Starting phenix.real_space_refine on Wed Aug 5 15:41:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11qc_75944/08_2026/11qc_75944.cif Found real_map, /net/cci-nas-00/data/ceres_data/11qc_75944/08_2026/11qc_75944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11qc_75944/08_2026/11qc_75944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11qc_75944/08_2026/11qc_75944.map" model { file = "/net/cci-nas-00/data/ceres_data/11qc_75944/08_2026/11qc_75944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11qc_75944/08_2026/11qc_75944.cif" } resolution = 2.4 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= 0.016 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 28 5.16 5 C 6536 2.51 5 N 1706 2.21 5 O 1928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10198 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5057 Classifications: {'peptide': 639} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Chain: "B" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5057 Classifications: {'peptide': 639} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.95, per 1000 atoms: 0.19 Number of scatterers: 10198 At special positions: 0 Unit cell: (116.82, 81.18, 96.36, 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 28 16.00 O 1928 8.00 N 1706 7.00 C 6536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 761 " - " ASN A 251 " " NAG A 762 " - " ASN A 317 " " NAG A 763 " - " ASN A 727 " " NAG B 761 " - " ASN B 251 " " NAG B 762 " - " ASN B 317 " " NAG B 763 " - " ASN B 727 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 343.7 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 45.0% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 123 through 136 Processing helix chain 'A' and resid 139 through 147 removed outlier: 3.691A pdb=" N THR A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 176 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 419 through 439 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.167A pdb=" N PHE A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 604 removed outlier: 4.029A pdb=" N ASP A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 removed outlier: 4.272A pdb=" N SER A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 635 Processing helix chain 'A' and resid 639 through 663 Processing helix chain 'A' and resid 667 through 684 removed outlier: 3.688A pdb=" N VAL A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU A 682 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR A 683 " --> pdb=" O MET A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 718 through 722 Processing helix chain 'A' and resid 727 through 751 removed outlier: 3.572A pdb=" N GLY A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 136 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.665A pdb=" N THR B 143 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 176 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 419 through 439 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 470 through 475 Processing helix chain 'B' and resid 502 through 513 removed outlier: 3.514A pdb=" N ASN B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.843A pdb=" N VAL B 532 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.142A pdb=" N PHE B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 582 through 604 removed outlier: 4.021A pdb=" N ASP B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 613 through 626 removed outlier: 3.734A pdb=" N GLN B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 663 Processing helix chain 'B' and resid 667 through 684 removed outlier: 3.860A pdb=" N VAL B 681 " --> pdb=" O ARG B 677 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLU B 682 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR B 683 " --> pdb=" O MET B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 717 Processing helix chain 'B' and resid 718 through 722 Processing helix chain 'B' and resid 727 through 751 Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 192 removed outlier: 3.526A pdb=" N LYS A 180 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A 447 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N HIS A 401 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 449 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A 403 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA A 451 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A 405 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N TRP A 453 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA A 407 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ALA A 478 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N ASP A 400 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N THR A 480 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR A 402 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ILE A 482 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 404 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 555 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 214 removed outlier: 7.209A pdb=" N ILE A 202 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU A 212 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL A 200 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.451A pdb=" N VAL A 255 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TYR A 282 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A 257 " --> pdb=" O TYR A 282 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 180 through 192 removed