: 79.7292 Evaluate side-chains 201 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 186 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 92 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9897 Z= 0.197 Angle : 0.734 32.307 13369 Z= 0.313 Chirality : 0.068 1.708 1471 Planarity : 0.004 0.034 1652 Dihedral : 12.052 176.607 1824 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.50 % Allowed : 19.56 % Favored : 77.94 % 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: 0.60 (0.25), residues: 1147 helix: 1.69 (0.25), residues: 450 sheet: 0.65 (0.36), residues: 209 loop : -0.96 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.005 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6278 (tmm) cc_final: 0.5919 (tmm) REVERT: A 280 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.6944 (ttm-80) REVERT: A 314 GLU cc_start: 0.7063 (mp0) cc_final: 0.6677 (mp0) REVERT: A 344 GLU cc_start: 0.7501 (tp30) cc_final: 0.6786 (tp30) REVERT: B 78 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7950 (mtmm) REVERT: B 84 SER cc_start: 0.7879 (OUTLIER) cc_final: 0.7654 (p) REVERT: B 212 ASP cc_start: 0.7647 (t0) cc_final: 0.7377 (t70) REVERT: B 217 MET cc_start: 0.7433 (ppp) cc_final: 0.6613 (ppp) REVERT: B 275 SER cc_start: 0.7963 (t) cc_final: 0.7691 (t) REVERT: B 289 TYR cc_start: 0.8445 (m-80) cc_final: 0.8140 (m-80) REVERT: B 298 ASP cc_start: 0.7306 (t0) cc_final: 0.6819 (t0) REVERT: B 316 SER cc_start: 0.8119 (t) cc_final: 0.7743 (p) REVERT: B 317 CYS cc_start: 0.8017 (p) cc_final: 0.7688 (p) REVERT: N 13 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: N 87 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8119 (mttp) REVERT: N 108 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7135 (m-80) REVERT: R 181 ARG cc_start: 0.7018 (mmm-85) cc_final: 0.6608 (mmm-85) REVERT: R 312 MET cc_start: 0.6668 (tmm) cc_final: 0.6378 (tmm) REVERT: R 360 LYS cc_start: 0.7701 (ttpp) cc_final: 0.7429 (ptpp) outliers start: 25 outliers final: 17 residues processed: 206 average time/residue: 0.2877 time to fit residues: 77.3411 Evaluate side-chains 208 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 9897 Z= 0.468 Angle : 0.832 32.290 13369 Z= 0.374 Chirality : 0.072 1.709 1471 Planarity : 0.004 0.033 1652 Dihedral : 12.221 176.548 1824 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.99 % Allowed : 20.36 % Favored : 75.65 % 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: 0.23 (0.25), residues: 1147 helix: 1.43 (0.25), residues: 434 sheet: 0.46 (0.34), residues: 220 loop : -1.17 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 329 HIS 0.006 0.001 HIS B 54 PHE 0.030 0.003 PHE R 335 TYR 0.027 0.002 TYR R 191 ARG 0.006 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6343 (tmm) cc_final: 0.5900 (tmm) REVERT: A 314 GLU cc_start: 0.7147 (mp0) cc_final: 0.6696 (mp0) REVERT: A 344 GLU cc_start: 0.7798 (tp30) cc_final: 0.7133 (tp30) REVERT: B 111 TYR cc_start: 0.8444 (m-80) cc_final: 0.7992 (m-80) REVERT: B 112 VAL cc_start: 0.8003 (t) cc_final: 0.7790 (p) REVERT: B 155 ASN cc_start: 0.6039 (m-40) cc_final: 0.5818 (t0) REVERT: B 171 ILE cc_start: 0.6530 (mm) cc_final: 0.6320 (mm) REVERT: B 217 MET cc_start: 0.7484 (ppp) cc_final: 0.6586 (ppp) REVERT: B 219 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7265 (mtt-85) REVERT: B 275 SER cc_start: 0.8069 (t) cc_final: 0.7805 (t) REVERT: B 289 TYR cc_start: 0.8658 (m-80) cc_final: 0.8351 (m-80) REVERT: B 298 ASP cc_start: 0.7461 (t0) cc_final: 0.7247 (t0) REVERT: B 316 SER cc_start: 0.8091 (t) cc_final: 0.7620 (p) REVERT: B 317 CYS cc_start: 0.7857 (p) cc_final: 0.7628 (p) REVERT: N 13 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: N 87 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8043 (mttp) REVERT: N 108 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: R 35 GLU cc_start: 0.7465 (mp0) cc_final: 0.6858 (mp0) REVERT: R 181 ARG cc_start: 0.7168 (mmm-85) cc_final: 0.6752 (mmm-85) REVERT: R 233 ARG cc_start: 0.7656 (ttp-170) cc_final: 0.7325 (ttt180) REVERT: R 312 MET cc_start: 0.6812 (tmm) cc_final: 0.6587 (tmm) REVERT: R 360 LYS cc_start: 0.7748 (ttpp) cc_final: 0.7516 (pttm) outliers start: 40 