Starting phenix.real_space_refine on Tue Jan 13 13:20:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8woy_37702/01_2026/8woy_37702.cif Found real_map, /net/cci-nas-00/data/ceres_data/8woy_37702/01_2026/8woy_37702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8woy_37702/01_2026/8woy_37702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8woy_37702/01_2026/8woy_37702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8woy_37702/01_2026/8woy_37702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8woy_37702/01_2026/8woy_37702.map" } resolution = 3.14 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= 0.008 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4064 2.51 5 N 1055 2.21 5 O 1198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6354 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4858 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.37, per 1000 atoms: 0.22 Number of scatterers: 6354 At special positions: 0 Unit cell: (99.44, 73.04, 115.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1198 8.00 N 1055 7.00 C 4064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 B 601 " - " ASN B 343 " Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 262.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1470 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 54.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 25 through 53 removed outlier: 3.627A pdb=" N GLN A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.819A pdb=" N LYS A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.691A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.599A pdb=" N ALA A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.557A pdb=" N LYS A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.717A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 removed outlier: 3.538A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.717A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 removed outlier: 3.756A pdb=" N GLU A 208 " --> pdb=" O ALA A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 220 through 231 removed outlier: 4.337A pdb=" N ASP A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.538A pdb=" N GLN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.672A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.811A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.738A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.571A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.661A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.834A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.643A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.987A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.578A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.934A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.688A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 371' Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.798A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 removed outlier: 3.574A pdb=" N PHE A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASN A 134 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLU A 140 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.901A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.519A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.703A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 735 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: 0.88 Time building geometry restraints manager: 0.78 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: 2045 1.34 - 1.46: 1646 1.46 - 1.58: 2782 1.58 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 6530 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C VAL B 367 " pdb=" O VAL B 367 " ideal model delta sigma weight residual 1.239 1.225 0.014 1.13e-02 7.83e+03 1.53e+00 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C3 NAG B 601 " pdb=" O3 NAG B 601 " ideal model delta sigma weight residual 1.403 1.424 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" C GLU B 516 " pdb=" N LEU B 517 " ideal model delta sigma weight residual 1.330 1.344 -0.014 1.36e-02 5.41e+03 1.02e+00 ... (remaining 6525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 8387 1.04 - 2.07: 394 2.07 - 3.11: 55 3.11 - 4.15: 23 4.15 - 5.19: 8 Bond angle restraints: 8867 Sorted by residual: angle pdb=" N GLY A 147 " pdb=" CA GLY A 147 " pdb=" C GLY A 147 " ideal model delta sigma weight residual 113.18 118.37 -5.19 2.37e+00 1.78e-01 4.79e+00 angle pdb=" N GLU A 483 " pdb=" CA GLU A 483 " pdb=" C GLU A 483 " ideal model delta sigma weight residual 111.36 113.69 -2.33 1.09e+00 8.42e-01 4.59e+00 angle pdb=" N SER A 136 " pdb=" CA SER A 136 " pdb=" CB SER A 136 " ideal model delta sigma weight residual 113.65 110.52 3.13 