outlier: 3.510A pdb=" N LYS B 180 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B 447 " --> pdb=" O PRO B 399 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS B 401 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE B 449 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 403 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA B 451 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 405 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TRP B 453 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA B 407 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ALA B 478 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N ASP B 400 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR B 480 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR B 402 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ILE B 482 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 404 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 209 through 214 removed outlier: 7.214A pdb=" N ILE B 202 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU B 212 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL B 200 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.460A pdb=" N VAL B 255 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N TYR B 282 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL B 257 " --> pdb=" O TYR B 282 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1296 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: 1.83 Time building geometry restraints manager: 1.11 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: 3230 1.34 - 1.45: 1447 1.45 - 1.57: 5715 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 10440 Sorted by residual: bond pdb=" CA THR A 310 " pdb=" C THR A 310 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 9.04e-01 bond pdb=" C THR B 310 " pdb=" N PRO B 311 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.40e-01 bond pdb=" CA THR B 310 " pdb=" C THR B 310 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.53e-01 bond pdb=" N ASN B 379 " pdb=" CA ASN B 379 " ideal model delta sigma weight residual 1.456 1.465 -0.009 1.27e-02 6.20e+03 5.18e-01 bond pdb=" N GLU B 682 " pdb=" CA GLU B 682 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.23e-02 6.61e+03 5.09e-01 ... (remaining 10435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 13528 1.53 - 3.06: 569 3.06 - 4.59: 49 4.59 - 6.12: 8 6.12 - 7.66: 4 Bond angle restraints: 14158 Sorted by residual: angle pdb=" N ASN A 251 " pdb=" CA ASN A 251 " pdb=" C ASN A 251 " ideal model delta sigma weight residual 110.80 117.13 -6.33 2.13e+00 2.20e-01 8.84e+00 angle pdb=" N ASN B 251 " pdb=" CA ASN B 251 " pdb=" C ASN B 251 " ideal model delta sigma weight residual 110.80 117.07 -6.27 2.13e+00 2.20e-01 8.67e+00 angle pdb=" N PRO A 314 " pdb=" CA PRO A 314 " pdb=" C PRO A 314 " ideal model delta sigma weight residual 112.47 117.68 -5.21 2.06e+00 2.36e-01 6.39e+00 angle pdb=" N PRO B 314 " pdb=" CA PRO B 314 " pdb=" C PRO B 314 " ideal model delta sigma weight residual 112.47 117.62 -5.15 2.06e+00 2.36e-01 6.25e+00 angle pdb=" N TYR B 402 " pdb=" CA TYR B 402 " pdb=" C TYR B 402 " ideal model delta sigma weight residual 108.99 112.91 -3.92 1.57e+00 4.06e-01 6.22e+00 ... (remaining 14153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5826 17.66 - 35.33: 337 35.33 - 52.99: 64 52.99 - 70.65: 18 70.65 - 88.32: 13 Dihedral angle restraints: 6258 sinusoidal: 2546 harmonic: 3712 Sorted by residual: dihedral pdb=" CA LEU A 474 " pdb=" C LEU A 474 " pdb=" N HIS A 475 " pdb=" CA HIS A 475 " ideal model delta harmonic sigma weight residual -180.00 -151.06 -28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LEU B 474 " pdb=" C LEU B 474 " pdb=" N HIS B 475 " pdb=" CA HIS B 475 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA THR B 319 " pdb=" C THR B 319 " pdb=" N GLN B 320 " pdb=" CA GLN B 320 " ideal model delta harmonic sigma weight residual 180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 6255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 879 0.036 - 0.071: 482 0.071 - 0.107: 147 0.107 - 0.143: 61 0.143 - 0.178: 9 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA ASN A 251 " pdb=" N ASN A 251 " pdb=" C ASN A 251 " pdb=" CB ASN A 251 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA ASN B 251 " pdb=" N ASN B 251 " pdb=" C ASN B 251 " pdb=" CB ASN B 251 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CA TRP B 740 " pdb=" N TRP B 740 " pdb=" C TRP B 740 " pdb=" CB TRP B 740 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 1575 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 446 " 0.235 9.50e-02 1.11e+02 1.06e-01 9.19e+00 pdb=" NE ARG A 446 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 446 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG A 446 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 446 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 446 " 0.216 9.50e-02 1.11e+02 9.76e-02 7.69e+00 pdb=" NE ARG B 446 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 446 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG B 446 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 446 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 740 " 0.023 2.00e-02 2.50e+03 1.68e-02 7.07e+00 pdb=" CG TRP B 740 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 740 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 740 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 740 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 