outliers final: 27 residues processed: 223 average time/residue: 0.2622 time to fit residues: 76.9015 Evaluate side-chains 219 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9897 Z= 0.271 Angle : 0.769 32.273 13369 Z= 0.334 Chirality : 0.069 1.711 1471 Planarity : 0.004 0.032 1652 Dihedral : 12.094 176.446 1824 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.79 % Allowed : 20.56 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1147 helix: 1.64 (0.25), residues: 434 sheet: 0.52 (0.34), residues: 215 loop : -1.18 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 329 HIS 0.004 0.001 HIS B 54 PHE 0.016 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.006 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 196 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6293 (tmm) cc_final: 0.5859 (tmm) REVERT: A 314 GLU cc_start: 0.7130 (mp0) cc_final: 0.6685 (mp0) REVERT: A 344 GLU cc_start: 0.7733 (tp30) cc_final: 0.7110 (tp30) REVERT: B 112 VAL cc_start: 0.8017 (t) cc_final: 0.7777 (p) REVERT: B 217 MET cc_start: 0.7516 (ppp) cc_final: 0.6631 (ppp) REVERT: B 219 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7217 (mtt-85) REVERT: B 275 SER cc_start: 0.8015 (t) cc_final: 0.7770 (t) REVERT: B 289 TYR cc_start: 0.8625 (m-80) cc_final: 0.8208 (m-80) REVERT: B 312 ASP cc_start: 0.6883 (t0) cc_final: 0.6678 (t0) REVERT: B 316 SER cc_start: 0.8137 (t) cc_final: 0.7673 (p) REVERT: B 317 CYS cc_start: 0.7948 (p) cc_final: 0.7668 (p) REVERT: B 327 VAL cc_start: 0.8270 (t) cc_final: 0.7991 (p) REVERT: N 13 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7725 (mp10) REVERT: N 87 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8082 (mttp) REVERT: N 108 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7207 (m-80) REVERT: R 35 GLU cc_start: 0.7475 (mp0) cc_final: 0.6827 (mp0) REVERT: R 181 ARG cc_start: 0.7038 (mmm-85) cc_final: 0.6627 (mmm-85) REVERT: R 312 MET cc_start: 0.6802 (tmm) cc_final: 0.6554 (tmm) REVERT: R 414 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7320 (mtp) REVERT: R 444 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7078 (mm-30) outliers start: 38 outliers final: 23 residues processed: 218 average time/residue: 0.2725 time to fit residues: 77.7905 Evaluate side-chains 213 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.0370 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 0.1980 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9897 Z= 0.209 Angle : 0.747 32.226 13369 Z= 0.319 Chirality : 0.069 1.718 1471 Planarity : 0.004 0.032 1652 Dihedral : 11.988 176.283 1824 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.79 % Allowed : 21.26 % Favored : 74.95 % 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 (0.25), residues: 1147 helix: 1.78 (0.25), residues: 434 sheet: 0.60 (0.34), residues: 216 loop : -1.16 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE R 335 TYR 0.021 0.001 TYR R 191 ARG 0.006 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 188 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6219 (tmm) cc_final: 0.5823 (tmm) REVERT: A 314 GLU cc_start: 0.7165 (mp0) cc_final: 0.6729 (mp0) REVERT: A 344 GLU cc_start: 0.7675 (tp30) cc_final: 0.7087 (tp30) REVERT: B 78 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7923 (mtmm) REVERT: B 111 TYR cc_start: 0.8440 (m-80) cc_final: 0.8022 (m-80) REVERT: B 155 ASN cc_start: 0.7039 (t0) cc_final: 0.6738 (t0) REVERT: B 212 ASP cc_start: 0.7894 (t0) cc_final: 0.7630 (t70) REVERT: B 217 MET cc_start: 0.7425 (ppp) cc_final: 0.6595 (ppp) REVERT: B 219 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7192 (mtt-85) REVERT: B 275 SER cc_start: 0.8026 (t) cc_final: 0.7766 (t) REVERT: B 289 TYR cc_start: 0.8592 (m-80) cc_final: 0.8175 (m-80) REVERT: B 316 SER cc_start: 0.8133 (t) cc_final: 0.7687 (p) REVERT: B 317 CYS cc_start: 0.7981 (p) cc_final: 0.7705 (p) REVERT: B 325 MET cc_start: 0.8001 (tpp) cc_final: 0.7712 (tpp) REVERT: B 327 VAL cc_start: 0.8260 (t) cc_final: 0.7977 (p) REVERT: N 13 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: N 87 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8107 (mttp) REVERT: N 108 