1.47e+00 4.63e-01 4.52e+00 angle pdb=" CA ARG A 177 " pdb=" C ARG A 177 " pdb=" N PRO A 178 " ideal model delta sigma weight residual 118.44 121.64 -3.20 1.59e+00 3.96e-01 4.05e+00 angle pdb=" N VAL A 364 " pdb=" CA VAL A 364 " pdb=" C VAL A 364 " ideal model delta sigma weight residual 111.91 110.18 1.73 8.90e-01 1.26e+00 3.77e+00 ... (remaining 8862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3553 17.75 - 35.51: 265 35.51 - 53.26: 43 53.26 - 71.02: 3 71.02 - 88.77: 6 Dihedral angle restraints: 3870 sinusoidal: 1579 harmonic: 2291 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -167.24 81.24 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CA GLU A 22 " pdb=" C GLU A 22 " pdb=" N GLU A 23 " pdb=" CA GLU A 23 " ideal model delta harmonic sigma weight residual 180.00 163.24 16.76 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CB GLU A 483 " pdb=" CG GLU A 483 " pdb=" CD GLU A 483 " pdb=" OE1 GLU A 483 " ideal model delta sinusoidal sigma weight residual 0.00 88.77 -88.77 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 477 0.027 - 0.053: 287 0.053 - 0.080: 103 0.080 - 0.107: 39 0.107 - 0.133: 19 Chirality restraints: 925 Sorted by residual: chirality pdb=" CB ILE A 291 " pdb=" CA ILE A 291 " pdb=" CG1 ILE A 291 " pdb=" CG2 ILE A 291 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" C PRO B 491 " pdb=" CB PRO B 491 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ARG A 177 " pdb=" N ARG A 177 " pdb=" C ARG A 177 " pdb=" CB ARG A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 922 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO A 500 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 537 " -0.032 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO A 538 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 538 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 538 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 490 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 491 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.024 5.00e-02 4.00e+02 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 56 2.66 - 3.22: 5729 3.22 - 3.78: 9023 3.78 - 4.34: 12479 4.34 - 4.90: 20776 Nonbonded interactions: 48063 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.098 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.101 2.230 nonbonded pdb=" CD GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.164 2.460 nonbonded pdb=" OG SER A 317 " pdb=" OD1 ASN A 546 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.296 3.040 ... (remaining 48058 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: 16.370 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.005 0.199 6538 Z= 0.189 Angle : 0.534 5.187 8880 Z= 0.302 Chirality : 0.041 0.133 925 Planarity : 0.004 0.051 1149 Dihedral : 12.815 88.769 2385 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.31), residues: 776 helix: 0.40 (0.29), residues: 364 sheet: 2.13 (0.76), residues: 44 loop : -0.94 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.014 0.001 TYR A 158 PHE 0.026 0.001 PHE A 400 TRP 0.011 0.001 TRP B 353 HIS 0.009 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6530) covalent geometry : angle 0.53224 ( 8867) SS BOND : bond 0.00156 ( 5) SS BOND : angle 1.00438 ( 10) hydrogen bonds : bond 0.20324 ( 264) hydrogen bonds : angle 6.27706 ( 735) metal coordination : bond 0.19883 ( 2) link_NAG-ASN : bond 0.00091 ( 1) link_NAG-ASN : angle 1.74202 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7451 (tt0) cc_final: 0.7247 (tt0) REVERT: A 63 ASN cc_start: 0.7986 (m-40) cc_final: 0.7505 (m-40) REVERT: A 154 LYS cc_start: 0.7234 (pttp) cc_final: 0.6922 (pttp) REVERT: A 182 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7477 (mm-30) REVERT: A 202 TYR cc_start: 0.8493 (t80) cc_final: 0.8211 (t80) REVERT: A 330 ASN cc_start: 0.8476 (m110) cc_final: 0.8206 (m110) REVERT: A 406 GLU cc_start: 0.7771 (tp30) cc_final: 0.7484 (tp30) REVERT: A 455 MET cc_start: 0.8301 (tmm) cc_final: 0.8054 (ttp) REVERT: A 476 LYS cc_start: 0.8086 (mmtm) cc_final: 0.7773 (mmtm) REVERT: A 484 ILE cc_start: 0.8883 (mm) cc_final: 0.8663 (mt) REVERT: A 559 ARG cc_start: 0.8191 (mtm110) cc_final: 0.7962 (mtm110) REVERT: A 580 ASP cc_start: 0.7554 (t0) cc_final: 0.7282 (t0) REVERT: B 350 VAL cc_start: 0.8987 (p) cc_final: 0.8738 (t) REVERT: B 374 PHE cc_start: 0.8653 (m-80) cc_final: 0.8306 (m-80) REVERT: B 393 THR cc_start: 0.7164 (m) cc_final: 0.6662 (p) REVERT: B 420 ASP cc_start: 0.7392 (m-30) cc_final: 0.7061 (m-30) REVERT: B 444 LYS cc_start: 0.8434 (mtmm) cc_final: 0.7994 (mtmm) REVERT: B 508 TYR cc_start: 0.8692 (m-80) cc_final: 0.8469 (m-80) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1028 time to fit residues: 27.5695 Evaluate side-chains 185 