740 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 740 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 740 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 740 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 740 " 0.006 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1664 2.77 - 3.31: 9686 3.31 - 3.84: 17040 3.84 - 4.37: 21768 4.37 - 4.90: 35485 Nonbonded interactions: 85643 Sorted by model distance: nonbonded pdb=" OD1 ASN B 626 " pdb=" OH TYR B 643 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASN A 626 " pdb=" OH TYR A 643 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR B 536 " pdb=" OD1 ASP B 538 " model vdw 2.340 3.040 nonbonded pdb=" OG1 THR A 536 " pdb=" OD1 ASP A 538 " model vdw 2.354 3.040 nonbonded pdb=" NH1 ARG A 446 " pdb=" O LEU A 601 " model vdw 2.357 3.120 ... (remaining 85638 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10446 Z= 0.151 Angle : 0.705 7.656 14176 Z= 0.427 Chirality : 0.050 0.178 1578 Planarity : 0.007 0.106 1812 Dihedral : 13.095 88.315 3870 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.98 % Favored : 96.86 % Rotamer: Outliers : 0.55 % Allowed : 1.37 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.19 (0.23), residues: 1274 helix: -0.17 (0.20), residues: 524 sheet: 0.72 (0.36), residues: 178 loop : 0.46 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG A 446 TYR 0.017 0.004 TYR B 222 PHE 0.021 0.002 PHE A 297 TRP 0.045 0.004 TRP B 740 HIS 0.004 0.001 HIS A 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (10440) covalent geometry : angle 0.69440 / 0.42 (14158) hydrogen bonds : bond 0.17744 / 11.13 ( 462) hydrogen bonds : angle 5.89877 / 4.13 ( 1296) link_NAG-ASN : bond 0.00415 / 0.22 ( 6) link_NAG-ASN : angle 3.44607 / 2.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 0.407 Fit side-chains REVERT: A 128 LYS cc_start: 0.8036 (ttpp) cc_final: 0.7605 (tttp) REVERT: A 150 ASN cc_start: 0.7640 (p0) cc_final: 0.7302 (m110) REVERT: A 194 ASP cc_start: 0.7156 (t0) cc_final: 0.6809 (t70) REVERT: A 261 LYS cc_start: 0.8112 (mptp) cc_final: 0.7571 (mtmt) REVERT: A 439 LYS cc_start: 0.8013 (mtmt) cc_final: 0.7791 (mtmm) REVERT: A 582 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6336 (mp0) REVERT: A 624 ASP cc_start: 0.7751 (m-30) cc_final: 0.7425 (m-30) REVERT: A 633 LYS cc_start: 0.7330 (ttmm) cc_final: 0.6916 (tttt) REVERT: A 694 GLU cc_start: 0.7177 (tt0) cc_final: 0.6751 (tm-30) REVERT: A 714 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7531 (pt0) REVERT: A 729 THR cc_start: 0.7644 (m) cc_final: 0.7383 (p) REVERT: B 128 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7676 (ttpp) REVERT: B 150 ASN cc_start: 0.7670 (p0) cc_final: 0.7169 (m110) REVERT: B 261 LYS cc_start: 0.8131 (mptp) cc_final: 0.7595 (mtmt) REVERT: B 439 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7784 (mtmm) REVERT: B 582 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6270 (mp0) REVERT: B 604 ASP cc_start: 0.6600 (t0) cc_final: 0.5817 (p0) REVERT: B 624 ASP cc_start: 0.7721 (m-30) cc_final: 0.7408 (m-30) REVERT: B 633 LYS cc_start: 0.7280 (ttmm) cc_final: 0.6933 (ttpt) REVERT: B 694 GLU cc_start: 0.7270 (tt0) cc_final: 0.6793 (tm-30) REVERT: B 729 THR cc_start: 0.7644 (m) cc_final: 0.7380 (p) outliers start: 6 outliers final: 2 residues processed: 182 average time/residue: 0.6366 time to fit residues: 123.1955 Evaluate side-chains 132 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain B residue 141 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 HIS A 515 HIS A 524 GLN A 627 GLN B 515 HIS B 520 GLN B 524 GLN B 627 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.159486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128955 restraints weight = 8912.658| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.35 r_work: 0.3298 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10446 Z= 0.185 Angle : 0.670 7.750 14176 Z= 0.366 Chirality : 0.050 0.179 1578 Planarity : 0.005 0.039 1812 Dihedral : 6.542 83.561 1504 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.01 % Allowed : 4.57 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.11 (0.23), residues: 1274 helix: 1.54 (0.23), residues: 504 sheet: 0.62 (0.35), residues: 200 loop : 0.17 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 719 TYR 0.017 0.002 TYR A 470 PHE 0.023 0.002 PHE A 297 TRP 0.033 0.004 TRP B 740 HIS 0.006 0.001 HIS B 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (10440) covalent geometry : angle 0.66439 / 0.36 (14158) hydrogen bonds : bond 0.06126 / 3.91 ( 462) hydrogen bonds : angle 4.24234 / 2.96 ( 1296) link_NAG-ASN : bond 0.00384 / 0.20 ( 6) link_NAG-ASN : angle 2.58923 / 1.50 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASN cc_start: 0.7595 (p0) cc_final: 0.7282 (m110) REVERT: A 163 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: A 261 LYS cc_start: 0.8092 (mptp) cc_final: 0.7610 (mtmt) REVERT: A 439 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7747 (mtmm) REVERT: A 471 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7376 (tt) REVERT: A 578 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: A 582 GLU cc_start: 0.7555 (mm-30) cc_final: 0.6592 (mp0) REVERT: A 624 ASP cc_start: 0.7483 (m-30) cc_final: 0.7266 (m-30) REVERT: A 633 LYS cc_start: 0.7261 (ttmm) cc_final: 0.6911 (ttpt) REVERT: B 128 LYS cc_start: 0.7834 (ttpp) cc_final: 0.7520 (ttpp) REVERT: B 150 ASN cc_start: 0.7639 (p0) cc_final: 0.7220 (m110) REVERT: B 163 