Starting phenix.real_space_refine on Fri Aug 22 20:18:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9now_49619/08_2025/9now_49619.cif Found real_map, /net/cci-nas-00/data/ceres_data/9now_49619/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9now_49619/08_2025/9now_49619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9now_49619/08_2025/9now_49619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9now_49619/08_2025/9now_49619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9now_49619/08_2025/9now_49619.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.94, per 1000 atoms: 0.25 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: 0.67 Conformation dependent library (CDL) restraints added in 330.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.32 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: 1.28 Time building geometry restraints manager: 0.91 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: 7.180 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (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 ARG 0.003 0.000 ARG B 498 TYR 0.049 0.002 TYR A 103 PHE 0.007 0.001 PHE A 236 TRP 0.009 0.001 TRP B 208 HIS 0.008 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7804) covalent geometry : angle 0.62637 (10609) SS BOND : bond 0.00441 ( 14) SS BOND : angle 0.97346 ( 28) hydrogen bonds : bond 0.14243 ( 276) hydrogen bonds : angle 5.71719 ( 768) link_NAG-ASN : bond 0.00494 ( 15) link_NAG-ASN : angle 2.67355 ( 45) *********************** 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 : 0.317 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: 0.1251 time to fit residues: 29.2015 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 : 0.296 ------------------------------------------------------------------------------- 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 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.120847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099722 restraints weight = 12352.727| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.24 r_work: 0.3167 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7833 Z= 0.137 Angle : 0.557 9.558 10682 Z= 0.268 Chirality : 0.044 0.270 1232 Planarity : 0.003 0.051 1338 Dihedral : 7.429 59.358 1332 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.51 % Allowed : 24.00 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.29), residues: 918 helix: 1.50 (0.29), residues: 340 sheet: -1.39 (0.42), residues: 143 loop : 0.58 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 467 TYR 0.014 0.001 TYR B 394 PHE 0.014 0.001 PHE B 159 TRP 0.010 0.001 TRP B 208 HIS 0.005 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7804) covalent geometry : angle 0.53512 (10609) SS BOND : bond 0.00148 ( 14) SS BOND : angle 0.85373 ( 28) hydrogen bonds : bond 0.03628 ( 276) hydrogen bonds : angle 4.38466 ( 768) link_NAG-ASN : bond 0.00394 ( 15) link_NAG-ASN : angle 2.40071 ( 45) *********************** 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 135 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.296 Fit side-chains REVERT: B 111 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7626 (tttt) REVERT: B 269 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8080 (mm110) REVERT: B 315 MET cc_start: 0.8703 (tpt) cc_final: 0.8299 (tpt) REVERT: B 379 GLN cc_start: 0.8801 (mp10) cc_final: 0.8477 (pt0) REVERT: B 469 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7408 (t70) REVERT: A 60 LYS cc_start: 0.8560 (ttmm) cc_final: 0.7909 (tptt) REVERT: A 142 ASP cc_start: 0.7819 (p0) cc_final: 0.6974 (t0) REVERT: A 397 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7571 (m170) outliers start: 37 outliers final: 16 residues processed: 131 average time/residue: 0.0866 time to fit residues: 15.9378 Evaluate side-chains 102 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 102 THR Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 269 GLN 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 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 371 LEU Chi-restraints excluded: chain A residue 397 HIS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.117433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096190 restraints weight = 12429.008| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.25 r_work: 0.3122 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7833 Z= 0.163 Angle : 0.557 9.636 10682 Z= 0.268 Chirality : 0.044 0.230 1232 Planarity : 0.003 0.038 1338 Dihedral : 7.196 59.998 1330 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 6.58 % Allowed : 23.14 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.29), residues: 918 helix: 1.45 (0.28), residues: 340 sheet: -1.14 (0.41), residues: 154 loop : 0.58 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.016 0.001 TYR A 389 PHE 0.012 0.001 PHE A 515 TRP 0.009 0.001 TRP B 208 HIS 0.004 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7804) covalent geometry : angle 