Starting phenix.real_space_refine on Mon Jun 16 22:46:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7y_29828/06_2025/8g7y_29828_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7y_29828/06_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_29828/06_2025/8g7y_29828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7y_29828/06_2025/8g7y_29828.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7y_29828/06_2025/8g7y_29828_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7y_29828/06_2025/8g7y_29828_trim.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} 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: 8.75, per 1000 atoms: 0.46 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: 4.56 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.45 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: 6.34 Time building geometry restraints manager: 5.61 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 609 or resid 901 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: 1.920 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: 0.300 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.760 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.260 ------------------------------------------------------------------------------- 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 : 10.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP A 438 HIS 0.008 0.001 HIS B 485 PHE 0.009 0.001 PHE B 373 TYR 0.012 0.001 TYR B 233 ARG 0.002 0.000 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 5) link_NAG-ASN : angle 1.32236 ( 15) hydrogen bonds : bond 0.25631 ( 366) hydrogen bonds : angle 9.73802 ( 990) SS BOND : bond 0.00221 ( 5) SS BOND : angle 0.99309 ( 10) covalent geometry : bond 0.00347 (10039) covalent geometry : angle 0.58283 (13684) *********************** 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 : 1.605 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: 0.4534 time to fit residues: 81.0012 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 : 1.901 ------------------------------------------------------------------------------- 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 105 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 500 HIS B 375 ASN B 412 ASN B 548 ASN ** 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 = 0.3407 r_free = 0.3407 target = 0.080485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.060206 restraints weight = 96209.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063373 restraints weight = 42161.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.065489 restraints weight = 25441.030| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10049 Z= 0.169 Angle : 0.586 5.934 13709 Z= 0.313 Chirality : 0.043 0.225 1504 Planarity : 0.005 0.051 1790 Dihedral : 5.626 51.228 1479 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.92 % Favored : 93.00 % Rotamer: Outliers : 1.89 % Allowed : 26.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1242 helix: 0.26 (0.26), residues: 392 sheet: -0.94 (0.38), residues: 188 loop : -1.26 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.006 0.001 HIS B 485 PHE 0.013 0.001 PHE C 152 TYR 0.012 0.001 TYR A 481 ARG 0.002 0.000 ARG B 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 5) link_NAG-ASN : angle 1.18039 ( 15) hydrogen bonds : bond 0.05893 ( 366) hydrogen bonds : angle 6.93821 ( 990) SS BOND : bond 0.00207 ( 5) SS BOND : angle 0.96262 ( 10) covalent geometry : bond 0.00365 (10039) covalent geometry : angle 0.58485 (13684) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.8583 (pm20) cc_final: 0.8083 (pm20) REVERT: B 180 MET cc_start: 0.7975 (mmm) cc_final: 0.7653 (mmm) REVERT: B 278 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.8682 (t-90) REVERT: C 98 TYR cc_start: 0.8758 (t80) cc_final: 0.8202 (t80) outliers start: 19 outliers final: 15 residues processed: 138 average time/residue: 0.4109 time to fit residues: 83.4700 Evaluate side-chains 128 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 269 SER Chi-restraints excluded: chain A residue 383 ASN 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 278 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 239 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 61 optimal weight: 0.0070 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- 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 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.080601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060283 restraints weight = 95771.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.063508 restraints weight = 41923.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065667 restraints weight = 25225.265| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1248 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= 0.146 Angle : 0.541 6.000 13709 Z= 0.285 Chirality : 0.042 0.222 1504 Planarity : 0.004 0.047 1790 Dihedral : 5.137 51.382 1477 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 1.99 % Allowed : 25.72 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.24), residues: 1242 helix: 0.68 (0.26), residues: 401 sheet: -1.06 (0.38), residues: 192 loop : -1.24 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 93 HIS 0.007 0.001 HIS B 485 PHE 0.011 0.001 PHE A 406 TYR 0.015 0.001 TYR B 435 ARG 0.002 0.000 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 5) link_NAG-ASN : angle 1.07941 ( 15) hydrogen bonds : bond 0.04974 ( 366) hydrogen bonds : angle 6.37662 ( 990) SS BOND : bond 0.00158 ( 5) SS BOND : angle 0.75102 ( 10) covalent geometry : bond 0.00319 (10039) covalent geometry : angle 0.54022 (13684) *********************** 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 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.8570 (pm20) cc_final: 0.8284 (pm20) REVERT: B 180 MET cc_start: 0.8040 (mmm) cc_final: 0.7721 (mmm) REVERT: B 332 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9040 (mmtp) REVERT: B 469 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8659 (tttp) REVERT: C 98 TYR cc_start: 0.8832 (t80) cc_final: 0.8254 (t80) outliers start: 20 outliers final: 15 residues processed: 142 average time/residue: 0.4627 time to fit residues: 96.0927 Evaluate side-chains 132 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 478 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 240 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 B 563 ASN C 169 ASN 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 = 0.079788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059590 restraints weight = 96041.