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: B 245 ASP cc_start: 0.7580 (m-30) cc_final: 0.7360 (m-30) REVERT: B 261 LYS cc_start: 0.8111 (mptp) cc_final: 0.7622 (mtmt) REVERT: B 439 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7793 (mtmm) REVERT: B 471 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7338 (tt) REVERT: B 508 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7860 (mtpt) REVERT: B 582 GLU cc_start: 0.7548 (mm-30) cc_final: 0.6553 (mp0) REVERT: B 624 ASP cc_start: 0.7350 (m-30) cc_final: 0.7088 (m-30) REVERT: B 633 LYS cc_start: 0.7283 (ttmm) cc_final: 0.6905 (ttpt) outliers start: 22 outliers final: 6 residues processed: 149 average time/residue: 0.6616 time to fit residues: 105.2631 Evaluate side-chains 136 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 622 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 98 optimal weight: 0.0270 chunk 100 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 HIS A 348 ASN A 372 ASN A 627 GLN B 318 HIS B 348 ASN B 372 ASN B 627 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.163411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133145 restraints weight = 8998.125| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.36 r_work: 0.3353 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10446 Z= 0.106 Angle : 0.505 5.618 14176 Z= 0.275 Chirality : 0.043 0.148 1578 Planarity : 0.003 0.029 1812 Dihedral : 5.760 82.510 1502 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.10 % Allowed : 5.94 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.58 (0.24), residues: 1274 helix: 2.10 (0.24), residues: 504 sheet: 0.86 (0.36), residues: 200 loop : 0.23 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 646 TYR 0.010 0.001 TYR A 309 PHE 0.017 0.001 PHE A 313 TRP 0.024 0.002 TRP B 740 HIS 0.003 0.001 HIS B 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (10440) covalent geometry : angle 0.50083 / 0.27 (14158) hydrogen bonds : bond 0.04417 / 2.82 ( 462) hydrogen bonds : angle 3.86731 / 2.68 ( 1296) link_NAG-ASN : bond 0.00318 / 0.17 ( 6) link_NAG-ASN : angle 1.87797 / 1.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7691 (ttpp) cc_final: 0.7410 (ttpp) REVERT: A 150 ASN cc_start: 0.7478 (p0) cc_final: 0.7235 (m110) REVERT: A 163 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: A 242 ASP cc_start: 0.8095 (m-30) cc_final: 0.7841 (m-30) REVERT: A 261 LYS cc_start: 0.8049 (mptp) cc_final: 0.7595 (mtmt) REVERT: A 439 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7745 (mtmm) REVERT: A 582 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6531 (mp0) REVERT: A 624 ASP cc_start: 0.7420 (m-30) cc_final: 0.7216 (m-30) REVERT: A 633 LYS cc_start: 0.7329 (ttmm) cc_final: 0.6980 (ttpt) REVERT: B 128 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7454 (ttpp) REVERT: B 150 ASN cc_start: 0.7566 (p0) cc_final: 0.7237 (m110) REVERT: B 163 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: B 184 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7847 (t0) REVERT: B 245 ASP cc_start: 0.7487 (m-30) cc_final: 0.7268 (m-30) REVERT: B 261 LYS cc_start: 0.8033 (mptp) cc_final: 0.7582 (mtmt) REVERT: B 582 GLU cc_start: 0.7572 (mm-30) cc_final: 0.6550 (mp0) REVERT: B 604 ASP cc_start: 0.7152 (t0) cc_final: 0.6147 (p0) REVERT: B 624 ASP cc_start: 0.7380 (m-30) cc_final: 0.7144 (m-30) REVERT: B 633 LYS cc_start: 0.7343 (ttmm) cc_final: 0.6983 (ttpt) outliers start: 23 outliers final: 4 residues processed: 150 average time/residue: 0.6160 time to fit residues: 99.1709 Evaluate side-chains 133 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 729 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 114 optimal weight: 0.0000 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 ASN A 524 GLN A 627 GLN B 348 ASN B 512 ASN B 627 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.161414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130686 restraints weight = 9063.438| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.38 r_work: 0.3322 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10446 Z= 0.127 Angle : 0.548 6.113 14176 Z= 0.295 Chirality : 0.045 0.162 1578 Planarity : 0.004 0.031 1812 Dihedral : 5.743 80.386 1502 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.29 % Allowed : 7.22 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.48 (0.24), residues: 1274 helix: 2.09 (0.23), residues: 504 sheet: 0.90 (0.36), residues: 200 loop : 0.06 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.012 0.001 TYR A 309 PHE 0.017 0.002 PHE A 297 TRP 0.022 0.002 TRP A 740 HIS 0.004 0.001 HIS B 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (10440) covalent geometry : angle 0.54387 / 0.29 (14158) hydrogen bonds : bond 0.04881 / 3.13 ( 462) hydrogen bonds : angle 3.90160 / 2.71 ( 1296) link_NAG-ASN : bond 0.00209 / 0.11 ( 6) link_NAG-ASN : angle 2.04499 / 1.