0.53599 (10609) SS BOND : bond 0.00236 ( 14) SS BOND : angle 1.01297 ( 28) hydrogen bonds : bond 0.03703 ( 276) hydrogen bonds : angle 4.20809 ( 768) link_NAG-ASN : bond 0.00365 ( 15) link_NAG-ASN : angle 2.27653 ( 45) *********************** 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 140 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 86 time to evaluate : 0.316 Fit side-chains REVERT: B 111 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7638 (tttt) REVERT: B 262 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7194 (mp10) REVERT: B 269 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8107 (mm110) REVERT: B 315 MET cc_start: 0.8833 (tpt) cc_final: 0.8490 (tpt) REVERT: B 451 ASP cc_start: 0.8546 (t0) cc_final: 0.8008 (p0) REVERT: B 469 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7650 (t70) REVERT: A 60 LYS cc_start: 0.8606 (ttmm) cc_final: 0.7876 (tptt) REVERT: A 244 GLN cc_start: 0.8012 (mp10) cc_final: 0.7795 (mp10) outliers start: 54 outliers final: 30 residues processed: 135 average time/residue: 0.0821 time to fit residues: 15.7341 Evaluate side-chains 113 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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 269 GLN Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 433 LEU 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 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 371 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 46 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.118931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097683 restraints weight = 12559.186| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.27 r_work: 0.3133 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7833 Z= 0.122 Angle : 0.512 9.529 10682 Z= 0.247 Chirality : 0.043 0.229 1232 Planarity : 0.003 0.029 1338 Dihedral : 6.952 57.204 1330 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.38 % Allowed : 24.12 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.29), residues: 918 helix: 1.55 (0.29), residues: 340 sheet: -1.11 (0.41), residues: 153 loop : 0.59 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 291 TYR 0.013 0.001 TYR B 394 PHE 0.011 0.001 PHE A 515 TRP 0.010 0.001 TRP B 208 HIS 0.003 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7804) covalent geometry : angle 0.49332 (10609) SS BOND : bond 0.00156 ( 14) SS BOND : angle 0.91409 ( 28) hydrogen bonds : bond 0.03279 ( 276) hydrogen bonds : angle 4.03839 ( 768) link_NAG-ASN : bond 0.00374 ( 15) link_NAG-ASN : angle 2.08953 ( 45) *********************** 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 126 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.304 Fit side-chains REVERT: B 111 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7543 (tttt) REVERT: B 269 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7964 (mm110) REVERT: B 315 MET cc_start: 0.8752 (tpt) cc_final: 0.8344 (tpt) REVERT: B 469 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7501 (t70) REVERT: A 60 LYS cc_start: 0.8625 (ttmm) cc_final: 0.7854 (tptt) REVERT: A 244 GLN cc_start: 0.7971 (mp10) cc_final: 0.7692 (mp10) outliers start: 36 outliers final: 22 residues processed: 120 average time/residue: 0.0849 time to fit residues: 14.4143 Evaluate side-chains 103 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 111 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 446 SER 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 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 371 LEU 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 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 49 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 43 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.119312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097067 restraints weight = 12320.238| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.29 r_work: 0.3120 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7833 Z= 0.122 Angle : 0.513 9.536 10682 Z= 0.245 Chirality : 0.043 0.228 1232 Planarity : 0.003 0.028 1338 Dihedral : 6.842 56.499 1330 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.99 % Allowed : 24.73 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.29), residues: 918 helix: 1.56 (0.29), residues: 340 sheet: -1.07 (0.40), residues: 153 loop : 0.62 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 291 TYR 0.014 0.001 TYR A 389 PHE 0.011 0.001 PHE A 515 TRP 0.009 0.001 TRP B 208 HIS 0.003 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7804) covalent geometry : angle 0.49306 (10609) SS BOND : bond 0.00170 ( 14) SS BOND : angle 0.82786 ( 28) hydrogen bonds : bond 0.03265 ( 276) hydrogen bonds : angle 3.94845 ( 768) link_NAG-ASN : bond 0.00549 ( 15) link_NAG-ASN : angle 2.19888 ( 45) *********************** 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: 41 poor density : 93 time to evaluate : 0.315 Fit side-chains REVERT: B 111 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7615 (tttt) REVERT: B 159 PHE cc_start: 0.9054 (t80) cc_final: 0.8758 (t80) REVERT: B 269 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8010 (mm110) REVERT: B 312 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8271 (mp) REVERT: B 315 MET cc_start: 0.8783 (tpt) cc_final: 0.8373 (tpt) REVERT: A 60 LYS cc_start: 0.8613 (ttmm) cc_final: 0.7852 (tptt) REVERT: A 244 GLN cc_start: 0.7978 (mp10) cc_final: 0.7689 (mp10) REVERT: A 256 ARG cc_start: 0.7779 (tpt90) cc_final: 0.7523 (tpt170) outliers start: 41 outliers final: 28 residues processed: 123 average time/residue: 0.0874 time to fit residues: 15.0167 Evaluate side-chains 117 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 108 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 446 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 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 264 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.119583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098108 restraints weight = 12407.987| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.21 r_work: 0.3133 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7833 Z= 0.120 Angle : 0.513 9.527 10682 Z= 0.245 Chirality : 0.043 0.227 1232 Planarity : 0.003 0.029 1338 Dihedral : 6.772 56.668 1328 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.87 % Allowed : 24.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.29), residues: 918 helix: 1.59 (0.28), residues: 340 sheet: -1.08 (0.40), residues: 153 loop : 0.62 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 291 TYR 0.013 0.001 TYR A 389 PHE 0.010 0.001 PHE A 515 TRP 0.009 0.001 TRP B 208 HIS 0.003 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7804) covalent geometry : angle 0.49432 (10609) SS BOND : bond 0.00143 ( 14) SS BOND : angle 0.72794 ( 28) hydrogen bonds : bond 0.03199 ( 276) hydrogen bonds : angle 3.91965 ( 768) link_NAG-ASN : bond 0.00422 ( 15) link_NAG-ASN : angle 2.12189 ( 45) *********************** 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 131 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.300 Fit side-chains REVERT: B 111 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7595 (tttt) REVERT: B 159 PHE cc_start: 0.9010 (t80) cc_final: 0.8735 (t80) REVERT: B 257 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8425 (tp40) REVERT: B 269 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8049 (mm-40) REVERT: B 315 MET cc_start: 0.8776 (tpt) cc_final: 0.8351 (tpt) REVERT: B 462 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7641 (pp30) REVERT: B 469 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7455 (t70) REVERT: A 60 LYS cc_start: 0.8613 (ttmm) cc_final: 0.7856 (tptt) REVERT: A 244 GLN cc_start: 0.8000 (mp10) cc_final: 0.7711 (mp10) outliers start: 40 outliers final: 28 residues processed: 123 average time/residue: 0.0863 time to fit residues: 15.0124 Evaluate side-chains 121 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 101 ASP 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 268 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 272 LEU 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 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 144 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 THR 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 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 18 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.115635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.093400 restraints weight = 12446.507| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.24 r_work: 0.3070 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7833 Z= 0.208 Angle : 0.587 9.494 10682 Z= 0.281 Chirality : 0.045 0.225 1232 Planarity : 0.003 0.029 1338 Dihedral : 7.084 59.233 1328 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.99 % Allowed : 24.97 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.28), residues: 918 helix: 1.31 (0.28), residues: 340 sheet: -1.00 (0.41), residues: 150 loop : 0.44 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 291 TYR 0.022 0.002 TYR A 389 PHE 0.011 0.001 PHE A 515 TRP 0.009 0.001 TRP B 208 HIS 0.004 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 7804) covalent geometry : angle 0.56726 (10609) SS BOND : bond 0.00261 ( 14) SS BOND : angle 1.04749 ( 28) hydrogen bonds : bond 0.03870 ( 276) hydrogen bonds : angle 4.15970 ( 768) link_NAG-ASN : bond 0.00350 ( 15) link_NAG-ASN : angle 2.29276 ( 45) *********************** 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 130 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.325 Fit side-chains REVERT: B 111 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7572 (tttt) REVERT: B 257 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8407 (tp40) REVERT: B 269 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8093 (mm-40) REVERT: B 312 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8250 (mp) REVERT: B 315 