Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 12:06:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/04_2023/8haf_34587_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/04_2023/8haf_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_34587/04_2023/8haf_34587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/04_2023/8haf_34587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/04_2023/8haf_34587_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haf_34587/04_2023/8haf_34587_updated.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 7.21, per 1000 atoms: 0.74 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: 4.53 Conformation dependent library (CDL) restraints added in 1.5 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: 0.80 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: 2.84 Time building geometry restraints manager: 4.64 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 - 20.32: 5304 20.32 - 40.64: 441 40.64 - 60.95: 93 60.95 - 81.27: 2 81.27 - 101.59: 2 Dihedral angle restraints: 5842 sinusoidal: 2446 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=" CA PHE R 311 " pdb=" C PHE R 311 " pdb=" N MET R 312 " pdb=" CA MET R 312 " ideal model delta harmonic sigma weight residual 180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C10 CLR R1516 " pdb=" C1 CLR R1516 " pdb=" C2 CLR R1516 " pdb=" C3 CLR R1516 " ideal model delta sinusoidal sigma weight residual -56.83 44.76 -101.59 1 3.00e+01 1.11e-03 1.28e+01 ... (remaining 5839 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: 1.270 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: 6.360 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.370 Find NCS groups from input model: 0.280 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.530 ------------------------------------------------------------------------------- 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 : 14.577 101.588 3636 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 % 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 *********************** 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 : 1.155 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 217 average time/residue: 0.2996 time to fit residues: 83.8427 Evaluate side-chains 191 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 188 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2134 time to fit residues: 2.5103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.0170 chunk 104 optimal weight: 0.5980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 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: 0.7233 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9897 Z= 0.203 Angle : 0.771 32.245 13369 Z= 0.335 Chirality : 0.070 1.774 1471 Planarity : 0.005 0.043 1652 Dihedral : 8.259 103.771 1488 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 2.40 % 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: 0.80 (0.25), residues: 1147 helix: 1.95 (0.24), residues: 453 sheet: 0.84 (0.37), residues: 210 loop : -1.02 (0.28), residues: 484 *********************** 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 217 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 1.126 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 208 average time/residue: 0.2610 time to fit residues: 72.1552 Evaluate side-chains 194 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0905 time to fit residues: 3.4895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 125 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 9897 Z= 0.279 Angle : 0.775 32.063 13369 Z= 0.341 Chirality : 0.071 1.791 1471 Planarity : 0.004 0.041 1652 Dihedral : 8.257 105.052 1488 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 2.20 % 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: 0.47 (0.25), residues: 1147 helix: 1.61 (0.25), residues: 450 sheet: 0.55 (0.37), residues: 208 loop : -1.04 (0.27), residues: 489 *********************** 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 222 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 1.069 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 212 average time/residue: 0.2747 time to fit residues: 77.2403 Evaluate side-chains 199 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1461 time to fit residues: 4.5992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 chunk 111 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 9897 Z= 0.252 Angle : 0.754 31.928 13369 Z= 0.328 Chirality : 0.071 1.805 1471 Planarity : 0.004 0.035 1652 Dihedral : 8.050 105.278 1488 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.60 % 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: 0.47 (0.25), residues: 1147 helix: 1.60 (0.25), residues: 446 sheet: 0.61 (0.35), residues: 211 loop : -1.06 (0.27), residues: 490 *********************** 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 195 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.093 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 188 average time/residue: 0.2701 time to fit residues: 67.3795 Evaluate side-chains 181 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0979 time to fit residues: 3.3453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 125 ASN G 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 9897 Z= 0.279 Angle : 0.770 31.852 13369 Z= 0.336 Chirality : 0.072 1.809 1471 Planarity : 0.004 0.036 1652 Dihedral : 7.982 105.580 1488 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.60 % 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: 0.41 (0.25), residues: 1147 helix: 1.61 (0.25), residues: 440 sheet: 0.65 (0.35), residues: 206 loop : -1.14 (0.27), residues: 501 *********************** 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 207 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 