Starting phenix.real_space_refine on Fri Jun 6 10:51:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9now_49619/06_2025/9now_49619.cif Found real_map, /net/cci-nas-00/data/ceres_data/9now_49619/06_2025/9now_49619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9now_49619/06_2025/9now_49619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9now_49619/06_2025/9now_49619.map" model { file = "/net/cci-nas-00/data/ceres_data/9now_49619/06_2025/9now_49619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9now_49619/06_2025/9now_49619.cif" } resolution = 3.1 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= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4861 2.51 5 N 1289 2.21 5 O 1422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7624 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3629 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 4 Chain: "A" Number of atoms: 3785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3785 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 21, 'TRANS': 447} Chain breaks: 3 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.92, per 1000 atoms: 0.78 Number of scatterers: 7624 At special positions: 0 Unit cell: (92.176, 88.061, 97.937, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1422 8.00 N 1289 7.00 C 4861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 517 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 518 " distance=2.02 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 102 " distance=2.02 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 513 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 517 " 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 601 " - " ASN A 487 " " NAG A 602 " - " ASN A 84 " " NAG A 603 " - " ASN A 428 " " NAG A 604 " - " ASN A 312 " " NAG A 605 " - " ASN A 248 " " NAG A 606 " - " ASN A 292 " " NAG A 607 " - " ASN A 368 " " NAG B 601 " - " ASN B 475 " " NAG B 602 " - " ASN B 285 " " NAG B 603 " - " ASN B 264 " " NAG B 604 " - " ASN B 411 " " NAG B 605 " - " ASN B 85 " " NAG B 606 " - " ASN B 130 " " NAG B 607 " - " ASN B 380 " " NAG B 608 " - " ASN B 432 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 948.6 milliseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 42.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.551A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.966A pdb=" N ALA B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 130 through 134 removed outlier: 3.911A pdb=" N GLN B 133 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 removed outlier: 4.183A pdb=" N PHE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.907A pdb=" N GLN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 234 removed outlier: 3.664A pdb=" N ALA B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.713A pdb=" N SER B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 300 through 305 removed outlier: 4.568A pdb=" N THR B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.524A pdb=" N MET B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 333 through 346 removed outlier: 3.748A pdb=" N THR B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 354 removed outlier: 3.593A pdb=" N CYS B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.636A pdb=" N ASP B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 388 through 408 removed outlier: 3.540A pdb=" N SER B 392 " --> pdb=" O HIS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 425 through 431 removed outlier: 4.371A pdb=" N ASN B 429 " --> pdb=" O GLN B 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.627A pdb=" N GLU A 61 " --> pdb=" O MET A 58 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 62 " --> pdb=" O CYS A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 62' Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.501A pdb=" N TYR A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.598A pdb=" N HIS A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 228 Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 280 through 292 removed outlier: 4.089A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 314 No H-bonds generated for 'chain 'A' and resid 313 through 314' Processing helix chain 'A' and resid 315 through 318 removed outlier: 4.119A pdb=" N HIS A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.931A pdb=" N SER A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 removed outlier: 3.643A pdb=" N GLY A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 404 removed outlier: 3.779A pdb=" N SER A 387 " --> pdb=" O ARG A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.807A