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.1980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 0.3980 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 572 ASN B 405 ASN B 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108036 restraints weight = 9754.967| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.11 r_work: 0.3303 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6538 Z= 0.141 Angle : 0.542 8.400 8880 Z= 0.281 Chirality : 0.041 0.226 925 Planarity : 0.004 0.051 1149 Dihedral : 4.403 36.102 875 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.32 % Allowed : 9.69 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.31), residues: 776 helix: 0.71 (0.29), residues: 364 sheet: 2.55 (0.74), residues: 41 loop : -0.94 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.014 0.001 TYR A 510 PHE 0.016 0.001 PHE B 490 TRP 0.010 0.001 TRP A 203 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6530) covalent geometry : angle 0.53743 ( 8867) SS BOND : bond 0.00702 ( 5) SS BOND : angle 1.94229 ( 10) hydrogen bonds : bond 0.05254 ( 264) hydrogen bonds : angle 4.30758 ( 735) metal coordination : bond 0.01058 ( 2) link_NAG-ASN : bond 0.00177 ( 1) link_NAG-ASN : angle 2.05060 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7845 (tt0) cc_final: 0.7586 (tt0) REVERT: A 31 LYS cc_start: 0.8359 (tptt) cc_final: 0.8136 (ttmm) REVERT: A 63 ASN cc_start: 0.8006 (m-40) cc_final: 0.7282 (m-40) REVERT: A 75 GLU cc_start: 0.8483 (tp30) cc_final: 0.8033 (tp30) REVERT: A 97 LEU cc_start: 0.8106 (tp) cc_final: 0.7797 (tp) REVERT: A 102 GLN cc_start: 0.7327 (mt0) cc_final: 0.7126 (mp10) REVERT: A 182 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7757 (mm-30) REVERT: A 313 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8365 (mtmm) REVERT: A 341 LYS cc_start: 0.8399 (mtmm) cc_final: 0.8186 (mtpp) REVERT: A 406 GLU cc_start: 0.8226 (tp30) cc_final: 0.7875 (tp30) REVERT: A 438 PHE cc_start: 0.8483 (t80) cc_final: 0.8249 (t80) REVERT: A 476 LYS cc_start: 0.8252 (mmtm) cc_final: 0.8028 (mmtp) REVERT: A 527 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7869 (tm-30) REVERT: A 559 ARG cc_start: 0.8301 (mtm110) cc_final: 0.8041 (mtm110) REVERT: A 580 ASP cc_start: 0.7815 (t0) cc_final: 0.7529 (t0) REVERT: A 596 LYS cc_start: 0.8048 (ttmt) cc_final: 0.7745 (mtmt) REVERT: B 393 THR cc_start: 0.7185 (m) cc_final: 0.6681 (p) REVERT: B 444 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8283 (mtmm) REVERT: B 508 TYR cc_start: 0.8634 (m-80) cc_final: 0.8408 (m-80) outliers start: 9 outliers final: 3 residues processed: 184 average time/residue: 0.0957 time to fit residues: 22.5299 Evaluate side-chains 171 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain B residue 470 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 74 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS A 524 GLN A 601 ASN B 405 ASN B 448 ASN B 450 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102109 restraints weight = 9819.748| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.14 r_work: 0.3207 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 6538 Z= 0.341 Angle : 0.675 10.000 8880 Z= 0.358 Chirality : 0.050 0.223 925 Planarity : 0.005 0.052 1149 Dihedral : 5.265 44.909 875 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.23 % Allowed : 12.78 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.30), residues: 776 helix: 0.42 (0.28), residues: 367 sheet: 2.53 (0.72), residues: 41 loop : -1.25 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 340 TYR 0.029 0.003 TYR B 423 PHE 0.022 0.002 PHE A 327 TRP 0.015 0.002 TRP B 353 HIS 0.014 0.002 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00801 ( 6530) covalent geometry : angle 0.66827 ( 8867) SS BOND : bond 0.00576 ( 5) SS BOND : angle 2.39289 ( 10) hydrogen bonds : bond 0.07499 ( 264) hydrogen bonds : angle 4.56296 ( 735) metal coordination : bond 0.00340 ( 2) link_NAG-ASN : bond 0.00634 ( 1) link_NAG-ASN : angle 3.16878 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7771 (tt0) cc_final: 0.7498 (tt0) REVERT: A 31 LYS cc_start: 0.8603 (tptt) cc_final: 0.8212 (tppp) REVERT: A 63 ASN cc_start: 0.8110 (m-40) cc_final: 0.7892 (m-40) REVERT: A 75 GLU cc_start: 0.8525 (tp30) cc_final: 0.8038 (tp30) REVERT: A 97 LEU cc_start: 0.8171 (tp) cc_final: 0.7406 (tp) REVERT: A 101 GLN cc_start: 0.8323 (mm110) cc_final: 0.7559 (mp10) REVERT: A 102 GLN cc_start: 0.7464 (mt0) cc_final: 0.7262 (mp10) REVERT: A 154 LYS cc_start: 0.7443 (pttp) cc_final: 0.7173 (pttp) REVERT: A 206 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7167 (t0) REVERT: A 313 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8462 (mtmm) REVERT: A 341 LYS cc_start: 0.8468 (mtmm) cc_final: 0.8239 (mtpp) REVERT: A 353 LYS cc_start: 0.8774 (mttt) cc_final: 0.8545 (mttm) REVERT: A 406 GLU cc_start: 0.8248 (tp30) cc_final: 0.7932 (tp30) REVERT: A 408 MET cc_start: 0.8202 (mmt) cc_final: 0.7811 (mmt) REVERT: A 484 ILE cc_start: 0.8903 (mm) cc_final: 0.8682 (mt) REVERT: A 559 ARG cc_start: 0.8292 (mtm110) cc_final: 0.8008 (mtm110) REVERT: A 580 ASP cc_start: 0.7896 (t0) cc_final: 0.7661 (t0) REVERT: A 589 GLU cc_start: 0.8088 (tp30) cc_final: 0.7751 (tp30) REVERT: A 596 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7892 (mtmm) REVERT: B 393 THR cc_start: 0.7354 (m) cc_final: 0.6890 (p) REVERT: B 444 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8296 (mtmm) REVERT: B 448 ASN cc_start: 0.8322 (m110) cc_final: 0.7857 (m-40) outliers start: 22 outliers final: 12 residues processed: 188 average time/residue: 0.0973 time to fit residues: 23.2073 Evaluate side-chains 181 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 366 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 16 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 62 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 0.0770 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 overall best weight: 0.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105417 restraints weight = 9879.430| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.15 r_work: 0.3257 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6538 Z= 0.156 Angle : 0.551 9.230 8880 Z= 0.287 Chirality : 0.042 0.152 925 Planarity : 0.004 0.049 1149 Dihedral : 4.579 34.316 875 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.08 % Allowed : 14.10 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.31), residues: 776 helix: 0.63 (0.29), residues: 373 sheet: 2.68 (0.73), residues: 41 loop : -1.05 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 340 TYR 0.014 0.001 TYR A 183 PHE 0.015 0.001 PHE B 490 TRP 0.012 0.001 TRP A 477 HIS 0.008 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6530) covalent geometry : angle 0.54694 ( 8867) SS BOND : bond 0.00665 ( 5) SS BOND : angle 1.63118 ( 10) hydrogen bonds : bond 0.05286 ( 264) hydrogen bonds : angle 4.19881 ( 735) metal coordination : bond 0.00136 ( 2) link_NAG-ASN : bond 0.00288 ( 1) link_NAG-ASN : angle 2.23195 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7815 (tt0) cc_final: 0.7540 (tt0) REVERT: A 31 LYS cc_start: 0.8543 (tptt) cc_final: 0.8291 (ttmm) REVERT: A 47 SER cc_start: 0.8892 (t) cc_final: 0.8674 (p) REVERT: A 63 ASN cc_start: 0.8006 (m-40) cc_final: 0.7797 (m-40) REVERT: A 75 GLU cc_start: 0.8555 (tp30) cc_final: 0.8255 (tp30) REVERT: A 97 LEU cc_start: 0.8076 (tp) cc_final: 0.7741 (tp) REVERT: A 202 TYR cc_start: 0.8587 (t80) cc_final: 0.8349 (t80) REVERT: A 206 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7141 (t0) REVERT: A 219 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7742 (mtm180) REVERT: A 330 ASN cc_start: 0.8406 (m110) cc_final: 0.8135 (m110) REVERT: A 341 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8228 (mtpp) REVERT: A 406 GLU cc_start: 0.8236 (tp30) cc_final: 0.7908 (tp30) REVERT: A 484 ILE cc_start: 0.8879 (mm) cc_final: 0.8632 (mt) REVERT: A 527 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7851 (tm-30) REVERT: A 559 ARG cc_start: 0.8268 (mtm110) cc_final: 0.7995 (mtm110) REVERT: A 568 LEU cc_start: 0.8619 (tt) cc_final: 0.8412 (tp) REVERT: A 580 ASP cc_start: 0.7906 (t0) cc_final: 0.7670 (t0) REVERT: A 596 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7818 (mtmm) REVERT: B 393 THR cc_start: 0.7311 (m) cc_final: 0.6912 (p) REVERT: B 439 ASN cc_start: 0.8483 (t0) cc_final: 0.8125 (t0) REVERT: B 444 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8191 (mtmm) REVERT: B 508 TYR cc_start: 0.8608 (m-80) cc_final: 0.8317 (m-80) outliers start: 21 outliers final: 11 residues processed: 177 average time/residue: 0.0958 time to fit residues: 21.6478 Evaluate side-chains 177 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 366 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 27 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 18 optimal weight: 0.0770 chunk 62 optimal weight: 0.0000 chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 overall best weight: 0.