Starting phenix.real_space_refine on Sun Aug 24 10:43:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7y_29828/08_2025/8g7y_29828_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7y_29828/08_2025/8g7y_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7y_29828/08_2025/8g7y_29828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7y_29828/08_2025/8g7y_29828.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7y_29828/08_2025/8g7y_29828_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7y_29828/08_2025/8g7y_29828_trim.cif" } 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-2.0-5787/lib/python3.9/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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 3.48, 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: 1.58 Conformation dependent library (CDL) restraints added in 603.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.52 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: 3.28 Time building geometry restraints manager: 2.20 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.670 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 aren 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 covalent geometry : bond 0.00347 (10039) covalent geometry : angle 0.58283 (13684) SS BOND : bond 0.00221 ( 5) SS BOND : angle 0.99309 ( 10) hydrogen bonds : bond 0.25631 ( 366) hydrogen bonds : angle 9.73802 ( 990) link_NAG-ASN : bond 0.00370 ( 5) link_NAG-ASN : angle 1.32236 ( 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 : 0.574 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: 0.1886 time to fit residues: 33.9492 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 : 0.447 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3392 r_free = 0.3392 target = 0.079662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059369 restraints weight = 97282.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062468 restraints weight = 43000.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.064563 restraints weight = 26087.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.065952 restraints weight = 18898.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066658 restraints weight = 15257.137| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0794 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= 0.220 Angle : 0.605 5.952 13709 Z= 0.329 Chirality : 0.043 0.221 1504 Planarity : 0.005 0.052 1790 Dihedral : 5.761 50.992 1479 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.57 % Favored : 92.35 % Rotamer: Outliers : 2.38 % Allowed : 26.81 % 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 aren not related in a simple way. whole: -1.28 (0.23), residues: 1242 helix: 0.03 (0.25), residues: 392 sheet: -0.96 (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 A 331 TYR 0.013 0.001 TYR A 481 PHE 0.009 0.001 PHE B 433 TRP 0.008 0.001 TRP B 93 HIS 0.007 0.001 HIS B 485 Details of bonding type rmsd covalent geometry : bond 0.00465 (10039) covalent geometry : angle 0.60330 (13684) SS BOND : bond 0.00286 ( 5) SS BOND : angle 1.00738 ( 10) hydrogen bonds : bond 0.06831 ( 366) hydrogen bonds : angle 7.28175 ( 990) link_NAG-ASN : bond 0.00301 ( 5) link_NAG-ASN : angle 1.26298 ( 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 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.327 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: A 503 GLU cc_start: 0.8621 (pm20) cc_final: 0.8101 (pm20) REVERT: B 233 TYR cc_start: 0.8404 (m-80) cc_final: 0.7798 (m-80) REVERT: B 278 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.8669 (t-90) REVERT: C 98 TYR cc_start: 0.8692 (t80) cc_final: 0.8220 (t80) outliers start: 24 outliers final: 19 residues processed: 134 average time/residue: 0.1757 time to fit residues: 34.5464 Evaluate side-chains 130 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 139 LEU 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: 6.9990 chunk 106 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3423 r_free = 0.3423 target = 0.081234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060588 restraints weight = 95764.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.063842 restraints weight = 42114.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.066033 restraints weight = 25513.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067470 restraints weight = 18421.