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.062732 restraints weight = 42355.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.064831 restraints weight = 25701.442| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1540 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= 0.194 Angle : 0.551 6.142 13709 Z= 0.290 Chirality : 0.042 0.233 1504 Planarity : 0.005 0.052 1790 Dihedral : 4.994 51.349 1477 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.41 % Favored : 92.51 % Rotamer: Outliers : 2.98 % Allowed : 25.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.24), residues: 1242 helix: 0.69 (0.26), residues: 396 sheet: -1.13 (0.38), residues: 195 loop : -1.27 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 93 HIS 0.006 0.001 HIS B 485 PHE 0.011 0.001 PHE A 541 TYR 0.010 0.001 TYR A 481 ARG 0.003 0.000 ARG C 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 5) link_NAG-ASN : angle 1.22359 ( 15) hydrogen bonds : bond 0.04187 ( 366) hydrogen bonds : angle 6.21437 ( 990) SS BOND : bond 0.00239 ( 5) SS BOND : angle 0.77337 ( 10) covalent geometry : bond 0.00415 (10039) covalent geometry : angle 0.55000 (13684) *********************** 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 149 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.591 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: 0.8548 (pm20) cc_final: 0.8223 (pm20) REVERT: B 180 MET cc_start: 0.8089 (mmm) cc_final: 0.7805 (mmm) REVERT: B 469 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8671 (tttp) REVERT: C 262 TYR cc_start: 0.7686 (t80) cc_final: 0.7355 (t80) outliers start: 30 outliers final: 25 residues processed: 143 average time/residue: 0.4226 time to fit residues: 88.3152 Evaluate side-chains 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 467 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 115 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 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 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 = 0.079529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.059045 restraints weight = 97334.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062211 restraints weight = 43121.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064341 restraints weight = 26222.308| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10049 Z= 0.193 Angle : 0.549 6.192 13709 Z= 0.290 Chirality : 0.042 0.227 1504 Planarity : 0.004 0.045 1790 Dihedral : 4.985 51.487 1477 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.92 % Favored : 93.00 % Rotamer: Outliers : 3.28 % Allowed : 25.82 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1242 helix: 0.75 (0.26), residues: 394 sheet: -1.19 (0.37), residues: 207 loop : -1.32 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 93 HIS 0.005 0.001 HIS B 485 PHE 0.012 0.001 PHE B 413 TYR 0.012 0.001 TYR B 435 ARG 0.002 0.000 ARG A 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 5) link_NAG-ASN : angle 1.14765 ( 15) hydrogen bonds : bond 0.04050 ( 366) hydrogen bonds : angle 6.11287 ( 990) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.74363 ( 10) covalent geometry : bond 0.00412 (10039) covalent geometry : angle 0.54816 (13684) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LYS 424 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 SER cc_start: 0.9248 (m) cc_final: 0.8900 (p) REVERT: A 503 GLU cc_start: 0.8511 (pm20) cc_final: 0.8210 (pm20) REVERT: B 278 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8775 (t-90) REVERT: B 372 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7101 (tm-30) outliers start: 33 outliers final: 29 residues processed: 143 average time/residue: 0.4522 time to fit residues: 96.7987 Evaluate side-chains 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 232 ASN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 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 278 HIS 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 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 81 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.079279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.058881 restraints weight = 97050.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.062041 restraints weight = 42603.