pdb=" N TRP A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.548A pdb=" N GLY B 39 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain 'B' and resid 124 through 126 Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 143 removed outlier: 6.460A pdb=" N GLN B 164 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.960A pdb=" N VAL B 209 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLU B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA B 211 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU B 242 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TRP B 208 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LEU B 272 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 210 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE B 274 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU B 212 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B 271 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TRP B 297 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE B 324 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ALA B 299 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N GLN B 326 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL B 321 " --> pdb=" O TRP B 459 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 454 " --> pdb=" O ARG B 473 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG B 473 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU B 456 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AA7, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AA8, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.149A pdb=" N LEU A 35 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 99 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLY A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU A 34 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE A 139 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY A 36 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ILE A 162 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 138 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN A 161 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.706A pdb=" N GLU A 63 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 233 through 240 removed outlier: 7.723A pdb=" N ILE A 206 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN A 237 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 208 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR A 239 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 210 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP A 205 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL A 273 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 207 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE A 275 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 209 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 272 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A 296 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU A 323 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TRP A 298 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ILE A 325 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA A 300 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ILE A 327 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N PHE A 322 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 448 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER A 467 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 450 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.610A pdb=" N PHE A 429 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 506 through 507 removed outlier: 3.822A pdb=" N LYS A 506 " --> pdb=" O GLU A 516 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2418 1.34 - 1.46: 1509 1.46 - 1.58: 3802 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 7804 Sorted by residual: bond pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" CA SER B 497 " pdb=" CB SER B 497 " ideal model delta sigma weight residual 1.531 1.488 0.043 1.37e-02 5.33e+03 9.65e+00 bond pdb=" N ILE A 486 " pdb=" CA ILE A 486 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.20e-02 6.94e+03 8.20e+00 bond pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.18e-02 7.18e+03 8.14e+00 bond pdb=" N ILE A 481 " pdb=" CA ILE A 481 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.20e-02 6.94e+03 7.83e+00 ... (remaining 7799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 10385 1.99 - 3.97: 199 3.97 - 5.96: 19 5.96 - 7.95: 3 7.95 - 9.94: 3 Bond angle