1.080 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 200 average time/residue: 0.2971 time to fit residues: 77.2070 Evaluate side-chains 193 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0976 time to fit residues: 2.9223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 9897 Z= 0.251 Angle : 0.755 31.721 13369 Z= 0.329 Chirality : 0.072 1.819 1471 Planarity : 0.004 0.036 1652 Dihedral : 7.935 105.742 1488 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1147 helix: 1.61 (0.25), residues: 446 sheet: 0.73 (0.35), residues: 204 loop : -1.13 (0.27), residues: 497 *********************** 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 205 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 1.085 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 197 average time/residue: 0.2937 time to fit residues: 75.5091 Evaluate side-chains 186 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 177 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0953 time to fit residues: 3.1728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 0.0470 chunk 81 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 0.0670 chunk 110 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- 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: 0.7342 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9897 Z= 0.200 Angle : 0.738 31.498 13369 Z= 0.318 Chirality : 0.071 1.835 1471 Planarity : 0.004 0.035 1652 Dihedral : 7.810 105.851 1488 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.70 % 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: 0.55 (0.25), residues: 1147 helix: 1.72 (0.25), residues: 445 sheet: 0.74 (0.36), residues: 204 loop : -1.08 (0.27), residues: 498 *********************** 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 202 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 185 time to evaluate : 1.078 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 197 average time/residue: 0.2851 time to fit residues: 73.3388 Evaluate side-chains 188 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 185 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1015 time to fit residues: 2.2165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7356 moved from start: 0.3669 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 31.366 13369 Z= 0.328 Chirality : 0.072 1.843 1471 Planarity : 0.004 0.041 1652 Dihedral : 7.801 106.078 1488 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1147 helix: 1.69 (0.25), residues: 446 sheet: 0.75 (0.36), residues: 204 loop : -1.09 (0.27), residues: 497 *********************** 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 190 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 180 time to evaluate : 1.163 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 184 average time/residue: 0.2984 time to fit residues: 71.5282 Evaluate side-chains 181 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 176 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0915 time to fit residues: 2.4338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 0.0870 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 0.0970 chunk 102 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN R 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3678 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= 0.173 Angle : 0.734 31.262 13369 Z= 0.315 Chirality : 0.071 1.851 1471 Planarity : 0.004 0.036 1652 Dihedral : 7.644 106.139 1488 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1147 helix: 1.85 (0.26), residues: 441 sheet: 0.72 (0.36), residues: 204 loop : -1.05 (0.27), residues: 502 *********************** 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 187 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 1.034 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 182 average time/residue: 0.3128 time to fit residues: 73.5924 Evaluate side-chains 181 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0898 time to fit residues: 2.0157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN R 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9897 Z= 0.228 Angle : 0.752 31.160 13369 Z= 0.325 Chirality : 0.072 1.857 1471 Planarity : 0.004 0.046 1652 Dihedral : 7.655 106.239 1488 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.60 % 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: 0.57 (0.25), residues: 1147 helix: 1.75 (0.26), residues: 446 sheet: 0.74 (0.35), residues: 204 loop : -1.09 (0.27), residues: 497 ********************** 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 191 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 1.157 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 188 average time/residue: 0.3066 time to fit residues: 74.6664 Evaluate side-chains 184 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1009 time to fit residues: 2.0573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.0050 chunk 5 optimal weight: 0.0770 overall best weight: 0.5152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN R 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115070 restraints weight = 13043.594| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.77 r_work: 0.3304 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9897 Z= 0.207 Angle : 0.748 31.069 13369 Z= 0.322 Chirality : 0.072 1.864 1471 Planarity : 0.004 0.041 1652 Dihedral : 7.611 106.265 1488 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.60 % 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: 0.55 (0.25), residues: 1147 helix: 1.74 (0.25), residues: 445 sheet: 0.74 (0.35), residues: 204 loop : -1.10 (0.28), residues: 498 =============================================================================== Job complete usr+sys time: 2497.41 seconds wall clock time: 45 minutes 54.08 seconds (2754.08 seconds total)