Starting phenix.real_space_refine on Sat Jul 4 07:13:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7y_29828/07_2026/8g7y_29828_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7y_29828/07_2026/8g7y_29828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g7y_29828/07_2026/8g7y_29828_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7y_29828/07_2026/8g7y_29828_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g7y_29828/07_2026/8g7y_29828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7y_29828/07_2026/8g7y_29828.map" } resolution = 3.92 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 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= 0.002 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 37 5.16 5 C 6245 2.51 5 N 1680 2.21 5 O 1820 1.98 5 H 9311 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19094 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 8228 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 35, 'TRANS': 507} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 8189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8189 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 35, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2606 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.51, per 1000 atoms: 0.18 Number of scatterers: 19094 At special positions: 0 Unit cell: (91.3, 124.5, 123.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 37 16.00 O 1820 8.00 N 1680 7.00 C 6245 6.00 H 9311 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 521 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 98 " " NAG A 902 " - " ASN A 522 " " NAG B 901 " - " ASN B 98 " " NAG B 902 " - " ASN B 522 " " NAG C 502 " - " ASN C 184 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 710.4 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 7 sheets defined 38.9% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.557A pdb=" N TYR A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 232 through 247 removed outlier: 3.559A pdb=" N LEU A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.548A pdb=" N LEU A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.601A pdb=" N LEU A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 392 through 397 removed outlier: 4.288A pdb=" N GLU A 396 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.563A pdb=" N ASP A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.585A pdb=" N ARG A 441 " --> pdb=" O TRP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 removed outlier: 3.840A pdb=" N LYS A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 474 removed outlier: 3.540A pdb=" N TYR A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 509 through 514 removed outlier: 3.703A pdb=" N VAL A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 544 Processing helix chain 'A' and resid 594 through 603 removed outlier: 3.545A pdb=" N PHE A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 removed outlier: 4.165A pdb=" N HIS A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 603 through 608' Processing helix chain 'B' and resid 115 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.532A pdb=" N PHE B 196 " --> pdb=" O GLY B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 206 removed outlier: 3.735A pdb=" N ALA B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.842A pdb=" N LEU B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 249 Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 265 through 277 removed outlier: 3.526A pdb=" N LEU B 276 " --> pdb=" O ASN B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 316 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'B' and resid 333 through 339 Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.624A pdb=" N GLN B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 removed outlier: 3.991A pdb=" N GLU B 396 " --> pdb=" O ASP B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.561A pdb=" N ASP B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.835A pdb=" N ASP B 440 " --> pdb=" O ASP B 437 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 441 " --> pdb=" O TRP B 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 437 through 441' Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 460 through 474 Processing helix chain 'B' and resid 502 through 508 removed outlier: 4.633A pdb=" N TYR B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 524 through 545 removed outlier: 3.721A pdb=" N THR B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 603 Processing helix chain 'B' and resid 603 through 608 removed outlier: 3.637A pdb=" N HIS B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 4.040A pdb=" N ARG C 105 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 7.040A pdb=" N ARG A 50 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 73 removed outlier: 3.788A pdb=" N GLY A 71 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU A 144 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 209 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A 212 