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7162 (m-80) REVERT: R 35 GLU cc_start: 0.7484 (mp0) cc_final: 0.6802 (mp0) REVERT: R 181 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6621 (mmm-85) REVERT: R 312 MET cc_start: 0.6766 (tmm) cc_final: 0.6504 (tmm) REVERT: R 414 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7328 (mtp) REVERT: R 444 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7026 (mm-30) outliers start: 38 outliers final: 26 residues processed: 210 average time/residue: 0.2754 time to fit residues: 75.5447 Evaluate side-chains 217 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9897 Z= 0.240 Angle : 0.754 32.194 13369 Z= 0.324 Chirality : 0.069 1.722 1471 Planarity : 0.004 0.032 1652 Dihedral : 11.952 176.418 1824 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.29 % Allowed : 21.36 % Favored : 74.35 % 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: 0.48 (0.25), residues: 1147 helix: 1.78 (0.25), residues: 434 sheet: 0.67 (0.34), residues: 214 loop : -1.19 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS B 54 PHE 0.013 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.006 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 184 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6225 (tmm) cc_final: 0.5828 (tmm) REVERT: A 309 GLU cc_start: 0.7716 (mp0) cc_final: 0.7242 (mp0) REVERT: A 314 GLU cc_start: 0.7169 (mp0) cc_final: 0.6734 (mp0) REVERT: A 344 GLU cc_start: 0.7690 (tp30) cc_final: 0.7103 (tp30) REVERT: B 155 ASN cc_start: 0.6812 (t0) cc_final: 0.6424 (t0) REVERT: B 217 MET cc_start: 0.7401 (ppp) cc_final: 0.6587 (ppp) REVERT: B 219 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7189 (mtt-85) REVERT: B 275 SER cc_start: 0.8029 (t) cc_final: 0.7766 (t) REVERT: B 289 TYR cc_start: 0.8612 (m-80) cc_final: 0.8249 (m-80) REVERT: B 316 SER cc_start: 0.8134 (t) cc_final: 0.7677 (p) REVERT: B 317 CYS cc_start: 0.7960 (p) cc_final: 0.7674 (p) REVERT: B 325 MET cc_start: 0.7992 (tpp) cc_final: 0.7738 (tpp) REVERT: N 13 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7739 (mp10) REVERT: N 46 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: N 87 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8114 (mttp) REVERT: N 108 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: R 35 GLU cc_start: 0.7491 (mp0) cc_final: 0.6826 (mp0) REVERT: R 181 ARG cc_start: 0.6995 (mmm-85) cc_final: 0.6572 (mmm-85) REVERT: R 312 MET cc_start: 0.6770 (tmm) cc_final: 0.6444 (tmm) REVERT: R 414 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7362 (mtp) REVERT: R 444 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7065 (mm-30) outliers start: 43 outliers final: 27 residues processed: 208 average time/residue: 0.2738 time to fit residues: 74.3815 Evaluate side-chains 217 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 93 optimal weight: 0.0170 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN R 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9897 Z= 0.144 Angle : 0.726 32.173 13369 Z= 0.306 Chirality : 0.068 1.727 1471 Planarity : 0.004 0.034 1652 Dihedral : 11.817 176.566 1824 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.19 % Allowed : 22.65 % Favored : 74.15 % 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 (0.25), residues: 1147 helix: 2.00 (0.26), residues: 433 sheet: 0.76 (0.35), residues: 207 loop : -1.15 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS R 420 PHE 0.010 0.001 PHE R 447 TYR 0.022 0.001 TYR R 191 ARG 0.007 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6214 (tmm) cc_final: 0.5791 (tmm) REVERT: A 309 GLU cc_start: 0.7731 (mp0) cc_final: 0.7265 (mp0) REVERT: A 314 GLU cc_start: 0.7152 (mp0) cc_final: 0.6746 (mp0) REVERT: A 344 GLU cc_start: 0.7567 (tp30) cc_final: 0.6972 (tp30) REVERT: B 78 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7842 (mtmm) REVERT: B 212 ASP cc_start: 0.7846 (t0) cc_final: 0.7632 (t70) REVERT: B 217 MET cc_start: 0.7407 (ppp) cc_final: 0.6589 (ppp) REVERT: B 219 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7140 (mtt-85) REVERT: B 275 SER cc_start: 0.7949 (t) cc_final: 0.7669 (t) REVERT: B 289 TYR cc_start: 0.8548 (m-80) cc_final: 0.8086 (m-80) REVERT: B 