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.064151 restraints weight = 25852.259| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10049 Z= 0.194 Angle : 0.547 6.233 13709 Z= 0.288 Chirality : 0.042 0.233 1504 Planarity : 0.004 0.044 1790 Dihedral : 4.963 51.741 1477 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.65 % Favored : 92.27 % Rotamer: Outliers : 3.38 % Allowed : 25.72 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.24), residues: 1242 helix: 0.78 (0.26), residues: 402 sheet: -1.21 (0.37), residues: 207 loop : -1.33 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 93 HIS 0.007 0.001 HIS A 582 PHE 0.015 0.002 PHE C 254 TYR 0.017 0.001 TYR B 435 ARG 0.002 0.000 ARG A 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 5) link_NAG-ASN : angle 1.18026 ( 15) hydrogen bonds : bond 0.03830 ( 366) hydrogen bonds : angle 5.98446 ( 990) SS BOND : bond 0.00253 ( 5) SS BOND : angle 0.74259 ( 10) covalent geometry : bond 0.00417 (10039) covalent geometry : angle 0.54596 (13684) *********************** 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 151 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 SER cc_start: 0.9251 (m) cc_final: 0.8883 (p) REVERT: A 503 GLU cc_start: 0.8473 (pm20) cc_final: 0.8177 (pm20) REVERT: B 180 MET cc_start: 0.8120 (mmm) cc_final: 0.7850 (mmm) REVERT: B 278 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8735 (t-90) REVERT: B 372 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: B 469 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8628 (tttp) REVERT: C 262 TYR cc_start: 0.7745 (t80) cc_final: 0.7381 (t80) outliers start: 34 outliers final: 28 residues processed: 145 average time/residue: 0.4614 time to fit residues: 100.9522 Evaluate side-chains 147 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 ASN 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 440 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 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 278 HIS 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 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 57 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 383 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.080379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.059840 restraints weight = 95609.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.063074 restraints weight = 41710.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.065209 restraints weight = 25296.058| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1914 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= 0.120 Angle : 0.525 9.198 13709 Z= 0.269 Chirality : 0.041 0.214 1504 Planarity : 0.004 0.043 1790 Dihedral : 4.832 52.208 1477 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 2.58 % Allowed : 26.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1242 helix: 1.09 (0.27), residues: 400 sheet: -1.14 (0.38), residues: 195 loop : -1.21 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 438 HIS 0.004 0.001 HIS A 485 PHE 0.012 0.001 PHE B 413 TYR 0.019 0.001 TYR B 435 ARG 0.002 0.000 ARG A 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 5) link_NAG-ASN : angle 0.99774 ( 15) hydrogen bonds : bond 0.03640 ( 366) hydrogen bonds : angle 5.71859 ( 990) SS BOND : bond 0.00115 ( 5) SS BOND : angle 0.85653 ( 10) covalent geometry : bond 0.00272 (10039) covalent geometry : angle 0.52343 (13684) *********************** 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 150 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 SER cc_start: 0.9217 (m) cc_final: 0.8853 (p) REVERT: B 212 LEU cc_start: 0.9148 (pt) cc_final: 0.8849 (pp) REVERT: B 278 HIS cc_start: 0.9004 (OUTLIER) cc_final: 0.8753 (t-90) REVERT: B 372 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: B 469 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8612 (tttt) REVERT: C 262 TYR cc_start: 0.7596 (t80) cc_final: 0.7321 (t80) outliers start: 26 outliers final: 20 residues processed: 146 average time/residue: 0.4197 time to fit residues: 90.4236 Evaluate side-chains 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 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 269 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain 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 15 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 383 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059480 restraints weight = 95891.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.062708 restraints weight = 41912.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.064850 restraints weight = 25271.378| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1998 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= 0.157 Angle : 0.529 6.509 13709 Z= 0.274 Chirality : 0.041 0.223 1504 Planarity : 0.004 0.043 1790 Dihedral : 4.739 52.331 1475 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.09 % Favored : 92.83 % Rotamer: Outliers : 3.08 % Allowed : 25.92 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1242 helix: 1.09 (0.27), residues: 400 sheet: -1.16 (0.37), residues: 207 loop : -1.25 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 93 HIS 0.005 0.001 HIS A 184 PHE 0.013 0.001 PHE C 254 TYR 0.012 0.001 TYR B 233 ARG 0.002 0.000 ARG A 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 5) link_NAG-ASN : angle 1.09132 ( 15) hydrogen bonds : bond 0.03564 ( 366) hydrogen bonds : angle 5.70309 ( 990) SS BOND : bond 0.00190 ( 5) SS BOND : angle 0.78533 ( 10) covalent geometry : bond 0.00343 (10039) covalent geometry : angle 0.52735 (13684) *********************** 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 147 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 1.652 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 269 SER cc_start: 0.9235 (m) cc_final: 0.8862 (p) REVERT: B 278 HIS cc_start: 0.9003 (OUTLIER) cc_final: 0.8750 (t-90) REVERT: B 372 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: C 262 TYR cc_start: 0.7602 (t80) cc_final: 0.7317 (t80) outliers start: 31 outliers final: 28 residues processed: 141 average time/residue: 0.4279 time to fit residues: 90.6834 Evaluate side-chains 146 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 383 ASN 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 A residue 548 ASN Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 211 THR 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 278 HIS 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 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 89 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.080495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.059901 restraints weight = 95904.