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS A 177 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLU A 257 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL A 179 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A 259 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 181 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A 261 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 183 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY A 263 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS A 286 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 259 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE A 288 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 261 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 378 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N TYR A 481 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 380 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE A 483 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 382 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N LEU A 581 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE A 480 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE A 583 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N THR A 482 " --> pdb=" O ILE A 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 46 removed outlier: 6.961A pdb=" N ARG B 50 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 54 through 56 Processing sheet with id=AA5, first strand: chain 'B' and resid 72 through 73 removed outlier: 4.768A pdb=" N LEU B 212 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS B 177 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU B 257 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL B 179 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE B 259 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU B 181 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE B 261 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU B 183 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY B 263 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS B 286 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 259 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ILE B 288 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 261 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLN B 290 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY B 263 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 381 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 382 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N LEU B 581 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE B 480 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 583 " --> pdb=" O PHE B 480 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N THR B 482 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG B 590 " --> pdb=" O TYR B 580 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 195 through 197 removed outlier: 6.236A pdb=" N ARG C 112 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR C 263 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA C 114 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C 261 " --> pdb=" O ALA C 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 159 through 162 removed outlier: 6.717A pdb=" N LEU C 139 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG C 128 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C 141 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASP C 130 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR C 242 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR C 98 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE C 245 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE C 96 " --> pdb=" O ILE C 245 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 990 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: 3.44 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9307 1.03 - 1.23: 21 1.23 - 1.42: 4315 1.42 - 1.62: 5647 1.62 - 1.81: 60 Bond restraints: 19350 Sorted by residual: bond pdb=" N PHE B 373 " pdb=" H PHE B 373 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" N LEU B 374 " pdb=" H LEU B 374 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" N ASN B 375 " pdb=" CA ASN B 375 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.38e+00 bond pdb=" N TYR B 376 " pdb=" H TYR B 376 " ideal model delta sigma weight residual 0.860 0.910 -0.050 2.00e-02 2.50e+03 6.34e+00 bond pdb=" N GLU B 372 " pdb=" H GLU B 372 " ideal model delta sigma weight residual 0.860 0.910 -0.050 2.00e-02 2.50e+03 6.32e+00 ... (remaining 19345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 34501 1.88 - 3.76: 290 3.76 - 5.64: 29 5.64 - 7.53: 2 7.53 - 9.41: 3 Bond angle restraints: 34825 Sorted by residual: angle pdb=" C GLN B 369 " pdb=" N GLN B 370 " pdb=" CA GLN B 370 " ideal model delta sigma weight residual 120.31 128.91 -8.60 1.52e+00 4.33e-01 3.20e+01 angle pdb=" CA GLN B 369 " pdb=" C GLN B 369 " pdb=" N GLN B 370 " ideal model delta sigma weight residual 117.07 