restraints: 10609 Sorted by residual: angle pdb=" CA THR A 485 " pdb=" CB THR A 485 " pdb=" OG1 THR A 485 " ideal model delta sigma weight residual 109.60 103.89 5.71 1.50e+00 4.44e-01 1.45e+01 angle pdb=" CA LYS A 412 " pdb=" C LYS A 412 " pdb=" O LYS A 412 " ideal model delta sigma weight residual 122.03 117.99 4.04 1.17e+00 7.31e-01 1.19e+01 angle pdb=" C ILE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.76 123.31 -3.55 1.03e+00 9.43e-01 1.19e+01 angle pdb=" N ILE B 288 " pdb=" CA ILE B 288 " pdb=" C ILE B 288 " ideal model delta sigma weight residual 110.72 107.25 3.47 1.01e+00 9.80e-01 1.18e+01 angle pdb=" N GLN A 109 " pdb=" CA GLN A 109 " pdb=" C GLN A 109 " ideal model delta sigma weight residual 113.25 109.00 4.25 1.30e+00 5.92e-01 1.07e+01 ... (remaining 10604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 4162 18.03 - 36.05: 490 36.05 - 54.08: 162 54.08 - 72.11: 35 72.11 - 90.13: 10 Dihedral angle restraints: 4859 sinusoidal: 2128 harmonic: 2731 Sorted by residual: dihedral pdb=" CB CYS A 495 " pdb=" SG CYS A 495 " pdb=" SG CYS A 514 " pdb=" CB CYS A 514 " ideal model delta sinusoidal sigma weight residual 93.00 -176.87 -90.13 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 102 " pdb=" CB CYS A 102 " ideal model delta sinusoidal sigma weight residual -86.00 -156.93 70.93 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS A 363 " pdb=" SG CYS A 363 " pdb=" SG CYS A 366 " pdb=" CB CYS A 366 " ideal model delta sinusoidal sigma weight residual -86.00 -145.11 59.11 1 1.00e+01 1.00e-02 4.67e+01 ... (remaining 4856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 974 0.050 - 0.099: 182 0.099 - 0.149: 58 0.149 - 0.199: 11 0.199 - 0.248: 7 Chirality restraints: 1232 Sorted by residual: chirality pdb=" C1 NAG B 608 " pdb=" ND2 ASN B 432 " pdb=" C2 NAG B 608 " pdb=" O5 NAG B 608 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA CYS B 499 " pdb=" N CYS B 499 " pdb=" C CYS B 499 " pdb=" CB CYS B 499 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ARG B 501 " pdb=" N ARG B 501 " pdb=" C ARG B 501 " pdb=" CB ARG B 501 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1229 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 487 " -0.129 2.00e-02 2.50e+03 1.45e-01 2.63e+02 pdb=" CG ASN A 487 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 487 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 487 " 0.233 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 170 " -0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C SER B 170 " 0.058 2.00e-02 2.50e+03 pdb=" O SER B 170 " -0.022 2.00e-02 2.50e+03 pdb=" N MET B 171 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 103 " 0.021 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR A 103 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 103 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 103 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 103 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 103 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 103 " 0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 103 " 0.000 2.00e-02 2.50e+03 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 3134 2.92 - 3.41: 7219 3.41 - 3.91: 12625 3.91 - 4.40: 14188 4.40 - 4.90: 24113 Nonbonded interactions: 61279 Sorted by model distance: nonbonded pdb=" OG1 THR A 485 " pdb=" O THR A 489 " model vdw 2.420 3.040 nonbonded pdb=" O TRP B 208 " pdb=" OG SER B 497 " model vdw 2.424 3.040 nonbonded pdb=" O ASP A 406 " pdb=" OD1 ASP A 406 " model vdw 2.462 3.040 nonbonded pdb=" OD1 ASN B 264 " pdb=" O5 NAG B 603 " model vdw 2.504 3.040 nonbonded pdb=" O MET B 171 " pdb=" NH2 ARG B 185 " model vdw 2.505 3.120 ... (remaining 61274 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.004 0.043 7833 Z= 0.237 Angle : 0.650 9.936 10682 Z= 0.367 Chirality : 0.048 0.248 1232 Planarity : 0.005 0.095 1338 Dihedral : 17.099 86.106 3045 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.97 % Allowed : 26.19 % Favored : 72.84 % 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: 0.46 (0.28), residues: 918 helix: 1.23 (0.28), residues: 343 sheet: -1.30 (0.45), residues: 135 loop : 0.25 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 208 HIS 0.008 0.001 HIS A 397 PHE 0.007 0.001 PHE A 236 TYR 0.049 0.002 TYR A 103 ARG 0.003 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 15) link_NAG-ASN : angle 2.67355 ( 45) hydrogen bonds : bond 0.14243 ( 276) hydrogen bonds : angle 5.71719 ( 768) SS BOND : bond 0.00441 ( 14) SS BOND : angle 0.97346 ( 28) covalent geometry : bond 0.00378 ( 7804) covalent geometry : angle 0.62637 (10609) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.740 Fit side-chains REVERT: B 111 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7909 (tttt) REVERT: B 516 SER cc_start: 0.9129 (m) cc_final: 0.8857 (t) REVERT: A 60 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8147 (tptt) REVERT: A 142 ASP cc_start: 0.7362 (p0) cc_final: 0.7043 (t0) REVERT: A 309 VAL cc_start: 0.9215 (p) cc_final: 0.8998 (t) outliers start: 8 outliers final: 4 residues processed: 183 average time/residue: 0.2460 time to fit residues: 57.3630 Evaluate side-chains 102 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain A residue 405 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.0000 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101320 restraints weight = 12293.617| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.28 r_work: 0.3186 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7833 Z= 0.113 Angle : 0.539 9.543 10682 Z= 0.259 Chirality : 0.044 0.269 1232 Planarity : 0.003 0.050 1338 Dihedral : 7.355 58.576 1332 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.14 % Allowed : 24.12 % Favored : 71.74 % 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: 0.68 (0.29), residues: 918 helix: 1.43 (0.29), residues: 346 sheet: -1.32 (0.43), residues: 138 loop : 0.44 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 208 HIS 0.005 0.001 HIS A 397 PHE 0.015 0.001 PHE B 159 TYR 0.013 0.001 TYR B 394 ARG 0.005 0.000 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 15) link_NAG-ASN : angle 2.31131 ( 45) hydrogen bonds : bond 0.03474 ( 276) hydrogen bonds : angle 4.33591 ( 768) SS BOND : bond 0.00142 ( 14) SS BOND : angle 0.76721 ( 28) covalent geometry : bond 0.00264 ( 7804) covalent geometry : angle 0.51829 (10609) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.852 Fit side-chains REVERT: B 111 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7635 (tttt) REVERT: B 115 MET cc_start: 0.7607 (tpp) cc_final: 0.7393 (tpp) REVERT: B 315 MET cc_start: 0.8699 (tpt) cc_final: 0.8273 (tpt) REVERT: B 379 GLN cc_start: 0.8808 (mp10) cc_final: 0.8502 (pt0) REVERT: B 469 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7402 (t70) REVERT: A 28 TYR cc_start: 0.7827 (t80) cc_final: 0.7585 (t80) REVERT: A 60 LYS cc_start: 0.8525 (ttmm) cc_final: 0.7848 (tptt) REVERT: A 142 ASP cc_start: 0.7719 (p0) cc_final: 0.6936 (t0) REVERT: A 256 ARG cc_start: 0.7934 (tpt170) cc_final: 0.7706 (tpt170) outliers start: 34 outliers final: 13 residues processed: 133 average time/residue: 0.1901 time to fit residues: 34.7942 Evaluate side-chains 107 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 508 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN B 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098252 restraints weight = 12555.091| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.32 r_work: 0.3142 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7833 Z= 0.134 Angle : 0.531 9.618 10682 Z= 0.256 Chirality : 0.043 0.227 1232 Planarity : 0.003 0.036 1338 Dihedral : 7.050 59.689 1330 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.99 % Allowed : 23.87 % Favored : 71.13 % 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: 0.89 (0.29), residues: 918 helix: 1.53 (0.29), residues: 340 sheet: -1.26 (0.42), residues: 143 loop : 0.69 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 208 HIS 0.004 0.001 HIS A 397 PHE 0.011 0.001 PHE B 159 TYR 0.014 0.001 TYR B 394 ARG 0.006 0.000 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 15) link_NAG-ASN : angle 2.14471 ( 45) hydrogen bonds : bond 0.03430 ( 276) hydrogen bonds : angle 4.09339 ( 768) SS BOND : bond 0.00193 ( 14) SS BOND : angle 0.87114 ( 28) covalent geometry : bond 0.00317 ( 7804) covalent geometry : angle 0.51186 (10609) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.781 Fit side-chains REVERT: B 111 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7601 (tttt) REVERT: B 315 MET cc_start: 0.8805 (tpt) cc_final: 0.8430 (tpt) REVERT: B 379 GLN cc_start: 0.8736 (mp10) cc_final: 0.8481 (pt0) REVERT: B 451 ASP cc_start: 0.8584 (t0) cc_final: 0.7976 (p0) REVERT: B 469 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.7518 (t70) REVERT: A 60 LYS cc_start: 0.8595 (ttmm) cc_final: 0.7859 (tptt) REVERT: A 256 ARG cc_start: 0.7940 (tpt170) cc_final: 0.7536 (tpt170) REVERT: A 313 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7520 (mp) outliers start: 41 outliers final: 26 residues processed: 134 average time/residue: 0.1784 time to fit residues: 33.0983 Evaluate side-chains 115 