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068365 restraints weight = 14838.739| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10049 Z= 0.126 Angle : 0.546 5.926 13709 Z= 0.287 Chirality : 0.042 0.216 1504 Planarity : 0.004 0.047 1790 Dihedral : 5.202 51.533 1477 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 1.79 % Allowed : 26.12 % 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 aren not related in a simple way. whole: -0.81 (0.24), residues: 1242 helix: 0.72 (0.26), residues: 401 sheet: -1.01 (0.37), residues: 192 loop : -1.18 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 109 TYR 0.014 0.001 TYR B 435 PHE 0.012 0.001 PHE A 455 TRP 0.006 0.001 TRP A 460 HIS 0.017 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00277 (10039) covalent geometry : angle 0.54508 (13684) SS BOND : bond 0.00123 ( 5) SS BOND : angle 0.81620 ( 10) hydrogen bonds : bond 0.05047 ( 366) hydrogen bonds : angle 6.34474 ( 990) link_NAG-ASN : bond 0.00290 ( 5) link_NAG-ASN : angle 1.03380 ( 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 149 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.467 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: 0.8585 (pm20) cc_final: 0.8015 (pm20) REVERT: B 180 MET cc_start: 0.8017 (mmm) cc_final: 0.7667 (mmm) REVERT: B 233 TYR cc_start: 0.8387 (m-80) cc_final: 0.7835 (m-80) REVERT: B 469 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8665 (tttp) REVERT: C 98 TYR cc_start: 0.8808 (t80) cc_final: 0.8245 (t80) outliers start: 18 outliers final: 12 residues processed: 146 average time/residue: 0.2078 time to fit residues: 43.2453 Evaluate side-chains 130 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 533 VAL 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 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: 4.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3396 r_free = 0.3396 target = 0.079901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059356 restraints weight = 97281.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.062543 restraints weight = 43349.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.064678 restraints weight = 26292.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.066086 restraints weight = 19059.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066946 restraints weight = 15416.965| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10049 Z= 0.200 Angle : 0.558 6.141 13709 Z= 0.296 Chirality : 0.042 0.230 1504 Planarity : 0.005 0.046 1790 Dihedral : 5.034 51.483 1477 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.09 % Favored : 92.83 % Rotamer: Outliers : 2.88 % Allowed : 25.12 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.24), residues: 1242 helix: 0.67 (0.26), residues: 396 sheet: -1.12 (0.38), residues: 192 loop : -1.27 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 232 TYR 0.010 0.001 TYR A 481 PHE 0.010 0.001 PHE B 413 TRP 0.009 0.001 TRP B 93 HIS 0.006 0.001 HIS B 485 Details of bonding type rmsd covalent geometry : bond 0.00428 (10039) covalent geometry : angle 0.55684 (13684) SS BOND : bond 0.00238 ( 5) SS BOND : angle 0.76713 ( 10) hydrogen bonds : bond 0.04445 ( 366) hydrogen bonds : angle 6.30198 ( 990) link_NAG-ASN : bond 0.00262 ( 5) link_NAG-ASN : angle 1.20338 ( 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 146 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.451 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: A 189 MET cc_start: 0.9030 (mtm) cc_final: 0.8783 (mtt) REVERT: A 269 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.8921 (p) REVERT: A 503 GLU cc_start: 0.8578 (pm20) cc_final: 0.8307 (pm20) REVERT: B 180 MET cc_start: 0.8107 (mmm) cc_final: 0.7801 (mmm) REVERT: C 98 TYR cc_start: 0.8726 (t80) cc_final: 0.8122 (t80) REVERT: C 262 TYR cc_start: 0.7652 (t80) cc_final: 0.7326 (t80) outliers start: 29 outliers final: 24 residues processed: 138 average time/residue: 0.1727 time to fit residues: 35.5703 Evaluate side-chains 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 269 SER 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 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 485 HIS 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: 4.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3388 r_free = 0.3388 target = 0.079532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.058962 restraints weight = 97133.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.062141 restraints weight = 42837.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.064265 restraints weight = 25987.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065668 restraints weight = 18832.