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7381 (ttpp) REVERT: A 150 ASN cc_start: 0.7500 (p0) cc_final: 0.7257 (m110) REVERT: A 163 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: A 183 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7924 (ttm170) REVERT: A 184 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7918 (t0) REVERT: A 194 ASP cc_start: 0.7183 (t0) cc_final: 0.6885 (t70) REVERT: A 245 ASP cc_start: 0.7519 (m-30) cc_final: 0.7303 (m-30) REVERT: A 261 LYS cc_start: 0.8058 (mptp) cc_final: 0.7608 (mtmt) REVERT: A 471 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7276 (tt) REVERT: A 582 GLU cc_start: 0.7573 (mm-30) cc_final: 0.6612 (mp0) REVERT: A 604 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6265 (p0) REVERT: A 624 ASP cc_start: 0.7440 (m-30) cc_final: 0.7235 (m-30) REVERT: A 633 LYS cc_start: 0.7334 (ttmm) cc_final: 0.6979 (ttpt) REVERT: B 128 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7422 (ttpp) REVERT: B 150 ASN cc_start: 0.7564 (p0) cc_final: 0.7245 (m110) REVERT: B 163 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: B 184 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7916 (t0) REVERT: B 245 ASP cc_start: 0.7472 (m-30) cc_final: 0.7259 (m-30) REVERT: B 261 LYS cc_start: 0.8058 (mptp) cc_final: 0.7600 (mtmt) REVERT: B 471 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7271 (tt) REVERT: B 508 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7845 (mtpt) REVERT: B 582 GLU cc_start: 0.7655 (mm-30) cc_final: 0.6594 (mp0) REVERT: B 604 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6165 (p0) REVERT: B 624 ASP cc_start: 0.7381 (m-30) cc_final: 0.7173 (m-30) REVERT: B 633 LYS cc_start: 0.7339 (ttmm) cc_final: 0.6976 (ttpt) outliers start: 25 outliers final: 6 residues processed: 146 average time/residue: 0.6431 time to fit residues: 100.4968 Evaluate side-chains 144 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 729 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 105 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 ASN A 627 GLN B 348 ASN B 627 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.159802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130876 restraints weight = 8942.249| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.41 r_work: 0.3308 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10446 Z= 0.157 Angle : 0.596 6.344 14176 Z= 0.320 Chirality : 0.047 0.170 1578 Planarity : 0.004 0.032 1812 Dihedral : 5.797 77.181 1502 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.92 % Allowed : 8.23 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.23 (0.23), residues: 1274 helix: 1.97 (0.23), residues: 504 sheet: 0.84 (0.36), residues: 200 loop : -0.21 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.013 0.002 TYR A 309 PHE 0.020 0.002 PHE B 297 TRP 0.023 0.003 TRP A 740 HIS 0.005 0.001 HIS B 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (10440) covalent geometry : angle 0.59121 / 0.32 (14158) hydrogen bonds : bond 0.05387 / 3.46 ( 462) hydrogen bonds : angle 3.99071 / 2.77 ( 1296) link_NAG-ASN : bond 0.00188 / 0.10 ( 6) link_NAG-ASN : angle 2.16297 / 1.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7693 (ttpp) cc_final: 0.7377 (ttpp) REVERT: A 150 ASN cc_start: 0.7515 (p0) cc_final: 0.7270 (m110) REVERT: A 163 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: A 183 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7961 (ttm170) REVERT: A 184 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7945 (t0) REVERT: A 194 ASP cc_start: 0.7196 (t0) cc_final: 0.6915 (t70) REVERT: A 261 LYS cc_start: 0.8088 (mptp) cc_final: 0.7601 (mtmt) REVERT: A 383 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: A 439 LYS cc_start: 0.8497 (mtmm) cc_final: 0.7995 (mttm) REVERT: A 471 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7299 (tt) REVERT: A 582 GLU cc_start: 0.7628 (mm-30) cc_final: 0.6670 (mp0) REVERT: A 604 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6303 (p0) REVERT: A 624 ASP cc_start: 0.7436 (m-30) cc_final: 0.7231 (m-30) REVERT: A 633 LYS cc_start: 0.7360 (ttmm) cc_final: 0.6998 (ttpt) REVERT: B 128 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7430 (ttpp) REVERT: B 150 ASN cc_start: 0.7566 (p0) cc_final: 0.7275 (m110) REVERT: B 163 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: B 184 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7929 (t0) REVERT: B 245 ASP cc_start: 0.7508 (m-30) cc_final: 0.7307 (m-30) REVERT: B 261 LYS cc_start: 0.8094 (mptp) cc_final: 0.7609 (mtmt) REVERT: B 383 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: B 439 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8009 (mttm) REVERT: B 471 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7276 (tt) REVERT: B 508 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7896 (mtpt) REVERT: B 582 GLU cc_start: 0.7723 (mm-30) cc_final: 0.6653 (mp0) REVERT: B 604 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6264 (p0) REVERT: B 624 ASP cc_start: 0.7324 (m-30) cc_final: 0.7121 (m-30) REVERT: B 633 LYS cc_start: 0.7337 (ttmm) cc_final: 0.6966 (ttpt) outliers start: 21 outliers final: 7 residues processed: 140 average time/residue: 0.5808 time to fit residues: 87.1174 Evaluate side-chains 146 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 729 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 520 GLN A 608 ASN A 627 GLN B 627 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.162439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132070 restraints weight = 9023.174| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.36 r_work: 0.3340 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10446 Z= 0.107 Angle : 0.504 5.267 14176 Z= 0.272 Chirality : 0.043 0.172 1578 Planarity : 0.003 0.030 1812 Dihedral : 5.398 73.072 1502 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.92 % Allowed : 8.87 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.43 (0.24), residues: 1274 helix: 2.18 (0.23), residues: 504 sheet: 0.93 (0.37), residues: 200 loop : -0.13 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.009 0.001 TYR A 309 PHE 0.015 0.001 PHE B 313 TRP 0.023 0.002 TRP A 740 HIS 0.003 0.001 HIS B 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (10440) covalent geometry : angle 0.49939 / 0.27 (14158) hydrogen bonds : bond 0.04313 / 2.77 ( 462) hydrogen bonds : angle 3.79048 / 2.62 ( 1296) link_NAG-ASN : bond 0.00256 / 0.14 ( 6) link_NAG-ASN : angle 1.87481 / 1.