110.95 6.12 1.14e+00 7.69e-01 2.88e+01 angle pdb=" O GLN B 369 " pdb=" C GLN B 369 " pdb=" N GLN B 370 " ideal model delta sigma weight residual 122.07 127.54 -5.47 1.03e+00 9.43e-01 2.83e+01 angle pdb=" CA LEU B 374 " pdb=" C LEU B 374 " pdb=" O LEU B 374 " ideal model delta sigma weight residual 122.63 116.67 5.96 1.29e+00 6.01e-01 2.14e+01 angle pdb=" N VAL B 359 " pdb=" CA VAL B 359 " pdb=" C VAL B 359 " ideal model delta sigma weight residual 113.53 109.26 4.27 9.80e-01 1.04e+00 1.90e+01 ... (remaining 34820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8197 17.89 - 35.78: 818 35.78 - 53.67: 244 53.67 - 71.55: 54 71.55 - 89.44: 13 Dihedral angle restraints: 9326 sinusoidal: 4976 harmonic: 4350 Sorted by residual: dihedral pdb=" CB CYS A 106 " pdb=" SG CYS A 106 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual -86.00 -51.91 -34.09 1 1.00e+01 1.00e-02 1.65e+01 dihedral pdb=" CB CYS B 487 " pdb=" SG CYS B 487 " pdb=" SG CYS B 521 " pdb=" CB CYS B 521 " ideal model delta sinusoidal sigma weight residual -86.00 -118.42 32.42 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA GLN C 95 " pdb=" C GLN C 95 " pdb=" N ILE C 96 " pdb=" CA ILE C 96 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1306 0.058 - 0.116: 182 0.116 - 0.174: 14 0.174 - 0.232: 0 0.232 - 0.290: 2 Chirality restraints: 1504 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 522 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1 NAG B 902 " pdb=" ND2 ASN B 522 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA GLN B 370 " pdb=" N GLN B 370 " pdb=" C GLN B 370 " pdb=" CB GLN B 370 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 1501 not shown) Planarity restraints: 2971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 370 " -0.197 2.00e-02 2.50e+03 2.21e-01 7.34e+02 pdb=" CD GLN B 370 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLN B 370 " 0.188 2.00e-02 2.50e+03 pdb=" NE2 GLN B 370 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 370 " 0.327 2.00e-02 2.50e+03 pdb="HE22 GLN B 370 " -0.335 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 369 " -0.015 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C GLN B 369 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN B 369 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN B 370 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 360 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO B 361 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 361 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 361 " 0.039 5.00e-02 4.00e+02 ... (remaining 2968 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 537 2.10 - 2.73: 33336 2.73 - 3.35: 56656 3.35 - 3.98: 70379 3.98 - 4.60: 109612 Nonbonded interactions: 270520 Sorted by model distance: nonbonded pdb=" O ILE B 366 " pdb=" OE1 GLN B 370 " model vdw 1.478 2.800 nonbonded pdb=" H ASN A 383 " pdb=" OE2 GLU A 386 " model vdw 1.538 2.450 nonbonded pdb=" OE1 GLU A 503 " pdb=" H GLU A 503 " model vdw 1.540 2.450 nonbonded pdb=" O LEU C 126 " pdb=" H GLY C 246 " model vdw 1.543 2.450 nonbonded pdb=" OD1 ASN A 60 " pdb=" H ILE A 62 " model vdw 1.550 2.450 ... (remaining 270515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 40 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11 or name HH12 or name HH21 or name HH22)) or resid 41 through 56 o \ r (resid 57 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 58 through 308 or (resid 309 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 310 through 486 or (resid \ 487 and (name N or name CA or name C or name O or name CB or name SG or name H \ or name HA or name HB2 or name HB3)) or resid 488 through 491 or (resid 492 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 493 through 520 or (resid 521 and (name N or name CA or name C or name O or n \ ame CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 522 th \ rough 581 or (resid 582 and (name N or name CA or name C or name O or name CB or \ name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 583 through \ 609 or resid 901 through 902)) selection = (chain 'B' and (resid 40 through 305 or (resid 306 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 307 through 556 or res \ id 562 through 564 or (resid 565 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 566 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.640 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 0.050 10049 Z= 0.166 Angle : 0.585 9.407 13709 Z= 0.319 Chirality : 0.042 0.290 1504 Planarity : 0.004 0.071 1790 Dihedral : 15.487 89.442 3635 Min Nonbonded Distance : 1.478 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 0.50 % Allowed : 29.59 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.23), residues: 1242 helix: -0.55 (0.26), residues: 376 sheet: -0.77 (0.38), residues: 196 loop : -1.32 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 180 TYR 0.012 0.001 TYR B 233 PHE 0.009 0.001 PHE B 373 TRP 0.007 0.001 TRP A 438 HIS 0.008 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (10039) covalent geometry : angle 0.58283 / 0.32 (13684) SS BOND : bond 0.00221 / 0.12 ( 5) SS BOND : angle 0.99309 / 0.53 ( 10) hydrogen bonds : bond 0.25631 / 17.48 ( 366) hydrogen bonds : angle 9.73802 / 6.99 ( 990) link_NAG-ASN : bond 0.00370 / 0.18 ( 5) link_NAG-ASN : angle 1.32236 / 0.66 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 TYR cc_start: 0.8485 (m-80) cc_final: 0.7728 (m-80) outliers start: 5 outliers final: 5 residues processed: 122 average time/residue: 0.1688 time to fit residues: 30.6545 Evaluate side-chains 120 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 376 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 500 HIS B 375 ASN B 412 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.079804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.059507 restraints weight = 97366.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.062624 restraints weight = 42887.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.064718 restraints weight = 25966.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.066084 restraints weight = 18837.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.067037 restraints weight = 15249.473| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10049 Z= 0.219 Angle : 0.610 5.990 13709 Z= 0.330 Chirality : 0.043 0.225 1504 Planarity : 0.005 0.051 1790 Dihedral : 5.721 51.029 1479 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.81 % Favored : 92.11 % Rotamer: Outliers : 2.38 % Allowed : 26.12 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.24), residues: 1242 helix: 0.07 (0.26), residues: 392 sheet: -1.00 (0.38), residues: 188 loop : -1.35 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 128 TYR 0.013 0.001 TYR A 481 PHE 0.012 0.001 PHE C 152 TRP 0.008 0.001 TRP B 93 HIS 0.007 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (10039) covalent geometry : angle 0.60830 / 0.33 (13684) SS BOND : bond 0.00277 / 0.14 ( 5) SS BOND : angle 1.01665 / 0.56 ( 10) hydrogen bonds : bond 0.05969 / 4.18 ( 366) hydrogen bonds : angle 7.11209 / 5.16 ( 990) link_NAG-ASN : bond 0.00351 / 0.18 ( 5) link_NAG-ASN : angle 1.30202 / 0.64 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 MET cc_start: 0.7953 (mmm) cc_final: 0.7675 (mmm) REVERT: B 233 TYR cc_start: 0.8421 (m-80) cc_final: 0.7824 (m-80) REVERT: B 278 HIS cc_start: 0.8884 (OUTLIER) cc_final: 0.8649 (t-90) REVERT: C 98 TYR cc_start: 0.8691 (t80) cc_final: 0.8163 (t80) outliers start: 24 outliers final: 19 residues processed: 135 average time/residue: 0.1823 time to fit residues: 36.6262 Evaluate side-chains 129 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 239 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 53 optimal weight: 0.0980 chunk 27 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS B 343 GLN B 412 ASN B 548 ASN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060928 restraints weight = 94823.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064185 restraints weight = 41326.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.066361 restraints weight = 24845.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067794 restraints weight = 17851.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.068749 restraints weight = 14322.594| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10049 Z= 0.123 Angle : 0.542 5.919 13709 Z= 0.285 Chirality : 0.042 0.215 1504 Planarity : 0.004 0.046 1790 Dihedral : 5.191 51.502 1477 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Rotamer: Outliers : 2.18 % Allowed : 25.72 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.24), residues: 1242 helix: 0.72 (0.26), residues: 400 sheet: -0.98 (0.38), residues: 189 loop : -1.22 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 180 TYR 0.011 0.001 TYR A 481 PHE 0.012 0.001 PHE A 455 TRP 0.006 0.001 TRP B 93 HIS 0.017 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10039) covalent geometry : angle 0.54059 / 0.28 (13684) SS BOND : bond 0.00118 / 0.07 ( 5) SS BOND : angle 0.81106 / 0.45 ( 10) hydrogen bonds : bond 0.05013 / 3.57 ( 366) hydrogen bonds : angle 6.36417 / 4.64 ( 990) link_NAG-ASN : bond 0.00279 / 0.15 ( 5) link_NAG-ASN : angle 0.99896 / 0.50 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.8582 (pm20) cc_final: 0.8045 (pm20) REVERT: B 180 MET cc_start: 0.7993 (mmm) cc_final: 0.7655 (mmm) REVERT: B 233 TYR cc_start: 0.8390 (m-80) cc_final: 0.7849 (m-80) REVERT: B 469 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8660 (tttp) REVERT: C 98 TYR cc_start: 0.8816 (t80) cc_final: 0.8255 (t80) outliers start: 22 outliers final: 16 residues processed: 146 average time/residue: 0.2006 time to fit residues: 42.7460 Evaluate side-chains 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 240 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 86 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN B 412 ASN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.079829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059613 restraints weight = 96388.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.062767 restraints weight = 42289.