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066603 restraints weight = 15220.688| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1620 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= 0.187 Angle : 0.546 6.212 13709 Z= 0.288 Chirality : 0.042 0.227 1504 Planarity : 0.004 0.045 1790 Dihedral : 4.970 51.610 1477 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 3.08 % Allowed : 25.42 % 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 aren not related in a simple way. whole: -0.92 (0.24), residues: 1242 helix: 0.78 (0.26), residues: 400 sheet: -1.17 (0.37), residues: 207 loop : -1.32 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.012 0.001 TYR B 435 PHE 0.013 0.001 PHE B 413 TRP 0.009 0.001 TRP B 93 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00401 (10039) covalent geometry : angle 0.54438 (13684) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.75829 ( 10) hydrogen bonds : bond 0.04062 ( 366) hydrogen bonds : angle 6.10773 ( 990) link_NAG-ASN : bond 0.00254 ( 5) link_NAG-ASN : angle 1.16074 ( 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 148 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.399 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: A 189 MET cc_start: 0.9043 (mtm) cc_final: 0.8813 (mtt) REVERT: A 269 SER cc_start: 0.9267 (OUTLIER) cc_final: 0.8928 (p) REVERT: A 503 GLU cc_start: 0.8521 (pm20) cc_final: 0.8293 (pm20) REVERT: B 180 MET cc_start: 0.8094 (mmm) cc_final: 0.7829 (mmm) REVERT: B 469 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8667 (tttp) REVERT: C 98 TYR cc_start: 0.8725 (t80) cc_final: 0.8122 (t80) outliers start: 31 outliers final: 27 residues processed: 140 average time/residue: 0.1835 time to fit residues: 38.7833 Evaluate side-chains 143 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 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 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 372 GLU 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 535 MET 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: 0.7980 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3406 r_free = 0.3406 target = 0.080487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060359 restraints weight = 95754.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.063557 restraints weight = 41660.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065686 restraints weight = 25174.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.067091 restraints weight = 18186.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.067789 restraints weight = 14644.832| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10049 Z= 0.128 Angle : 0.523 6.100 13709 Z= 0.272 Chirality : 0.041 0.214 1504 Planarity : 0.004 0.044 1790 Dihedral : 4.858 51.944 1477 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % 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 aren not related in a simple way. whole: -0.73 (0.25), residues: 1242 helix: 1.01 (0.27), residues: 398 sheet: -1.13 (0.38), residues: 195 loop : -1.23 (0.25), residues: 649 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 0.011 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 covalent geometry : bond 0.00286 (10039) covalent geometry : angle 0.52188 (13684) SS BOND : bond 0.00123 ( 5) SS BOND : angle 0.69715 ( 10) hydrogen bonds : bond 0.03825 ( 366) hydrogen bonds : angle 5.87880 ( 990) link_NAG-ASN : bond 0.00267 ( 5) link_NAG-ASN : angle 1.01552 ( 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 144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.493 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 189 MET cc_start: 0.9066 (mtm) cc_final: 0.8827 (mtt) REVERT: A 269 SER cc_start: 0.9241 (m) cc_final: 0.8883 (p) REVERT: A 503 GLU cc_start: 0.8457 (pm20) cc_final: 0.8233 (pm20) REVERT: B 180 MET cc_start: 0.8088 (mmm) cc_final: 0.7816 (mmm) outliers start: 26 outliers final: 23 residues processed: 139 average time/residue: 0.1834 time to fit residues: 38.0645 Evaluate side-chains 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 374 LEU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 485 HIS Chi-restraints excluded: chain B residue 535 MET 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=2.50 ------------------------------------------------------------------------------- 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: 0.0050 chunk 83 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 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 = 0.3406 r_free = 0.3406 target = 0.080419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.060189 restraints weight = 96223.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.063397 restraints weight = 41876.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.065528 restraints weight = 25263.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066935 restraints weight = 18206.