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.063186 restraints weight = 41841.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.065361 restraints weight = 25237.213| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10049 Z= 0.128 Angle : 0.520 6.090 13709 Z= 0.270 Chirality : 0.041 0.216 1504 Planarity : 0.004 0.043 1790 Dihedral : 4.764 52.511 1475 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 2.68 % Allowed : 26.02 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1242 helix: 1.18 (0.27), residues: 400 sheet: -1.22 (0.36), residues: 211 loop : -1.18 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 438 HIS 0.004 0.001 HIS A 485 PHE 0.012 0.001 PHE B 433 TYR 0.019 0.001 TYR B 233 ARG 0.002 0.000 ARG A 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 5) link_NAG-ASN : angle 1.02612 ( 15) hydrogen bonds : bond 0.03516 ( 366) hydrogen bonds : angle 5.60083 ( 990) SS BOND : bond 0.00138 ( 5) SS BOND : angle 0.70462 ( 10) covalent geometry : bond 0.00287 (10039) covalent geometry : angle 0.51945 (13684) *********************** 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 147 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 SER cc_start: 0.9209 (m) cc_final: 0.8845 (p) REVERT: A 383 ASN cc_start: 0.8520 (m-40) cc_final: 0.7945 (p0) REVERT: A 386 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8102 (mt-10) REVERT: B 212 LEU cc_start: 0.9170 (pt) cc_final: 0.8867 (pp) REVERT: B 278 HIS cc_start: 0.9010 (OUTLIER) cc_final: 0.8757 (t-90) REVERT: B 372 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: C 262 TYR cc_start: 0.7572 (t80) cc_final: 0.7280 (t80) outliers start: 27 outliers final: 25 residues processed: 142 average time/residue: 0.5062 time to fit residues: 108.3709 Evaluate side-chains 144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 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 A residue 548 ASN Chi-restraints excluded: chain B residue 145 ASN 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 278 HIS 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 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 93 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 overall best weight: 1.0960 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.080816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.060520 restraints weight = 94890.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.063775 restraints weight = 41450.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.065935 restraints weight = 25024.629| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10049 Z= 0.113 Angle : 0.518 6.104 13709 Z= 0.266 Chirality : 0.041 0.210 1504 Planarity : 0.004 0.042 1790 Dihedral : 4.681 52.776 1475 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.38 % Allowed : 26.71 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1242 helix: 1.24 (0.27), residues: 400 sheet: -1.03 (0.38), residues: 194 loop : -1.20 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.005 0.001 HIS A 582 PHE 0.016 0.001 PHE A 541 TYR 0.017 0.001 TYR B 435 ARG 0.002 0.000 ARG A 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 5) link_NAG-ASN : angle 0.99005 ( 15) hydrogen bonds : bond 0.03434 ( 366) hydrogen bonds : angle 5.54922 ( 990) SS BOND : bond 0.00104 ( 5) SS BOND : angle 0.69869 ( 10) covalent geometry : bond 0.00259 (10039) covalent geometry : angle 0.51711 (13684) ********************** 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 142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.462 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 269 SER cc_start: 0.9215 (m) cc_final: 0.8845 (p) REVERT: A 383 ASN cc_start: 0.8462 (m-40) cc_final: 0.7843 (p0) REVERT: B 212 LEU cc_start: 0.9170 (pt) cc_final: 0.8871 (pp) REVERT: B 278 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.8745 (t-90) REVERT: B 446 MET cc_start: 0.8744 (tpp) cc_final: 0.8347 (tpp) REVERT: C 262 TYR cc_start: 0.7554 (t80) cc_final: 0.7255 (t80) outliers start: 24 outliers final: 22 residues processed: 138 average time/residue: 0.4420 time to fit residues: 91.6716 Evaluate side-chains 140 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 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 A residue 548 ASN Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 374 LEU 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 52 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.080712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060371 restraints weight = 95084.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.063626 restraints weight = 41243.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065783 restraints weight = 24834.546| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10049 Z= 0.128 Angle : 0.522 6.336 13709 Z= 0.268 Chirality : 0.041 0.212 1504 Planarity : 0.004 0.042 1790 Dihedral : 4.446 52.910 1472 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.48 % Allowed : 26.81 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1242 helix: 1.23 (0.27), residues: 400 sheet: -1.16 (0.37), residues: 198 loop : -1.15 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 93 HIS 0.006 0.001 HIS A 184 PHE 0.016 0.001 PHE A 541 TYR 0.019 0.001 TYR B 233 ARG 0.002 0.000 ARG A 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 5) link_NAG-ASN : angle 1.02866 ( 15) hydrogen bonds : bond 0.03401 ( 366) hydrogen bonds : angle 5.53542 ( 990) SS BOND : bond 0.00147 ( 5) SS BOND : angle 0.67784 ( 10) covalent geometry : bond 0.00288 (10039) covalent geometry : angle 0.52126 (13684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6833.01 seconds wall clock time: 123 minutes 40.07 seconds (7420.07 seconds total)