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7632 (ttpp) cc_final: 0.7322 (ttpp) REVERT: A 150 ASN cc_start: 0.7491 (p0) cc_final: 0.7283 (m110) REVERT: A 163 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: A 183 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7905 (ttm170) REVERT: A 184 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7948 (t0) REVERT: A 194 ASP cc_start: 0.7067 (t0) cc_final: 0.6798 (t70) REVERT: A 242 ASP cc_start: 0.8107 (m-30) cc_final: 0.7829 (m-30) REVERT: A 261 LYS cc_start: 0.8006 (mptp) cc_final: 0.7570 (mtmt) REVERT: A 318 HIS cc_start: 0.7034 (m90) cc_final: 0.6830 (m-70) REVERT: A 383 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: A 471 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7266 (tt) REVERT: A 582 GLU cc_start: 0.7600 (mm-30) cc_final: 0.6634 (mp0) REVERT: A 604 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6231 (p0) REVERT: A 624 ASP cc_start: 0.7400 (m-30) cc_final: 0.7191 (m-30) REVERT: A 633 LYS cc_start: 0.7349 (ttmm) cc_final: 0.6990 (ttpt) REVERT: B 128 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7365 (ttpp) REVERT: B 150 ASN cc_start: 0.7513 (p0) cc_final: 0.7269 (m110) REVERT: B 163 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: B 184 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7906 (t0) REVERT: B 194 ASP cc_start: 0.6983 (t0) cc_final: 0.6677 (t70) REVERT: B 261 LYS cc_start: 0.8011 (mptp) cc_final: 0.7571 (mtmt) REVERT: B 318 HIS cc_start: 0.6979 (m90) cc_final: 0.6775 (m-70) REVERT: B 383 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: B 471 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7239 (tt) REVERT: B 508 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7779 (mtpt) REVERT: B 604 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6237 (p0) REVERT: B 624 ASP cc_start: 0.7282 (m-30) cc_final: 0.7075 (m-30) REVERT: B 633 LYS cc_start: 0.7322 (ttmm) cc_final: 0.6952 (ttpt) outliers start: 21 outliers final: 6 residues processed: 140 average time/residue: 0.6013 time to fit residues: 90.3220 Evaluate side-chains 145 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 622 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 627 GLN B 627 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.161710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.131252 restraints weight = 8941.146| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.36 r_work: 0.3330 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10446 Z= 0.116 Angle : 0.524 5.495 14176 Z= 0.281 Chirality : 0.044 0.177 1578 Planarity : 0.004 0.031 1812 Dihedral : 5.338 67.652 1502 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.38 % Allowed : 9.23 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.41 (0.23), residues: 1274 helix: 2.16 (0.23), residues: 504 sheet: 0.96 (0.37), residues: 196 loop : -0.15 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.010 0.001 TYR B 470 PHE 0.015 0.001 PHE A 297 TRP 0.021 0.002 TRP A 740 HIS 0.004 0.001 HIS B 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (10440) covalent geometry : angle 0.52003 / 0.28 (14158) hydrogen bonds : bond 0.04525 / 2.91 ( 462) hydrogen bonds : angle 3.80582 / 2.63 ( 1296) link_NAG-ASN : bond 0.00207 / 0.11 ( 6) link_NAG-ASN : angle 1.89933 / 1.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7661 (ttpp) cc_final: 0.7340 (ttpp) REVERT: A 150 ASN cc_start: 0.7504 (p0) cc_final: 0.7292 (m110) REVERT: A 163 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: A 183 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7909 (ttm170) REVERT: A 184 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7948 (t0) REVERT: A 194 ASP cc_start: 0.7005 (t0) cc_final: 0.6665 (t70) REVERT: A 261 LYS cc_start: 0.7996 (mptp) cc_final: 0.7568 (mtmt) REVERT: A 383 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: A 439 LYS cc_start: 0.8495 (mtmm) cc_final: 0.7953 (mttm) REVERT: A 471 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7270 (tt) REVERT: A 582 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6669 (mp0) REVERT: A 604 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6201 (p0) REVERT: A 633 LYS cc_start: 0.7337 (ttmm) cc_final: 0.6973 (ttpt) REVERT: A 666 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7104 (p) REVERT: B 128 LYS cc_start: 0.7699 (ttpp) cc_final: 0.7369 (ttpp) REVERT: B 150 ASN cc_start: 0.7527 (p0) cc_final: 0.7287 (m110) REVERT: B 163 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: B 184 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7911 (t0) REVERT: B 194 ASP cc_start: 0.6973 (t0) cc_final: 0.6674 (t70) REVERT: B 261 LYS cc_start: 0.8004 (mptp) cc_final: 0.7580 (mtmt) REVERT: B 318 HIS cc_start: 0.7016 (m90) cc_final: 0.6801 (m-70) REVERT: B 383 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: B 439 LYS cc_start: 0.8464 (mtmm) cc_final: 0.7929 (mttm) REVERT: B 471 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7257 (tt) REVERT: B 508 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7813 (mtpt) REVERT: B 604 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6210 (p0) REVERT: B 633 LYS cc_start: 0.7319 (ttmm) cc_final: 0.6948 (ttpt) outliers start: 26 outliers final: 10 residues processed: 139 average time/residue: 0.6286 time to fit residues: 93.8141 Evaluate side-chains 148 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 729 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 HIS A 524 GLN A 627 GLN B 627 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.162480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132111 restraints weight = 8928.163| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.36 r_work: 0.3337 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10446 Z= 0.109 Angle : 0.508 5.240 14176 Z= 0.273 Chirality : 0.043 0.189 1578 Planarity : 0.004 0.031 1812 Dihedral : 5.195 60.834 1502 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.29 % Allowed : 9.14 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.49 (0.24), residues: 1274 helix: 2.17 (0.23), residues: 506 sheet: 1.16 (0.38), residues: 188 loop : -0.10 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.009 0.001 TYR B 470 PHE 0.015 0.001 PHE A 313 TRP 0.021 0.002 TRP A 740 HIS 0.003 0.001 HIS B 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10440) covalent geometry : angle 0.50401 / 0.27 (14158) hydrogen bonds : bond 0.04316 / 2.78 ( 462) hydrogen bonds : angle 3.77054 / 2.60 ( 1296) link_NAG-ASN : bond 0.00222 / 0.12 ( 6) link_NAG-ASN : angle 1.84971 / 1.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7642 (ttpp) cc_final: 0.7308 (ttpp) REVERT: A 150 ASN cc_start: 0.7495 (p0) cc_final: 0.7294 (m110) REVERT: A 163 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: A 183 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7901 (ttm170) REVERT: A 184 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7935 (t0) REVERT: A 194 ASP cc_start: 0.6951 (t0) cc_final: 0.6643 (t70) REVERT: A 242 ASP cc_start: 0.8165 (m-30) cc_final: 0.7884 (m-30) REVERT: A 261 LYS cc_start: 0.7972 (mptp) cc_final: 0.7554 (mtmt) REVERT: A 383 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: A 439 LYS cc_start: 0.8446 (mtmm) cc_final: 0.7891 (mtmm) REVERT: A 471 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7276 (tt) REVERT: A 582 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6632 (mp0) REVERT: A 604 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6199 (p0) REVERT: A 633 LYS cc_start: 0.7347 (ttmm) cc_final: 0.6982 (ttpt) REVERT: A 666 THR cc_start: 0.7293 (OUTLIER) cc_final: 0.7075 (p) REVERT: B 128 LYS cc_start: 0.7697 (ttpp) cc_final: 0.7350 (ttpp) REVERT: B 150 ASN cc_start: 0.7521 (p0) cc_final: 0.7286 (m110) REVERT: B 163 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: B 184 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7886 (t0) REVERT: B 194 ASP cc_start: 0.6956 (t0) cc_final: 0.6683 (t70) REVERT: B 242 ASP cc_start: 0.8146 (m-30) cc_final: 0.7847 (m-30) REVERT: B 261 LYS cc_start: 0.7980 (mptp) cc_final: 0.7560 (mtmt) REVERT: B 318 HIS cc_start: 0.7018 (m90) cc_final: 0.6808 (m-70) REVERT: B 383 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: B 439 LYS cc_start: 0.8452 (mtmm) cc_final: 0.7865 (mtmm) REVERT: B 471 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7247 (tt) REVERT: B 508 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7830 (mtpt) REVERT: B 604 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6217 (p0) REVERT: B 633 LYS cc_start: 0.7315 (ttmm) cc_final: 0.6943 (ttpt) outliers start: 25 outliers final: 7 residues processed: 139 average time/residue: 0.6045 time to fit residues: 90.0401 Evaluate side-chains 146 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 622 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.0000 chunk 19 optimal weight: 0.6980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 HIS A 627 GLN B 627 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.164530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134423 restraints weight = 8933.708| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.36 r_work: 0.3369 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10446 Z= 0.093 Angle : 0.469 4.906 14176 Z= 0.252 Chirality : 0.042 0.195 1578 Planarity : 0.003 0.032 1812 Dihedral : 4.897 51.889 1502 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.92 % Allowed : 9.96 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.62 (0.24), residues: 1274 helix: 2.29 (0.23), residues: 506 sheet: 1.23 (0.38), residues: 188 loop : -0.04 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.008 0.001 TYR B 470 PHE 0.016 0.001 PHE B 313 TRP 0.021 0.002 TRP B 740 HIS 0.003 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (10440) covalent geometry : angle 0.46550 / 0.25 (14158) hydrogen bonds : bond 0.03764 / 2.43 ( 462) hydrogen bonds : angle 3.65511 / 2.51 ( 1296) link_NAG-ASN : bond 0.00254 / 0.14 ( 6) link_NAG-ASN : angle 1.68252 / 0.