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064885 restraints weight = 25551.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.066276 restraints weight = 18432.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066981 restraints weight = 14827.233| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10049 Z= 0.208 Angle : 0.556 6.137 13709 Z= 0.296 Chirality : 0.042 0.232 1504 Planarity : 0.005 0.045 1790 Dihedral : 5.043 51.274 1477 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.09 % Favored : 92.83 % Rotamer: Outliers : 2.78 % Allowed : 25.52 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.24), residues: 1242 helix: 0.64 (0.26), residues: 401 sheet: -1.15 (0.38), residues: 195 loop : -1.28 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 232 TYR 0.011 0.001 TYR A 481 PHE 0.011 0.001 PHE B 413 TRP 0.009 0.001 TRP B 93 HIS 0.007 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (10039) covalent geometry : angle 0.55520 / 0.30 (13684) SS BOND : bond 0.00243 / 0.13 ( 5) SS BOND : angle 0.75761 / 0.42 ( 10) hydrogen bonds : bond 0.04416 / 3.12 ( 366) hydrogen bonds : angle 6.35648 / 4.65 ( 990) link_NAG-ASN : bond 0.00248 / 0.13 ( 5) link_NAG-ASN : angle 1.18881 / 0.59 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.8586 (pm20) cc_final: 0.8234 (pm20) REVERT: B 180 MET cc_start: 0.8108 (mmm) cc_final: 0.7812 (mmm) REVERT: B 233 TYR cc_start: 0.8438 (m-80) cc_final: 0.7917 (m-80) REVERT: C 98 TYR cc_start: 0.8738 (t80) cc_final: 0.8127 (t80) REVERT: C 262 TYR cc_start: 0.7663 (t80) cc_final: 0.7338 (t80) outliers start: 28 outliers final: 24 residues processed: 137 average time/residue: 0.1763 time to fit residues: 36.4014 Evaluate side-chains 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 240 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 28 optimal weight: 0.0060 chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN C 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.080796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.060393 restraints weight = 95760.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.063631 restraints weight = 42061.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065805 restraints weight = 25433.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.067240 restraints weight = 18349.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067968 restraints weight = 14742.439| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10049 Z= 0.128 Angle : 0.522 6.091 13709 Z= 0.271 Chirality : 0.041 0.214 1504 Planarity : 0.004 0.045 1790 Dihedral : 4.848 51.775 1477 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 2.68 % Allowed : 25.62 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.25), residues: 1242 helix: 0.99 (0.27), residues: 395 sheet: -1.13 (0.37), residues: 195 loop : -1.20 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.011 0.001 TYR A 481 PHE 0.012 0.001 PHE B 413 TRP 0.006 0.001 TRP B 93 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10039) covalent geometry : angle 0.52063 / 0.27 (13684) SS BOND : bond 0.00133 / 0.08 ( 5) SS BOND : angle 0.72472 / 0.41 ( 10) hydrogen bonds : bond 0.03995 / 2.85 ( 366) hydrogen bonds : angle 5.95858 / 4.37 ( 990) link_NAG-ASN : bond 0.00272 / 0.14 ( 5) link_NAG-ASN : angle 1.00239 / 0.50 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.8889 (p) REVERT: A 503 GLU cc_start: 0.8481 (pm20) cc_final: 0.8237 (pm20) REVERT: B 180 MET cc_start: 0.8050 (mmm) cc_final: 0.7757 (mmm) REVERT: B 469 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8623 (tttp) outliers start: 27 outliers final: 22 residues processed: 143 average time/residue: 0.1837 time to fit residues: 38.9648 Evaluate side-chains 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 597 LYS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 268 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 109 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN C 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.080702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060408 restraints weight = 95165.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063688 restraints weight = 41701.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.065855 restraints weight = 24985.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.067295 restraints weight = 17942.