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106764 restraints weight = 10027.113| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.18 r_work: 0.3281 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6538 Z= 0.123 Angle : 0.538 10.315 8880 Z= 0.276 Chirality : 0.041 0.203 925 Planarity : 0.004 0.048 1149 Dihedral : 4.450 33.541 875 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.20 % Allowed : 16.59 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.31), residues: 776 helix: 0.77 (0.29), residues: 372 sheet: 2.70 (0.74), residues: 41 loop : -0.87 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.013 0.001 TYR A 183 PHE 0.011 0.001 PHE B 490 TRP 0.009 0.001 TRP A 477 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6530) covalent geometry : angle 0.53638 ( 8867) SS BOND : bond 0.00539 ( 5) SS BOND : angle 1.38432 ( 10) hydrogen bonds : bond 0.04668 ( 264) hydrogen bonds : angle 4.00814 ( 735) metal coordination : bond 0.00038 ( 2) link_NAG-ASN : bond 0.01607 ( 1) link_NAG-ASN : angle 1.26188 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7787 (tt0) cc_final: 0.7519 (tt0) REVERT: A 31 LYS cc_start: 0.8440 (tptt) cc_final: 0.8202 (ttmm) REVERT: A 47 SER cc_start: 0.8929 (t) cc_final: 0.8726 (p) REVERT: A 63 ASN cc_start: 0.7973 (m-40) cc_final: 0.7771 (m-40) REVERT: A 75 GLU cc_start: 0.8590 (tp30) cc_final: 0.8301 (tp30) REVERT: A 97 LEU cc_start: 0.8036 (tp) cc_final: 0.7717 (tp) REVERT: A 102 GLN cc_start: 0.7124 (mt0) cc_final: 0.6709 (mp10) REVERT: A 129 THR cc_start: 0.8541 (t) cc_final: 0.8331 (t) REVERT: A 190 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7714 (ttp) REVERT: A 202 TYR cc_start: 0.8611 (t80) cc_final: 0.8386 (t80) REVERT: A 206 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7154 (t0) REVERT: A 330 ASN cc_start: 0.8368 (m110) cc_final: 0.8063 (m110) REVERT: A 341 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8213 (mtpp) REVERT: A 406 GLU cc_start: 0.8259 (tp30) cc_final: 0.7938 (tp30) REVERT: A 559 ARG cc_start: 0.8269 (mtm110) cc_final: 0.8034 (mtm110) REVERT: A 580 ASP cc_start: 0.7875 (t0) cc_final: 0.7641 (t0) REVERT: A 596 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7751 (mtmm) REVERT: B 393 THR cc_start: 0.7302 (m) cc_final: 0.6910 (p) REVERT: B 439 ASN cc_start: 0.8420 (t0) cc_final: 0.8130 (t0) REVERT: B 444 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8171 (mtmm) REVERT: B 508 TYR cc_start: 0.8593 (m-80) cc_final: 0.8241 (m-80) outliers start: 15 outliers final: 10 residues processed: 170 average time/residue: 0.0958 time to fit residues: 20.7331 Evaluate side-chains 173 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 421 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 54 optimal weight: 0.1980 chunk 24 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 0.0170 chunk 40 optimal weight: 0.5980 overall best weight: 0.2618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105823 restraints weight = 9904.960| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.17 r_work: 0.3262 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6538 Z= 0.167 Angle : 0.564 10.949 8880 Z= 0.290 Chirality : 0.043 0.150 925 Planarity : 0.004 0.048 1149 Dihedral : 4.510 32.739 875 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.67 % Allowed : 16.45 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.31), residues: 776 helix: 0.77 (0.29), residues: 372 sheet: 2.74 (0.75), residues: 41 loop : -1.04 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.016 0.001 TYR A 183 PHE 0.014 0.001 PHE A 327 TRP 0.011 0.001 TRP A 477 HIS 0.009 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6530) covalent geometry : angle 0.56183 ( 8867) SS BOND : bond 0.00670 ( 5) SS BOND : angle 1.42555 ( 10) hydrogen bonds : bond 0.05283 ( 264) hydrogen bonds : angle 4.05497 ( 735) metal coordination : bond 0.00069 ( 2) link_NAG-ASN : bond 0.01189 ( 1) link_NAG-ASN : angle 0.89009 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7765 (tt0) cc_final: 0.7522 (tt0) REVERT: A 31 LYS cc_start: 0.8533 (tptt) cc_final: 0.8272 (ttmm) REVERT: A 75 GLU cc_start: 0.8593 (tp30) cc_final: 0.8301 (tp30) REVERT: A 97 LEU cc_start: 0.8076 (tp) cc_final: 0.7750 (tp) REVERT: A 102 GLN cc_start: 0.7101 (mt0) cc_final: 0.6703 (mp10) REVERT: A 129 THR cc_start: 0.8528 (t) cc_final: 0.8292 (t) REVERT: A 150 GLU cc_start: 0.8151 (tp30) cc_final: 0.7822 (tp30) REVERT: A 190 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7788 (ttp) REVERT: A 202 TYR cc_start: 0.8637 (t80) cc_final: 0.8434 (t80) REVERT: A 206 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7107 (t0) REVERT: A 330 ASN cc_start: 0.8436 (m110) cc_final: 0.8121 (m110) REVERT: A 341 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8241 (mtpp) REVERT: A 406 GLU cc_start: 0.8253 (tp30) cc_final: 0.7938 (tp30) REVERT: A 509 ASP cc_start: 0.7593 (p0) cc_final: 0.7184 (p0) REVERT: A 527 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8015 (tp30) REVERT: A 559 ARG cc_start: 0.8285 (mtm110) cc_final: 0.8027 (mtm110) REVERT: A 577 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7916 (tttp) REVERT: A 580 ASP cc_start: 0.7874 (t0) cc_final: 0.7618 (t0) REVERT: A 596 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7963 (mtmt) REVERT: B 393 THR cc_start: 0.7231 (m) cc_final: 0.6759 (p) REVERT: B 444 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8160 (mtmm) REVERT: B 508 TYR cc_start: 0.8630 (m-80) cc_final: 0.8375 (m-80) outliers start: 25 outliers final: 15 residues processed: 171 average time/residue: 0.0932 time to fit residues: 20.2520 Evaluate side-chains 176 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 366 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.1980 chunk 35 optimal weight: 0.4980 chunk 48 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 37 optimal weight: 0.3980 chunk 43 optimal weight: 0.0670 chunk 26 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 overall best weight: 0.1494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN B 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.107783 restraints weight = 9914.568| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.17 r_work: 0.3293 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6538 Z= 0.117 Angle : 0.531 12.281 8880 Z= 0.270 Chirality : 0.040 0.135 925 Planarity : 0.004 0.047 1149 Dihedral : 4.264 30.529 875 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.94 % Allowed : 18.36 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.32), residues: 776 helix: 0.97 (0.29), residues: 368 sheet: 2.57 (0.74), residues: 41 loop : -0.98 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 482 TYR 0.013 0.001 TYR A 183 PHE 0.009 0.001 PHE B 490 TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6530) covalent geometry : angle 0.52972 ( 8867) SS BOND : bond 0.00517 ( 5) SS BOND : angle 1.20173 ( 10) hydrogen bonds : bond 0.04320 ( 264) hydrogen bonds : angle 3.89778 ( 735) metal coordination : bond 0.00065 ( 2) link_NAG-ASN : bond 0.00848 ( 1) link_NAG-ASN : angle 0.77588 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8429 (tptt) cc_final: 0.8194 (ttmm) REVERT: A 55 THR cc_start: 0.6880 (OUTLIER) cc_final: 0.6632 (p) REVERT: A 75 GLU cc_start: 0.8582 (tp30) cc_final: 0.8309 (tp30) REVERT: A 94 LYS cc_start: 0.8836 (tttt) cc_final: 0.8483 (tttm) REVERT: A 97 LEU cc_start: 0.8059 (tp) cc_final: 0.7749 (tp) REVERT: A 102 GLN cc_start: 0.7088 (mt0) cc_final: 0.6681 (mp10) REVERT: A 129 THR cc_start: 0.8497 (t) cc_final: 0.8246 (t) REVERT: A 150 GLU cc_start: 0.8104 (tp30) cc_final: 0.7784 (tp30) REVERT: A 190 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7694 (ttp) REVERT: A 206 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7117 (t0) REVERT: A 219 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7866 (mtm-85) REVERT: A 330 ASN cc_start: 0.8411 (m110) cc_final: 0.8080 (m110) REVERT: A 335 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7430 (tm-30) REVERT: A 341 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8226 (mtpp) REVERT: A 406 GLU cc_start: 0.8230 (tp30) cc_final: 0.7924 (tp30) REVERT: A 529 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8420 (mp) REVERT: A 557 MET cc_start: 0.8591 (ttp) cc_final: 0.8317 (ttp) REVERT: A 559 ARG cc_start: 0.8267 (mtm110) cc_final: 0.8012 (mtm110) REVERT: A 580 ASP cc_start: 0.7828 (t0) cc_final: 0.7608 (t0) REVERT: A 596 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7890 (mtmt) REVERT: B 393 THR cc_start: 0.7179 (m) cc_final: 0.6712 (p) REVERT: B 444 LYS cc_start: 0.8632 (mtmm) cc_final: 0.8143 (mtmm) REVERT: B 508 TYR cc_start: 0.8594 (m-80) cc_final: 0.8328 (m-80) outliers start: 20 outliers final: 13 residues processed: 168 average time/residue: 0.0935 time to fit residues: 20.0825 Evaluate side-chains 174 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.0980 chunk 67 optimal weight: 0.1980 chunk 70 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 39 optimal weight: 0.3980 chunk 17 optimal weight: 0.1980 chunk 3 optimal weight: 0.0970 chunk 61 optimal weight: 0.1980 chunk 69 optimal weight: 0.1980 chunk 46 optimal weight: 0.5980 overall best weight: 0.1578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107770 restraints weight = 9884.853| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.17 r_work: 0.3293 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6538 Z= 0.123 Angle : 0.537 11.934 8880 Z= 0.275 Chirality : 0.041 0.139 925 Planarity : 0.004 0.046 1149 Dihedral : 4.227 30.654 875 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.08 % Allowed : 18.65 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.32), residues: 776 helix: 1.01 (0.29), residues: 370 sheet: 2.58 (0.75), residues: 41 loop : -0.98 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 600 TYR 0.017 0.001 TYR A 202 PHE 0.010 0.001 PHE A 243 TRP 0.010 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6530) covalent geometry : angle 0.53592 ( 8867) SS BOND : bond 0.00611 ( 5) SS BOND : angle 1.21929 ( 10) hydrogen bonds : bond 0.04387 ( 264) hydrogen bonds : angle 3.87440 ( 735) metal coordination : bond 0.00044 ( 2) link_NAG-ASN : bond 