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.067686 restraints weight = 14677.663| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10049 Z= 0.140 Angle : 0.524 6.175 13709 Z= 0.271 Chirality : 0.041 0.219 1504 Planarity : 0.004 0.044 1790 Dihedral : 4.600 52.024 1474 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.44 % Favored : 93.48 % Rotamer: Outliers : 2.88 % Allowed : 25.52 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.25), residues: 1242 helix: 1.05 (0.27), residues: 400 sheet: -1.11 (0.37), residues: 204 loop : -1.24 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 258 TYR 0.011 0.001 TYR B 435 PHE 0.011 0.001 PHE B 413 TRP 0.007 0.001 TRP B 93 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00310 (10039) covalent geometry : angle 0.52351 (13684) SS BOND : bond 0.00149 ( 5) SS BOND : angle 0.65341 ( 10) hydrogen bonds : bond 0.03674 ( 366) hydrogen bonds : angle 5.79892 ( 990) link_NAG-ASN : bond 0.00256 ( 5) link_NAG-ASN : angle 1.04071 ( 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 144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.541 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 189 MET cc_start: 0.9071 (mtm) cc_final: 0.8835 (mtt) REVERT: A 269 SER cc_start: 0.9237 (m) cc_final: 0.8884 (p) REVERT: A 503 GLU cc_start: 0.8461 (pm20) cc_final: 0.8259 (pm20) REVERT: C 262 TYR cc_start: 0.7517 (t80) cc_final: 0.7232 (t80) outliers start: 29 outliers final: 28 residues processed: 139 average time/residue: 0.1761 time to fit residues: 36.5264 Evaluate side-chains 142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 315 VAL Chi-restraints excluded: chain A residue 417 LEU 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 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 535 MET 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: 0.9990 chunk 118 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 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 = 0.3407 r_free = 0.3407 target = 0.080422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.060079 restraints weight = 95546.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.063307 restraints weight = 41465.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.065457 restraints weight = 24964.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.066879 restraints weight = 17970.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.067700 restraints weight = 14461.306| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1969 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= 0.138 Angle : 0.522 6.899 13709 Z= 0.269 Chirality : 0.041 0.218 1504 Planarity : 0.004 0.043 1790 Dihedral : 4.559 52.239 1474 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 3.18 % Allowed : 25.22 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.25), residues: 1242 helix: 1.15 (0.27), residues: 400 sheet: -1.11 (0.37), residues: 204 loop : -1.22 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.010 0.001 TYR A 481 PHE 0.013 0.001 PHE C 152 TRP 0.007 0.001 TRP B 93 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00305 (10039) covalent geometry : angle 0.52113 (13684) SS BOND : bond 0.00148 ( 5) SS BOND : angle 0.64599 ( 10) hydrogen bonds : bond 0.03553 ( 366) hydrogen bonds : angle 5.70367 ( 990) link_NAG-ASN : bond 0.00264 ( 5) link_NAG-ASN : angle 1.02992 ( 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 152 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.570 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 189 MET cc_start: 0.9104 (mtm) cc_final: 0.8864 (mtt) REVERT: A 269 SER cc_start: 0.9255 (m) cc_final: 0.8906 (p) REVERT: C 262 TYR cc_start: 0.7519 (t80) cc_final: 0.7231 (t80) outliers start: 32 outliers final: 28 residues processed: 146 average time/residue: 0.1609 time to fit residues: 35.6736 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 : 0.334 ------------------------------------------------------------------------------- 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 295 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 417 LEU 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 274 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.080041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059773 restraints weight = 95512.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.062967 restraints weight = 41504.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.065097 restraints weight = 25074.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.066507 restraints weight = 18095.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.067264 restraints weight = 14566.941| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10049 Z= 0.168 Angle : 0.540 6.238 13709 Z= 0.281 Chirality : 0.041 0.224 1504 Planarity : 0.004 0.042 1790 Dihedral : 4.540 52.291 1472 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.84 % Favored : 93.08 % Rotamer: Outliers : 2.78 % Allowed : 25.72 % 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 aren not related in a simple way. whole: -0.72 (0.25), residues: 1242 helix: 1.09 (0.27), residues: 400 sheet: -1.18 (0.37), residues: 204 loop : -1.26 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.010 0.001 TYR A 481 PHE 0.011 0.001 PHE B 413 TRP 0.008 0.001 TRP B 93 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00363 (10039) covalent geometry : angle 