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068257 restraints weight = 14392.168| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10049 Z= 0.133 Angle : 0.525 6.130 13709 Z= 0.272 Chirality : 0.041 0.215 1504 Planarity : 0.004 0.043 1790 Dihedral : 4.596 51.866 1474 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.76 % Favored : 93.16 % Rotamer: Outliers : 2.58 % Allowed : 26.32 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.25), residues: 1242 helix: 1.02 (0.27), residues: 400 sheet: -1.11 (0.37), residues: 195 loop : -1.19 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 331 TYR 0.010 0.001 TYR A 481 PHE 0.011 0.001 PHE B 433 TRP 0.007 0.001 TRP A 438 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10039) covalent geometry : angle 0.52385 / 0.27 (13684) SS BOND : bond 0.00129 / 0.07 ( 5) SS BOND : angle 0.67157 / 0.37 ( 10) hydrogen bonds : bond 0.03796 / 2.71 ( 366) hydrogen bonds : angle 5.86814 / 4.30 ( 990) link_NAG-ASN : bond 0.00257 / 0.14 ( 5) link_NAG-ASN : angle 1.02287 / 0.52 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 SER cc_start: 0.9251 (m) cc_final: 0.8906 (p) REVERT: A 503 GLU cc_start: 0.8503 (pm20) cc_final: 0.8272 (pm20) REVERT: C 98 TYR cc_start: 0.8705 (t80) cc_final: 0.8110 (t80) outliers start: 26 outliers final: 23 residues processed: 142 average time/residue: 0.1829 time to fit residues: 38.6898 Evaluate side-chains 140 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 597 LYS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 268 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 116 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 61 optimal weight: 0.0570 chunk 83 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 HIS B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.081328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.060976 restraints weight = 94907.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.064280 restraints weight = 40894.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066484 restraints weight = 24459.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067943 restraints weight = 17481.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.068711 restraints weight = 13990.340| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10049 Z= 0.116 Angle : 0.520 6.109 13709 Z= 0.266 Chirality : 0.041 0.209 1504 Planarity : 0.004 0.041 1790 Dihedral : 4.481 52.151 1474 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 2.28 % Allowed : 26.22 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.25), residues: 1242 helix: 1.24 (0.27), residues: 399 sheet: -1.04 (0.38), residues: 192 loop : -1.12 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.010 0.001 TYR A 481 PHE 0.012 0.001 PHE B 433 TRP 0.006 0.001 TRP A 438 HIS 0.003 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (10039) covalent geometry : angle 0.51900 / 0.27 (13684) SS BOND : bond 0.00105 / 0.06 ( 5) SS BOND : angle 0.62176 / 0.35 ( 10) hydrogen bonds : bond 0.03577 / 2.56 ( 366) hydrogen bonds : angle 5.64935 / 4.15 ( 990) link_NAG-ASN : bond 0.00284 / 0.15 ( 5) link_NAG-ASN : angle 0.96084 / 0.49 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 SER cc_start: 0.9219 (m) cc_final: 0.8876 (p) REVERT: B 469 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8579 (tttt) REVERT: C 262 TYR cc_start: 0.7461 (t80) cc_final: 0.7181 (t80) outliers start: 23 outliers final: 21 residues processed: 145 average time/residue: 0.1946 time to fit residues: 41.4665 Evaluate side-chains 142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 597 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 268 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.059198 restraints weight = 96942.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.062371 restraints weight = 42519.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.064477 restraints weight = 25685.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.065860 restraints weight = 18535.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066775 restraints weight = 14929.484| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10049 Z= 0.254 Angle : 0.579 6.370 13709 Z= 0.306 Chirality : 0.042 0.242 1504 Planarity : 0.005 0.045 1790 Dihedral : 4.708 51.907 1474 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.57 % Favored : 92.35 % Rotamer: Outliers : 2.88 % Allowed : 26.42 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.24), residues: 1242 helix: 0.85 (0.26), residues: 401 sheet: -1.20 (0.37), residues: 207 loop : -1.29 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.012 0.002 TYR A 580 PHE 0.011 0.002 PHE B 519 TRP 0.011 0.001 TRP B 93 HIS 0.006 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.25 (10039) covalent geometry : angle 0.57776 / 0.31 (13684) SS BOND : bond 0.00334 / 0.17 ( 5) SS BOND : angle 0.71885 / 0.40 ( 10) hydrogen bonds : bond 0.03794 / 2.66 ( 366) hydrogen bonds : angle 5.94113 / 4.36 ( 990) link_NAG-ASN : bond 0.00274 / 0.14 ( 5) link_NAG-ASN : angle 1.26614 / 0.64 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 SER cc_start: 0.9292 (m) cc_final: 0.8933 (p) REVERT: B 184 HIS cc_start: 0.8024 (p90) cc_final: 0.7333 (p90) REVERT: B 469 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8631 (tttp) REVERT: C 262 TYR cc_start: 0.7581 (t80) cc_final: 0.7282 (t80) outliers start: 29 outliers final: 27 residues processed: 137 average time/residue: 0.1903 time to fit residues: 38.8717 Evaluate side-chains 143 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 485 HIS Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 597 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.059907 restraints weight = 95429.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.063141 restraints weight = 41599.