MET cc_start: 0.8749 (tpt) cc_final: 0.8401 (tpt) REVERT: B 462 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7559 (pp30) REVERT: B 469 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7615 (t70) REVERT: A 60 LYS cc_start: 0.8770 (ttmm) cc_final: 0.7790 (tptt) REVERT: A 244 GLN cc_start: 0.8015 (mp10) cc_final: 0.7695 (mp10) outliers start: 41 outliers final: 28 residues processed: 123 average time/residue: 0.0909 time to fit residues: 15.5349 Evaluate side-chains 119 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 101 ASP 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 268 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 312 LEU 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 446 SER 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 242 THR 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 374 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 48 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.118544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096714 restraints weight = 12398.136| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.25 r_work: 0.3119 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7833 Z= 0.115 Angle : 0.518 9.504 10682 Z= 0.249 Chirality : 0.043 0.227 1232 Planarity : 0.003 0.030 1338 Dihedral : 6.850 56.521 1328 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.29), residues: 918 helix: 1.52 (0.29), residues: 340 sheet: -1.06 (0.40), residues: 153 loop : 0.46 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 291 TYR 0.014 0.001 TYR A 389 PHE 0.009 0.001 PHE A 515 TRP 0.010 0.001 TRP B 303 HIS 0.003 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7804) covalent geometry : angle 0.50067 (10609) SS BOND : bond 0.00118 ( 14) SS BOND : angle 0.66758 ( 28) hydrogen bonds : bond 0.03235 ( 276) hydrogen bonds : angle 3.98967 ( 768) link_NAG-ASN : bond 0.00411 ( 15) link_NAG-ASN : angle 2.08055 ( 45) *********************** 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 128 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.317 Fit side-chains REVERT: B 111 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7583 (tttt) REVERT: B 257 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8444 (tp40) REVERT: B 269 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8084 (mm-40) REVERT: B 292 LEU cc_start: 0.7708 (tp) cc_final: 0.7463 (tp) REVERT: B 312 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8257 (mp) REVERT: B 315 MET cc_start: 0.8799 (tpt) cc_final: 0.8415 (tpt) REVERT: B 451 ASP cc_start: 0.8340 (t0) cc_final: 0.7600 (p0) REVERT: B 462 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7585 (pp30) REVERT: B 469 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7465 (t70) REVERT: A 60 LYS cc_start: 0.8823 (ttmm) cc_final: 0.7830 (tptt) REVERT: A 244 GLN cc_start: 0.8001 (mp10) cc_final: 0.7681 (mp10) outliers start: 38 outliers final: 26 residues processed: 121 average time/residue: 0.0980 time to fit residues: 16.2060 Evaluate side-chains 118 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 101 ASP 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 268 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 312 LEU 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 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 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 306 ILE 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 510 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.115863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.093951 restraints weight = 12414.576| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.23 r_work: 0.3085 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7833 Z= 0.179 Angle : 0.572 10.383 10682 Z= 0.273 Chirality : 0.044 0.233 1232 Planarity : 0.003 0.029 1338 Dihedral : 6.983 58.790 1328 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.29), residues: 918 helix: 1.36 (0.28), residues: 340 sheet: -0.94 (0.40), residues: 156 loop : 0.45 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 291 TYR 0.019 0.001 TYR A 389 PHE 0.020 0.001 PHE B 159 TRP 0.009 0.001 TRP B 208 HIS 0.004 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 7804) covalent geometry : angle 0.55458 (10609) SS BOND : bond 0.00223 ( 14) SS BOND : angle 0.89841 ( 28) hydrogen bonds : bond 0.03646 ( 276) hydrogen bonds : angle 4.06034 ( 768) link_NAG-ASN : bond 0.00345 ( 15) link_NAG-ASN : angle 2.16598 ( 45) *********************** 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 123 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 0.325 Fit side-chains REVERT: B 111 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7596 (tttt) REVERT: B 257 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8427 (tp40) REVERT: B 269 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8125 (mm-40) REVERT: B 292 LEU cc_start: 0.7734 (tp) cc_final: 0.7475 (tp) REVERT: B 312 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8271 (mp) REVERT: B 315 MET cc_start: 0.8768 (tpt) cc_final: 0.8404 (tpt) REVERT: B 451 ASP cc_start: 0.8387 (t0) cc_final: 0.7653 (p0) REVERT: B 462 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7676 (pp30) REVERT: B 469 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.7517 (t70) REVERT: A 60 LYS cc_start: 0.8833 (ttmm) cc_final: 0.7840 (tptt) REVERT: A 244 GLN cc_start: 0.8033 (mp10) cc_final: 0.7707 (mp10) outliers start: 38 outliers final: 29 residues processed: 116 average time/residue: 0.0883 time to fit residues: 14.2948 Evaluate side-chains 117 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 101 ASP 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 268 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 312 LEU 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 434 THR 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 144 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 THR 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 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 45 optimal weight: 5.9990 chunk 25 optimal weight: 0.0470 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 0.0370 chunk 22 optimal weight: 2.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.120152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097788 restraints weight = 12355.357| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.30 r_work: 0.3138 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7833 Z= 0.101 Angle : 0.515 9.856 10682 Z= 0.246 Chirality : 0.042 0.228 1232 Planarity : 0.003 0.030 1338 Dihedral : 6.742 59.160 1328 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.38 % Allowed : 25.70 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.29), residues: 918 helix: 1.57 (0.29), residues: 340 sheet: -1.02 (0.41), residues: 153 loop : 0.56 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 291 TYR 0.010 0.001 TYR B 394 PHE 0.018 0.001 PHE B 159 TRP 0.011 0.001 TRP B 303 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7804) covalent geometry : angle 0.49966 (10609) SS BOND : bond 0.00113 ( 14) SS BOND : angle 0.61092 ( 28) hydrogen bonds : bond 0.03022 ( 276) hydrogen bonds : angle 3.90422 ( 768) link_NAG-ASN : bond 0.00430 ( 15) link_NAG-ASN : angle 1.96287 ( 45) ********************** 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 128 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.303 Fit side-chains REVERT: B 111 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7485 (tttt) REVERT: B 257 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8447 (tp40) REVERT: B 269 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7991 (mm-40) REVERT: B 312 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8244 (mp) REVERT: B 315 MET cc_start: 0.8756 (tpt) cc_final: 0.8336 (tpt) REVERT: B 451 ASP cc_start: 0.8350 (t0) cc_final: 0.7540 (p0) REVERT: B 469 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7425 (t70) REVERT: A 60 LYS cc_start: 0.8789 (ttmm) cc_final: 0.7780 (tptt) REVERT: A 244 GLN cc_start: 0.7980 (mp10) cc_final: 0.7721 (mp10) outliers start: 36 outliers final: 29 residues processed: 120 average time/residue: 0.0921 time to fit residues: 15.3701 Evaluate side-chains 121 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 101 ASP 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 268 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 272 LEU 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 446 SER 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 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 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 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 38 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 0.0070 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3580 r_free = 0.3580 target = 0.119922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097597 restraints weight = 12395.709| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.31 r_work: 0.3131 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 7833 Z= 0.175 Angle : 0.930 59.154 10682 Z= 0.538 Chirality : 0.044 0.337 1232 Planarity : 0.003 0.030 1338 Dihedral : 6.806 59.212 1328 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.02 % Allowed : 25.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.29), residues: 918 helix: 1.56 (0.29), residues: 340 sheet: -1.02 (0.41), residues: 153 loop : 0.57 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.010 0.001 TYR A 389 PHE 0.016 0.001 PHE B 159 TRP 0.010 0.001 TRP B 303 HIS 0.002 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7804) covalent geometry : angle 0.92428 (10609) SS BOND : bond 0.00112 ( 14) SS BOND : angle 0.59931 ( 28) hydrogen bonds : bond 0.03047 ( 276) hydrogen bonds : angle 3.90614 ( 768) link_NAG-ASN : bond 0.00421 ( 15) link_NAG-ASN : angle 1.96177 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1856.05 seconds wall clock time: 32 minutes 43.33 seconds (1963.33 seconds total)