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7261 (ttpp) REVERT: A 163 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: A 183 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7845 (ttm170) REVERT: A 184 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7863 (t0) REVERT: A 194 ASP cc_start: 0.6858 (t0) cc_final: 0.6622 (t70) REVERT: A 242 ASP cc_start: 0.8107 (m-30) cc_final: 0.7798 (m-30) REVERT: A 261 LYS cc_start: 0.7927 (mptp) cc_final: 0.7526 (mtmt) REVERT: A 439 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7830 (mtmm) REVERT: A 471 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7262 (tt) REVERT: A 582 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6624 (mp0) REVERT: A 604 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6157 (p0) REVERT: A 633 LYS cc_start: 0.7328 (ttmm) cc_final: 0.6964 (ttpt) REVERT: A 666 THR cc_start: 0.7183 (OUTLIER) cc_final: 0.6950 (p) REVERT: B 128 LYS cc_start: 0.7632 (ttpp) cc_final: 0.7289 (ttpp) REVERT: B 163 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: B 184 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7823 (t0) REVERT: B 194 ASP cc_start: 0.6833 (t0) cc_final: 0.6586 (t70) REVERT: B 242 ASP cc_start: 0.8106 (m-30) cc_final: 0.7789 (m-30) REVERT: B 261 LYS cc_start: 0.7930 (mptp) cc_final: 0.7534 (mtmt) REVERT: B 318 HIS cc_start: 0.6923 (m90) cc_final: 0.6701 (m-70) REVERT: B 439 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7821 (mtmm) REVERT: B 471 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7245 (tt) REVERT: B 508 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7761 (mtpt) REVERT: B 604 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6083 (p0) REVERT: B 633 LYS cc_start: 0.7305 (ttmm) cc_final: 0.6933 (ttpt) outliers start: 21 outliers final: 3 residues processed: 140 average time/residue: 0.5937 time to fit residues: 89.1873 Evaluate side-chains 142 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 604 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 627 GLN B 150 ASN B 627 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.159145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128706 restraints weight = 8850.274| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.35 r_work: 0.3298 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10446 Z= 0.175 Angle : 0.621 6.380 14176 Z= 0.331 Chirality : 0.048 0.174 1578 Planarity : 0.004 0.033 1812 Dihedral : 5.423 44.328 1502 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.65 % Allowed : 10.69 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.17 (0.23), residues: 1274 helix: 1.92 (0.23), residues: 506 sheet: 0.84 (0.37), residues: 186 loop : -0.23 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.013 0.002 TYR A 309 PHE 0.021 0.002 PHE B 297 TRP 0.017 0.003 TRP B 740 HIS 0.006 0.001 HIS B 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (10440) covalent geometry : angle 0.61625 / 0.33 (14158) hydrogen bonds : bond 0.05553 / 3.57 ( 462) hydrogen bonds : angle 4.03367 / 2.79 ( 1296) link_NAG-ASN : bond 0.00171 / 0.09 ( 6) link_NAG-ASN : angle 2.13848 / 1.20 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7762 (ttpp) cc_final: 0.7288 (tttp) REVERT: A 163 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: A 183 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7981 (ttm170) REVERT: A 194 ASP cc_start: 0.6995 (t0) cc_final: 0.6677 (t70) REVERT: A 261 LYS cc_start: 0.8079 (mptp) cc_final: 0.7592 (mtmt) REVERT: A 439 LYS cc_start: 0.8503 (mtmm) cc_final: 0.7935 (mtmm) REVERT: A 471 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7337 (tt) REVERT: A 604 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6226 (p0) REVERT: A 633 LYS cc_start: 0.7357 (ttmm) cc_final: 0.6992 (ttpt) REVERT: A 666 THR cc_start: 0.7340 (OUTLIER) cc_final: 0.7138 (p) REVERT: B 128 LYS cc_start: 0.7741 (ttpp) cc_final: 0.7385 (ttpp) REVERT: B 134 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7628 (mttp) REVERT: B 163 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: B 194 ASP cc_start: 0.7008 (t0) cc_final: 0.6638 (t70) REVERT: B 242 ASP cc_start: 0.8171 (m-30) cc_final: 0.7929 (m-30) REVERT: B 261 LYS cc_start: 0.8088 (mptp) cc_final: 0.7603 (mtmt) REVERT: B 439 LYS cc_start: 0.8497 (mtmm) cc_final: 0.7929 (mtmm) REVERT: B 471 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7311 (tt) REVERT: B 508 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7902 (mtpt) REVERT: B 604 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6245 (p0) REVERT: B 633 LYS cc_start: 0.7325 (ttmm) cc_final: 0.6954 (ttpt) outliers start: 18 outliers final: 6 residues processed: 136 average time/residue: 0.6100 time to fit residues: 88.6861 Evaluate side-chains 140 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 729 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 85 optimal weight: 0.0050 chunk 68 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 318 HIS A 627 GLN B 150 ASN B 627 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.160600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130178 restraints weight = 8920.033| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.36 r_work: 0.3316 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10446 Z= 0.130 Angle : 0.550 5.538 14176 Z= 0.295 Chirality : 0.045 0.188 1578 Planarity : 0.004 0.031 1812 Dihedral : 5.251 40.007 1502 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.74 % Allowed : 10.69 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.18 (0.23), residues: 1274 helix: 1.94 (0.23), residues: 506 sheet: 0.84 (0.38), residues: 186 loop : -0.23 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.011 0.001 TYR A 309 PHE 0.017 0.002 PHE B 297 TRP 0.020 0.002 TRP B 740 HIS 0.004 0.001 HIS A 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (10440) covalent geometry : angle 0.54564 / 0.29 (14158) hydrogen bonds : bond 0.04811 / 3.10 ( 462) hydrogen bonds : angle 3.92913 / 2.71 ( 1296) link_NAG-ASN : bond 0.00231 / 0.12 ( 6) link_NAG-ASN : angle 1.99327 / 1.13 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.89 seconds wall clock time: 66 minutes 50.78 seconds (4010.78 seconds total)