0.53875 (13684) SS BOND : bond 0.00353 ( 5) SS BOND : angle 0.82140 ( 10) hydrogen bonds : bond 0.03583 ( 366) hydrogen bonds : angle 5.70292 ( 990) link_NAG-ASN : bond 0.00262 ( 5) link_NAG-ASN : angle 1.09672 ( 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 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.529 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 189 MET cc_start: 0.9090 (mtm) cc_final: 0.8855 (mtt) REVERT: A 269 SER cc_start: 0.9260 (m) cc_final: 0.8895 (p) REVERT: C 262 TYR cc_start: 0.7588 (t80) cc_final: 0.7296 (t80) outliers start: 28 outliers final: 27 residues processed: 140 average time/residue: 0.1701 time to fit residues: 35.7257 Evaluate side-chains 143 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 295 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 417 LEU 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 274 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 485 HIS Chi-restraints excluded: chain B residue 535 MET 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: 0.7980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3418 r_free = 0.3418 target = 0.081033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.060727 restraints weight = 93897.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.064000 restraints weight = 40991.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.066158 restraints weight = 24662.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.067595 restraints weight = 17770.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.068466 restraints weight = 14273.197| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2158 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= 0.107 Angle : 0.520 6.951 13709 Z= 0.266 Chirality : 0.041 0.205 1504 Planarity : 0.004 0.042 1790 Dihedral : 4.408 52.811 1472 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 2.09 % Allowed : 26.51 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.25), residues: 1242 helix: 1.30 (0.27), residues: 401 sheet: -1.06 (0.38), residues: 194 loop : -1.18 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.013 0.001 TYR B 435 PHE 0.016 0.001 PHE C 152 TRP 0.006 0.001 TRP A 122 HIS 0.006 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00248 (10039) covalent geometry : angle 0.51870 (13684) SS BOND : bond 0.00137 ( 5) SS BOND : angle 0.82110 ( 10) hydrogen bonds : bond 0.03420 ( 366) hydrogen bonds : angle 5.48051 ( 990) link_NAG-ASN : bond 0.00280 ( 5) link_NAG-ASN : angle 0.91604 ( 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 144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.563 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: A 269 SER cc_start: 0.9270 (m) cc_final: 0.8911 (p) REVERT: C 98 TYR cc_start: 0.8776 (t80) cc_final: 0.8240 (t80) REVERT: C 262 TYR cc_start: 0.7530 (t80) cc_final: 0.7250 (t80) outliers start: 21 outliers final: 20 residues processed: 139 average time/residue: 0.1737 time to fit residues: 36.6477 Evaluate side-chains 140 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 A residue 548 ASN 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 485 HIS Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 535 MET 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: 5.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 104 optimal weight: 0.0980 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.081006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060569 restraints weight = 94646.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.063893 restraints weight = 41244.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.066101 restraints weight = 24605.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067583 restraints weight = 17607.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.068470 restraints weight = 14068.295| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 10049 Z= 0.158 Angle : 0.820 59.199 13709 Z= 0.496 Chirality : 0.041 0.206 1504 Planarity : 0.004 0.042 1790 Dihedral : 4.388 52.796 1472 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 1.99 % Allowed : 26.81 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.25), residues: 1242 helix: 1.31 (0.27), residues: 401 sheet: -1.06 (0.38), residues: 194 loop : -1.18 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.011 0.001 TYR A 481 PHE 0.013 0.001 PHE B 433 TRP 0.005 0.001 TRP B 93 HIS 0.005 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00306 (10039) covalent geometry : angle 0.81992 (13684) SS BOND : bond 0.00128 ( 5) SS BOND : angle 0.76773 ( 10) hydrogen bonds : bond 0.03415 ( 366) hydrogen bonds : angle 5.48330 ( 990) link_NAG-ASN : bond 0.00279 ( 5) link_NAG-ASN : angle 0.91866 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2908.41 seconds wall clock time: 50 minutes 20.95 seconds (3020.95 seconds total)