316 SER cc_start: 0.8138 (t) cc_final: 0.7720 (p) REVERT: B 317 CYS cc_start: 0.8055 (p) cc_final: 0.7785 (p) REVERT: B 325 MET cc_start: 0.7946 (tpp) cc_final: 0.7665 (tpp) REVERT: N 13 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: N 34 MET cc_start: 0.7976 (mmm) cc_final: 0.7757 (mtp) REVERT: N 46 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: N 87 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8148 (mttp) REVERT: N 108 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6994 (m-80) REVERT: R 35 GLU cc_start: 0.7492 (mp0) cc_final: 0.6802 (mp0) REVERT: R 181 ARG cc_start: 0.6871 (mmm-85) cc_final: 0.6517 (mmm-85) REVERT: R 226 LEU cc_start: 0.7494 (tp) cc_final: 0.7189 (tp) REVERT: R 312 MET cc_start: 0.6722 (tmm) cc_final: 0.6411 (tmm) REVERT: R 444 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7042 (mm-30) outliers start: 32 outliers final: 25 residues processed: 205 average time/residue: 0.2850 time to fit residues: 76.1504 Evaluate side-chains 211 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9897 Z= 0.235 Angle : 0.753 32.164 13369 Z= 0.323 Chirality : 0.069 1.727 1471 Planarity : 0.004 0.033 1652 Dihedral : 11.827 176.713 1824 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.49 % Allowed : 22.95 % Favored : 73.55 % 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: 0.62 (0.25), residues: 1147 helix: 1.93 (0.25), residues: 434 sheet: 0.67 (0.34), residues: 214 loop : -1.12 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS B 54 PHE 0.013 0.002 PHE R 335 TYR 0.022 0.001 TYR R 191 ARG 0.007 0.000 ARG A 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6201 (tmm) cc_final: 0.5809 (tmm) REVERT: A 309 GLU cc_start: 0.7725 (mp0) cc_final: 0.7254 (mp0) REVERT: A 314 GLU cc_start: 0.7163 (mp0) cc_final: 0.6738 (mp0) REVERT: A 344 GLU cc_start: 0.7609 (tp30) cc_final: 0.7053 (tp30) REVERT: B 212 ASP cc_start: 0.7903 (t0) cc_final: 0.7630 (t70) REVERT: B 217 MET cc_start: 0.7423 (ppp) cc_final: 0.6604 (ppp) REVERT: B 219 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7165 (mtt-85) REVERT: B 275 SER cc_start: 0.8091 (t) cc_final: 0.7809 (t) REVERT: B 289 TYR cc_start: 0.8600 (m-80) cc_final: 0.8186 (m-80) REVERT: B 316 SER cc_start: 0.8144 (t) cc_final: 0.7686 (p) REVERT: B 317 CYS cc_start: 0.7963 (p) cc_final: 0.7654 (p) REVERT: B 325 MET cc_start: 0.8003 (tpp) cc_final: 0.7783 (tpp) REVERT: N 13 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: N 46 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: N 87 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8119 (mttp) REVERT: N 108 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7170 (m-80) REVERT: R 35 GLU cc_start: 0.7508 (mp0) cc_final: 0.6871 (mp0) REVERT: R 181 ARG cc_start: 0.6976 (mmm-85) cc_final: 0.6564 (mmm-85) REVERT: R 233 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7645 (ttp80) REVERT: R 312 MET cc_start: 0.6746 (tmm) cc_final: 0.6439 (tmm) REVERT: R 343 ARG cc_start: 0.7299 (tpt-90) cc_final: 0.6821 (tpp80) REVERT: R 444 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7063 (mm-30) outliers start: 35 outliers final: 27 residues processed: 201 average time/residue: 0.2811 time to fit residues: 73.1601 Evaluate side-chains 210 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 0.0050 chunk 5 optimal weight: 0.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115134 restraints weight = 13032.293| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.77 r_work: 0.3294 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9897 Z= 0.188 Angle : 0.739 32.162 13369 Z= 0.315 Chirality : 0.069 1.729 1471 Planarity : 0.004 0.033 1652 Dihedral : 11.782 176.636 1824 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.29 % Allowed : 23.15 % Favored : 73.55 % 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 (0.25), residues: 1147 helix: 2.01 (0.25), residues: 433 sheet: 0.71 (0.35), residues: 209 loop : -1.16 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE B 151 TYR 0.023 0.001 TYR R 191 ARG 0.007 0.000 ARG A 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2578.79 seconds wall clock time: 46 minutes 53.63 seconds (2813.63 seconds total)