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.091345 restraints weight = 12660.580| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.16 r_work: 0.3039 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 7833 Z= 0.306 Angle : 0.693 9.578 10682 Z= 0.336 Chirality : 0.048 0.237 1232 Planarity : 0.004 0.037 1338 Dihedral : 7.655 57.921 1330 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 6.09 % Allowed : 22.90 % Favored : 71.01 % 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: 0.30 (0.28), residues: 918 helix: 0.94 (0.28), residues: 339 sheet: -1.26 (0.39), residues: 157 loop : 0.37 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 208 HIS 0.006 0.001 HIS A 484 PHE 0.012 0.002 PHE A 429 TYR 0.026 0.002 TYR A 389 ARG 0.006 0.001 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 15) link_NAG-ASN : angle 2.67399 ( 45) hydrogen bonds : bond 0.04628 ( 276) hydrogen bonds : angle 4.48487 ( 768) SS BOND : bond 0.00377 ( 14) SS BOND : angle 1.41157 ( 28) covalent geometry : bond 0.00730 ( 7804) covalent geometry : angle 0.66916 (10609) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 89 time to evaluate : 0.844 Fit side-chains REVERT: B 111 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7560 (tttp) REVERT: B 301 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8451 (mm-30) REVERT: B 315 MET cc_start: 0.8727 (tpt) cc_final: 0.8379 (tpt) REVERT: B 469 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7624 (t70) REVERT: A 60 LYS cc_start: 0.8761 (ttmm) cc_final: 0.7850 (tptt) REVERT: A 256 ARG cc_start: 0.8010 (tpt170) cc_final: 0.7643 (tpt170) outliers start: 50 outliers final: 32 residues processed: 132 average time/residue: 0.1736 time to fit residues: 32.2050 Evaluate side-chains 116 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 281 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095311 restraints weight = 12469.408| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.24 r_work: 0.3097 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7833 Z= 0.129 Angle : 0.528 9.508 10682 Z= 0.255 Chirality : 0.044 0.226 1232 Planarity : 0.003 0.029 1338 Dihedral : 7.192 56.924 1330 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 4.51 % Allowed : 25.09 % Favored : 70.40 % 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: 0.57 (0.28), residues: 918 helix: 1.32 (0.29), residues: 340 sheet: -1.26 (0.39), residues: 155 loop : 0.44 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 208 HIS 0.003 0.001 HIS A 484 PHE 0.011 0.001 PHE A 515 TYR 0.015 0.001 TYR A 389 ARG 0.006 0.000 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 15) link_NAG-ASN : angle 2.17309 ( 45) hydrogen bonds : bond 0.03462 ( 276) hydrogen bonds : angle 4.09813 ( 768) SS BOND : bond 0.00351 ( 14) SS BOND : angle 0.79787 ( 28) covalent geometry : bond 0.00306 ( 7804) covalent geometry : angle 0.50881 (10609) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.875 Fit side-chains REVERT: B 111 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7490 (tttt) REVERT: B 257 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8400 (tp40) REVERT: B 315 MET cc_start: 0.8755 (tpt) cc_final: 0.8428 (tpt) REVERT: B 469 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7492 (t70) REVERT: A 60 LYS cc_start: 0.8800 (ttmm) cc_final: 0.7828 (tptt) outliers start: 37 outliers final: 27 residues processed: 126 average time/residue: 0.2042 time to fit residues: 34.8887 Evaluate side-chains 117 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 510 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093502 restraints weight = 12514.885| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.25 r_work: 0.3068 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7833 Z= 0.189 Angle : 0.599 11.752 10682 Z= 0.284 Chirality : 0.054 1.074 1232 Planarity : 0.004 0.031 1338 Dihedral : 7.378 58.711 1328 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.99 % Allowed : 24.85 % Favored : 70.16 % 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: 0.50 (0.28), residues: 918 helix: 1.25 (0.28), residues: 340 sheet: -1.21 (0.39), residues: 155 loop : 0.38 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 208 HIS 0.003 0.001 HIS A 484 PHE 0.012 0.001 PHE A 293 TYR 0.019 0.002 TYR A 282 ARG 0.007 0.000 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 15) link_NAG-ASN : angle 3.14162 ( 45) hydrogen bonds : bond 0.03863 ( 276) hydrogen bonds : angle 4.15454 ( 768) SS BOND : bond 0.00227 ( 14) SS BOND : angle 0.94014 ( 28) covalent geometry : bond 0.00452 ( 7804) covalent geometry : angle 