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065269 restraints weight = 24983.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066709 restraints weight = 17978.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.067560 restraints weight = 14415.231| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10049 Z= 0.175 Angle : 0.543 6.237 13709 Z= 0.283 Chirality : 0.042 0.229 1504 Planarity : 0.004 0.044 1790 Dihedral : 4.687 52.324 1474 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.78 % Allowed : 26.32 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.25), residues: 1242 helix: 0.96 (0.27), residues: 400 sheet: -1.21 (0.37), residues: 207 loop : -1.26 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.012 0.001 TYR A 481 PHE 0.011 0.001 PHE B 413 TRP 0.008 0.001 TRP B 93 HIS 0.004 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (10039) covalent geometry : angle 0.54137 / 0.28 (13684) SS BOND : bond 0.00221 / 0.11 ( 5) SS BOND : angle 0.84787 / 0.42 ( 10) hydrogen bonds : bond 0.03651 / 2.58 ( 366) hydrogen bonds : angle 5.76320 / 4.23 ( 990) link_NAG-ASN : bond 0.00253 / 0.13 ( 5) link_NAG-ASN : angle 1.10345 / 0.55 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 SER cc_start: 0.9256 (m) cc_final: 0.8889 (p) REVERT: C 262 TYR cc_start: 0.7586 (t80) cc_final: 0.7296 (t80) outliers start: 28 outliers final: 24 residues processed: 142 average time/residue: 0.1880 time to fit residues: 39.9386 Evaluate side-chains 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 597 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 78 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 72 optimal weight: 0.0270 chunk 93 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.081480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.061310 restraints weight = 93744.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.064651 restraints weight = 40703.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066861 restraints weight = 24205.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068334 restraints weight = 17265.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.069289 restraints weight = 13761.724| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10049 Z= 0.102 Angle : 0.526 6.804 13709 Z= 0.268 Chirality : 0.042 0.204 1504 Planarity : 0.004 0.041 1790 Dihedral : 4.404 52.914 1472 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Rotamer: Outliers : 1.79 % Allowed : 27.41 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.25), residues: 1242 helix: 1.30 (0.27), residues: 401 sheet: -1.12 (0.37), residues: 198 loop : -1.11 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 447 TYR 0.012 0.001 TYR A 481 PHE 0.016 0.001 PHE C 152 TRP 0.008 0.001 TRP A 122 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (10039) covalent geometry : angle 0.52486 / 0.27 (13684) SS BOND : bond 0.00079 / 0.05 ( 5) SS BOND : angle 0.81249 / 0.40 ( 10) hydrogen bonds : bond 0.03432 / 2.46 ( 366) hydrogen bonds : angle 5.44451 / 4.00 ( 990) link_NAG-ASN : bond 0.00297 / 0.16 ( 5) link_NAG-ASN : angle 0.90344 / 0.46 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 SER cc_start: 0.9227 (m) cc_final: 0.8859 (p) REVERT: C 262 TYR cc_start: 0.7495 (t80) cc_final: 0.7212 (t80) outliers start: 18 outliers final: 17 residues processed: 142 average time/residue: 0.1958 time to fit residues: 41.0317 Evaluate side-chains 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 597 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN B 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059983 restraints weight = 95248.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.063219 restraints weight = 41319.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065355 restraints weight = 24799.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.066769 restraints weight = 17816.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067544 restraints weight = 14301.563| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10049 Z= 0.180 Angle : 0.544 6.207 13709 Z= 0.283 Chirality : 0.041 0.232 1504 Planarity : 0.004 0.041 1790 Dihedral : 4.491 52.807 1472 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.24 % Rotamer: Outliers : 2.09 % Allowed : 27.21 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.25), residues: 1242 helix: 1.17 (0.27), residues: 402 sheet: -1.20 (0.37), residues: 201 loop : -1.18 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.010 0.001 TYR A 580 PHE 0.017 0.001 PHE C 254 TRP 0.009 0.001 TRP B 93 HIS 0.006 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (10039) covalent geometry : angle 0.54313 / 0.28 (13684) SS BOND : bond 0.00248 / 0.13 ( 5) SS BOND : angle 0.73565 / 0.37 ( 10) hydrogen bonds : bond 0.03494 / 2.48 ( 366) hydrogen bonds : angle 5.57875 / 4.09 ( 990) link_NAG-ASN : bond 0.00255 / 0.13 ( 5) link_NAG-ASN : angle 1.13665 / 0.57 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.16 seconds wall clock time: 51 minutes 10.77 seconds (3070.77 seconds total)