0.00905 ( 1) link_NAG-ASN : angle 0.65577 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8413 (tptt) cc_final: 0.8178 (ttmm) REVERT: A 55 THR cc_start: 0.6800 (OUTLIER) cc_final: 0.6356 (p) REVERT: A 64 ASP cc_start: 0.8138 (m-30) cc_final: 0.7871 (m-30) REVERT: A 75 GLU cc_start: 0.8573 (tp30) cc_final: 0.8309 (tp30) REVERT: A 94 LYS cc_start: 0.8833 (tttt) cc_final: 0.8481 (tttm) REVERT: A 97 LEU cc_start: 0.8061 (tp) cc_final: 0.7751 (tp) REVERT: A 102 GLN cc_start: 0.7106 (mt0) cc_final: 0.6702 (mp10) REVERT: A 129 THR cc_start: 0.8519 (t) cc_final: 0.8272 (t) REVERT: A 150 GLU cc_start: 0.8124 (tp30) cc_final: 0.7783 (tp30) REVERT: A 190 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7738 (ttp) REVERT: A 206 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7124 (t0) REVERT: A 313 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8031 (mtmm) REVERT: A 330 ASN cc_start: 0.8399 (m110) cc_final: 0.8057 (m110) REVERT: A 335 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7398 (tm-30) REVERT: A 341 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8261 (mtpp) REVERT: A 401 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.8361 (t-90) REVERT: A 406 GLU cc_start: 0.8241 (tp30) cc_final: 0.7936 (tp30) REVERT: A 527 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8007 (tp30) REVERT: A 529 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8439 (mp) REVERT: A 559 ARG cc_start: 0.8250 (mtm110) cc_final: 0.8005 (mtm110) REVERT: A 580 ASP cc_start: 0.7861 (t0) cc_final: 0.7611 (t0) REVERT: A 596 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7906 (mtmt) REVERT: B 393 THR cc_start: 0.7219 (m) cc_final: 0.6815 (p) REVERT: B 444 LYS cc_start: 0.8632 (mtmm) cc_final: 0.8144 (mtmm) REVERT: B 508 TYR cc_start: 0.8602 (m-80) cc_final: 0.8339 (m-80) outliers start: 21 outliers final: 11 residues processed: 168 average time/residue: 0.0956 time to fit residues: 20.6146 Evaluate side-chains 171 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 366 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 0.3980 chunk 68 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 72 optimal weight: 0.0570 chunk 71 optimal weight: 0.1980 chunk 21 optimal weight: 0.1980 chunk 58 optimal weight: 0.1980 chunk 37 optimal weight: 0.0980 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 0.0970 chunk 18 optimal weight: 0.2980 overall best weight: 0.1296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN B 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.108354 restraints weight = 9993.129| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.16 r_work: 0.3303 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6538 Z= 0.114 Angle : 0.535 12.518 8880 Z= 0.273 Chirality : 0.040 0.155 925 Planarity : 0.004 0.046 1149 Dihedral : 4.136 29.864 875 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.79 % Allowed : 19.24 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.32), residues: 776 helix: 1.03 (0.29), residues: 375 sheet: 2.64 (0.75), residues: 41 loop : -0.93 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.012 0.001 TYR A 183 PHE 0.010 0.001 PHE A 243 TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6530) covalent geometry : angle 0.53437 ( 8867) SS BOND : bond 0.00624 ( 5) SS BOND : angle 1.13621 ( 10) hydrogen bonds : bond 0.04094 ( 264) hydrogen bonds : angle 3.81580 ( 735) metal coordination : bond 0.00039 ( 2) link_NAG-ASN : bond 0.00831 ( 1) link_NAG-ASN : angle 0.68586 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8295 (mp) cc_final: 0.7982 (mt) REVERT: A 31 LYS cc_start: 0.8380 (tptt) cc_final: 0.8153 (ttmm) REVERT: A 55 THR cc_start: 0.6710 (OUTLIER) cc_final: 0.6325 (p) REVERT: A 64 ASP cc_start: 0.8118 (m-30) cc_final: 0.7848 (m-30) REVERT: A 75 GLU cc_start: 0.8555 (tp30) cc_final: 0.8305 (tp30) REVERT: A 94 LYS cc_start: 0.8821 (tttt) cc_final: 0.8462 (tttm) REVERT: A 97 LEU cc_start: 0.8065 (tp) cc_final: 0.7762 (tp) REVERT: A 102 GLN cc_start: 0.7065 (mt0) cc_final: 0.6675 (mp10) REVERT: A 129 THR cc_start: 0.8510 (t) cc_final: 0.8275 (t) REVERT: A 150 GLU cc_start: 0.8100 (tp30) cc_final: 0.7755 (tp30) REVERT: A 190 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7713 (ttp) REVERT: A 206 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7103 (t0) REVERT: A 313 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8246 (mtmm) REVERT: A 330 ASN cc_start: 0.8325 (m110) cc_final: 0.8011 (m110) REVERT: A 335 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 341 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8262 (mtpp) REVERT: A 527 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7990 (tp30) REVERT: A 529 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8439 (mp) REVERT: A 559 ARG cc_start: 0.8244 (mtm110) cc_final: 0.8037 (mtm110) REVERT: A 580 ASP cc_start: 0.7814 (t0) cc_final: 0.7574 (t0) REVERT: A 596 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7871 (mtmt) REVERT: B 393 THR cc_start: 0.7218 (m) cc_final: 0.6811 (p) REVERT: B 444 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8126 (mtmm) REVERT: B 508 TYR cc_start: 0.8583 (m-80) cc_final: 0.8318 (m-80) outliers start: 19 outliers final: 12 residues processed: 167 average time/residue: 0.0932 time to fit residues: 19.9548 Evaluate side-chains 175 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 0.0870 chunk 71 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 0.0040 chunk 26 optimal weight: 0.0870 chunk 38 optimal weight: 0.0980 chunk 54 optimal weight: 0.0970 chunk 40 optimal weight: 0.0570 overall best weight: 0.0604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110139 restraints weight = 9840.838| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.19 r_work: 0.3332 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6538 Z= 0.099 Angle : 0.519 12.880 8880 Z= 0.265 Chirality : 0.039 0.200 925 Planarity : 0.004 0.046 1149 Dihedral : 3.925 25.632 875 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.06 % Allowed : 20.12 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.32), residues: 776 helix: 1.14 (0.29), residues: 374 sheet: 2.48 (0.76), residues: 43 loop : -0.82 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.021 0.001 TYR A 202 PHE 0.008 0.001 PHE B 400 TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 6530) covalent geometry : angle 0.51828 ( 8867) SS BOND : bond 0.00574 ( 5) SS BOND : angle 1.03311 ( 10) hydrogen bonds : bond 0.03418 ( 264) hydrogen bonds : angle 3.70942 ( 735) metal coordination : bond 0.00023 ( 2) link_NAG-ASN : bond 0.00690 ( 1) link_NAG-ASN : angle 0.78102 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8294 (tptt) cc_final: 0.8071 (ttmm) REVERT: A 55 THR cc_start: 0.6433 (OUTLIER) cc_final: 0.6033 (p) REVERT: A 64 ASP cc_start: 0.8076 (m-30) cc_final: 0.7825 (m-30) REVERT: A 75 GLU cc_start: 0.8571 (tp30) cc_final: 0.8342 (tp30) REVERT: A 94 LYS cc_start: 0.8808 (tttt) cc_final: 0.8450 (tttm) REVERT: A 97 LEU cc_start: 0.8010 (tp) cc_final: 0.7730 (tp) REVERT: A 102 GLN cc_start: 0.7028 (mt0) cc_final: 0.6630 (mp10) REVERT: A 129 THR cc_start: 0.8468 (t) cc_final: 0.8229 (t) REVERT: A 190 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7697 (ttp) REVERT: A 313 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8201 (mtmm) REVERT: A 330 ASN cc_start: 0.8311 (m110) cc_final: 0.8029 (m110) REVERT: A 335 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 341 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8225 (mtpp) REVERT: A 527 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8050 (tp30) REVERT: A 529 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8394 (mp) REVERT: A 559 ARG cc_start: 0.8253 (mtm110) cc_final: 0.8019 (mtm110) REVERT: A 580 ASP cc_start: 0.7825 (t0) cc_final: 0.7559 (t0) REVERT: A 596 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7776 (mtmt) REVERT: B 393 THR cc_start: 0.7193 (m) cc_final: 0.6781 (p) REVERT: B 444 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8160 (mtmm) outliers start: 14 outliers final: 7 residues processed: 167 average time/residue: 0.0919 time to fit residues: 19.7103 Evaluate side-chains 167 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 21 optimal weight: 0.0370 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 0.1980 chunk 14 optimal weight: 0.3980 chunk 43 optimal weight: 0.2980 chunk 39 optimal weight: 0.0270 chunk 69 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107714 restraints weight = 9946.325| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.19 r_work: 0.3291 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6538 Z= 0.137 Angle : 0.549 13.216 8880 Z= 0.281 Chirality : 0.041 0.164 925 Planarity : 0.004 0.045 1149 Dihedral : 4.146 28.504 875 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.76 % Allowed : 20.41 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.32), residues: 776 helix: 1.15 (0.29), residues: 375 sheet: 2.74 (0.76), residues: 39 loop : -0.92 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.012 0.001 TYR A 183 PHE 0.012 0.001 PHE A 243 TRP 0.010 0.001 TRP A 477 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6530) covalent geometry : angle 0.54770 ( 8867) SS BOND : bond 0.00591 ( 5) SS BOND : angle 1.18172 ( 10) hydrogen bonds : bond 0.04452 ( 264) hydrogen bonds : angle 3.82648 ( 735) metal coordination : bond 0.00040 ( 2) link_NAG-ASN : bond 0.00968 ( 1) link_NAG-ASN : angle 0.67818 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.76 seconds wall clock time: 37 minutes 6.21 seconds (2226.21 seconds total)