0.56315 (10609) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.806 Fit side-chains REVERT: B 111 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7521 (tttt) REVERT: B 257 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8405 (tp40) REVERT: B 301 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8362 (mm-30) REVERT: B 312 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8330 (mp) REVERT: B 315 MET cc_start: 0.8750 (tpt) cc_final: 0.8392 (tpt) REVERT: B 462 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7535 (pp30) REVERT: B 469 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7558 (t70) REVERT: A 60 LYS cc_start: 0.8816 (ttmm) cc_final: 0.7805 (tptt) outliers start: 41 outliers final: 30 residues processed: 121 average time/residue: 0.1970 time to fit residues: 32.7159 Evaluate side-chains 121 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 26 optimal weight: 0.0370 chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095941 restraints weight = 12359.529| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.25 r_work: 0.3108 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7833 Z= 0.118 Angle : 0.541 12.616 10682 Z= 0.258 Chirality : 0.046 0.593 1232 Planarity : 0.003 0.031 1338 Dihedral : 7.171 56.872 1328 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.87 % Allowed : 25.21 % 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: 0.69 (0.28), residues: 918 helix: 1.44 (0.29), residues: 340 sheet: -1.06 (0.42), residues: 140 loop : 0.35 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 208 HIS 0.003 0.001 HIS A 189 PHE 0.010 0.001 PHE A 515 TYR 0.016 0.001 TYR A 282 ARG 0.007 0.000 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 15) link_NAG-ASN : angle 2.93158 ( 45) hydrogen bonds : bond 0.03417 ( 276) hydrogen bonds : angle 4.02326 ( 768) SS BOND : bond 0.00134 ( 14) SS BOND : angle 0.69120 ( 28) covalent geometry : bond 0.00281 ( 7804) covalent geometry : angle 0.50684 (10609) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.779 Fit side-chains REVERT: B 111 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7492 (tttt) REVERT: B 257 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8412 (tp40) REVERT: B 315 MET cc_start: 0.8760 (tpt) cc_final: 0.8408 (tpt) REVERT: B 462 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7600 (pp30) REVERT: B 469 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.7315 (t70) REVERT: A 60 LYS cc_start: 0.8822 (ttmm) cc_final: 0.7792 (tptt) outliers start: 40 outliers final: 31 residues processed: 126 average time/residue: 0.1871 time to fit residues: 32.4410 Evaluate side-chains 122 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.096337 restraints weight = 12595.013| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.27 r_work: 0.3114 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7833 Z= 0.123 Angle : 0.543 12.594 10682 Z= 0.258 Chirality : 0.045 0.465 1232 Planarity : 0.003 0.031 1338 Dihedral : 7.037 58.513 1328 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.99 % Allowed : 25.21 % Favored : 69.79 % 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: 0.82 (0.29), residues: 918 helix: 1.51 (0.29), residues: 340 sheet: -0.78 (0.42), residues: 139 loop : 0.38 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 208 HIS 0.002 0.001 HIS A 484 PHE 0.018 0.001 PHE B 159 TYR 0.013 0.001 TYR A 389 ARG 0.006 0.000 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 15) link_NAG-ASN : angle 2.82321 ( 45) hydrogen bonds : bond 0.03358 ( 276) hydrogen bonds : angle 3.99231 ( 768) SS BOND : bond 0.00141 ( 14) SS BOND : angle 0.67731 ( 28) covalent geometry : bond 0.00296 ( 7804) covalent geometry : angle 0.51224 (10609) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.795 Fit side-chains REVERT: B 111 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7529 (tttp) REVERT: B 257 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8449 (tp40) REVERT: B 315 MET cc_start: 0.8761 (tpt) cc_final: 0.8386 (tpt) REVERT: B 462 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7618 (pp30) REVERT: B 469 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7253 (t70) REVERT: A 60 LYS cc_start: 0.8797 (ttmm) cc_final: 0.7766 (tptt) outliers start: 41 outliers final: 32 residues processed: 123 average time/residue: 0.1950 time to fit residues: 32.9984 Evaluate side-chains 124 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.117976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096761 restraints weight = 12641.514| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.27 r_work: 0.3119 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7833 Z= 0.121 Angle : 0.540 12.195 10682 Z= 0.256 Chirality : 0.045 0.418 1232 Planarity : 0.003 0.031 1338 Dihedral : 6.876 59.871 1328 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.63 % Allowed : 25.46 % 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: 0.78 (0.29), residues: 918 helix: 1.56 (0.29), residues: 340 sheet: -1.06 (0.41), residues: 145 loop : 0.41 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 303 HIS 0.002 0.001 HIS A 484 PHE 0.019 0.001 PHE B 159 TYR 0.014 0.001 TYR A 389 ARG 0.005 0.000 ARG B 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 15) link_NAG-ASN : angle 2.70447 ( 45) hydrogen bonds : bond 0.03266 ( 276) hydrogen bonds : angle 3.91826 ( 768) SS BOND : bond 0.00137 ( 14) SS BOND : angle 0.68848 ( 28) covalent geometry : bond 0.00293 ( 7804) covalent geometry : angle 0.51117 (10609) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 1.293 Fit side-chains REVERT: B 111 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7501 (tttp) REVERT: B 257 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8433 (tp40) REVERT: B 315 MET cc_start: 0.8731 (tpt) cc_final: 0.8353 (tpt) REVERT: B 462 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7671 (pp30) REVERT: B 469 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7276 (t70) REVERT: A 60 LYS cc_start: 0.8777 (ttmm) cc_final: 0.7762 (tptt) REVERT: A 256 ARG cc_start: 0.7997 (tpt170) cc_final: 0.7678 (tpt170) outliers start: 38 outliers final: 31 residues processed: 124 average time/residue: 0.2895 time to fit residues: 49.3533 Evaluate side-chains 122 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 68 optimal weight: 0.0980 chunk 60 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097882 restraints weight = 12575.931| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.27 r_work: 0.3135 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7833 Z= 0.107 Angle : 0.537 12.086 10682 Z= 0.254 Chirality : 0.044 0.387 1232 Planarity : 0.003 0.031 1338 Dihedral : 6.746 58.854 1328 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.51 % Allowed : 25.94 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.29), residues: 918 helix: 1.79 (0.29), residues: 334 sheet: -0.84 (0.43), residues: 142 loop : 0.48 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 303 HIS 0.002 0.001 HIS A 484 PHE 0.017 0.001 PHE B 159 TYR 0.011 0.001 TYR A 389 ARG 0.004 0.000 ARG B 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 15) link_NAG-ASN : angle 2.63964 ( 45) hydrogen bonds : bond 0.03102 ( 276) hydrogen bonds : angle 3.85000 ( 768) SS BOND : bond 0.00119 ( 14) SS BOND : angle 0.59352 ( 28) covalent geometry : bond 0.00256 ( 7804) covalent geometry : angle 0.50998 (10609) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.782 Fit side-chains REVERT: B 111 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7445 (tttp) REVERT: B 257 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8450 (tp40) REVERT: B 315 MET cc_start: 0.8703 (tpt) cc_final: 0.8290 (tpt) REVERT: B 462 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7747 (pp30) REVERT: A 60 LYS cc_start: 0.8749 (ttmm) cc_final: 0.7727 (tptt) outliers start: 37 outliers final: 27 residues processed: 122 average time/residue: 0.1946 time to fit residues: 33.1806 Evaluate side-chains 118 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097659 restraints weight = 12451.193| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.25 r_work: 0.3135 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 7833 Z= 0.157 Angle : 0.932 59.192 10682 Z= 0.535 Chirality : 0.046 0.431 1232 Planarity : 0.003 0.031 1338 Dihedral : 6.797 58.805 1328 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.90 % Allowed : 26.07 % Favored : 70.04 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.01 (0.29), residues: 918 helix: 1.78 (0.29), residues: 334 sheet: -0.83 (0.43), residues: 142 loop : 0.48 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 303 HIS 0.002 0.001 HIS A 484 PHE 0.016 0.001 PHE B 159 TYR 0.012 0.001 TYR A 389 ARG 0.004 0.000 ARG B 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 15) link_NAG-ASN : angle 2.63879 ( 45) hydrogen bonds : bond 0.03129 ( 276) hydrogen bonds : angle 3.85125 ( 768) SS BOND : bond 0.00117 ( 14) SS BOND : angle 0.58402 ( 28) covalent geometry : bond 0.00345 ( 7804) covalent geometry : angle 0.91830 (10609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3692.64 seconds wall clock time: 65 minutes 24.84 seconds (3924.84 seconds total)