Starting phenix.real_space_refine on Wed Aug 5 19:46:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11rn_75980/08_2026/11rn_75980.cif Found real_map, /net/cci-nas-00/data/ceres_data/11rn_75980/08_2026/11rn_75980.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 { model { file = "/net/cci-nas-00/data/ceres_data/11rn_75980/08_2026/11rn_75980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11rn_75980/08_2026/11rn_75980.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11rn_75980/08_2026/11rn_75980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11rn_75980/08_2026/11rn_75980.map" } 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= 0.001 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 7182 2.51 5 N 1864 2.21 5 O 2126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 11200 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5036 Classifications: {'peptide': 637} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 611} Chain: "B" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5036 Classifications: {'peptide': 637} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 611} Chain: "X" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 522 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "Y" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 522 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 59} 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: 2.20, per 1000 atoms: 0.20 Number of scatterers: 11200 At special positions: 0 Unit cell: (102.3, 135.96, 97.68, 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 2126 8.00 N 1864 7.00 C 7182 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 801 " - " ASN A 251 " " NAG A 802 " - " ASN A 317 " " NAG A 803 " - " ASN A 727 " " NAG B 801 " - " ASN B 251 " " NAG B 802 " - " ASN B 317 " " NAG B 803 " - " ASN B 727 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 249.3 milliseconds 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 47.6% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 123 through 136 Processing helix chain 'A' and resid 139 through 147 removed outlier: 3.579A 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 440 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 511 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.688A pdb=" N LYS A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.442A 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 603 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 626 removed outlier: 3.748A 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 680 removed outlier: 3.502A pdb=" N ARG A 680 " --> pdb=" O ASP A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 686 Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 718 through 721 Processing helix chain 'A' and resid 727 through 751 removed outlier: 3.854A pdb=" N GLY A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 756 removed outlier: 3.660A pdb=" N ILE A 756 " --> pdb=" O VAL A 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 136 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.549A 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 removed outlier: 3.502A pdb=" N THR B 319 " --> pdb=" O PHE B 316 " (cutoff:3.500A) 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 440 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 511 Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.724A pdb=" N LYS B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.462A 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 603 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: 3.742A 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 680 removed outlier: 3.533A pdb=" N ARG B 680 " --> pdb=" O ASP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 708 through 717 Processing helix chain 'B' and resid 718 through 721 Processing helix chain 'B' and resid 727 through 750 Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.642A pdb=" N ILE B 756 " --> pdb=" O VAL B 753 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 32 Processing helix chain 'X' and resid 34 through 44 Processing helix chain 'X' and resid 55 through 57 No H-bonds generated for 'chain 'X' and resid 55 through 57' Processing helix chain 'X' and resid 58 through 67 Processing helix chain 'Y' and resid 13 through 31 Processing helix chain 'Y' and resid 34 through 44 removed outlier: 3.696A pdb=" N LYS Y 42 " --> pdb=" O ILE Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 57 through 68 removed outlier: 4.543A pdb=" N ASP Y 61 " --> pdb=" O SER Y 57 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN Y 68 " --> pdb=" O ALA Y 64 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 192 removed outlier: 3.683A pdb=" N LYS A 180 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 447 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS A 401 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE A 449 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 403 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA A 451 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 405 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N TRP A 453 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA A 407 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ALA A 478 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 11.374A pdb=" N ASP A 400 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N THR A 480 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TYR A 402 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ILE A 482 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 404 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE A 555 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 214 removed outlier: 6.730A pdb=" N VAL A 200 " --> pdb=" O VAL A 213 " (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: 6.477A pdb=" N VAL A 255 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR A 282 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.428A 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: 3.715A pdb=" N LYS B 180 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B 447 " --> pdb=" O PRO B 399 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N HIS B 401 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE B 449 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B 403 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ALA B 451 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL B 405 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N TRP B 453 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 407 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N ALA B 478 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N ASP B 400 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N THR B 480 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B 402 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ILE B 482 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 404 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 210 through 214 removed outlier: 6.756A pdb=" N VAL B 200 " --> pdb=" O VAL B 213 " (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: 6.485A pdb=" N VAL B 255 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N TYR B 282 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 257 " --> pdb=" O TYR B 282 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1470 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: 1.51 Time building geometry restraints manager: 1.00 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: 3571 1.34 - 1.45: 1584 1.45 - 1.57: 6263 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 11466 Sorted by residual: bond pdb=" CB THR A 708 " pdb=" CG2 THR A 708 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.08e-01 bond pdb=" CG PRO B 330 " pdb=" CD PRO B 330 " ideal model delta sigma weight residual 1.503 1.526 -0.023 3.40e-02 8.65e+02 4.72e-01 bond pdb=" CB ASP Y 43 " pdb=" CG ASP Y 43 " ideal model delta sigma weight residual 1.516 1.533 -0.017 2.50e-02 1.60e+03 4.57e-01 bond pdb=" CG PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 1.503 1.525 -0.022 3.40e-02 8.65e+02 4.27e-01 bond pdb=" CA PHE A 298 " pdb=" CB PHE A 298 " ideal model delta sigma weight residual 1.534 1.549 -0.015 2.33e-02 1.84e+03 4.09e-01 ... (remaining 11461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 14742 1.35 - 2.69: 707 2.69 - 4.04: 81 4.04 - 5.39: 15 5.39 - 6.73: 9 Bond angle restraints: 15554 Sorted by residual: angle pdb=" N HIS B 475 " pdb=" CA HIS B 475 " pdb=" CB HIS B 475 " ideal model delta sigma weight residual 110.49 104.21 6.28 1.69e+00 3.50e-01 1.38e+01 angle pdb=" N HIS A 475 " pdb=" CA HIS A 475 " pdb=" CB HIS A 475 " ideal model delta sigma weight residual 110.49 104.65 5.84 1.69e+00 3.50e-01 1.19e+01 angle pdb=" N HIS A 475 " pdb=" CA HIS A 475 " pdb=" C HIS A 475 " ideal model delta sigma weight residual 110.80 116.20 -5.40 2.13e+00 2.20e-01 6.43e+00 angle pdb=" C LEU A 474 " pdb=" N HIS A 475 " pdb=" CA HIS A 475 " ideal model delta sigma weight residual 121.54 126.35 -4.81 1.91e+00 2.74e-01 6.35e+00 angle pdb=" N ASN A 722 " pdb=" CA ASN A 722 " pdb=" C ASN A 722 " ideal model delta sigma weight residual 110.80 115.98 -5.18 2.13e+00 2.20e-01 5.90e+00 ... (remaining 15549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6331 17.81 - 35.63: 420 35.63 - 53.44: 70 53.44 - 71.26: 17 71.26 - 89.07: 26 Dihedral angle restraints: 6864 sinusoidal: 2792 harmonic: 4072 Sorted by residual: 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 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ARG B 183 " pdb=" C ARG B 183 " pdb=" N ASP B 184 " pdb=" CA ASP B 184 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA THR A 319 " pdb=" C THR A 319 " pdb=" N GLN A 320 " pdb=" CA GLN A 320 " ideal model delta harmonic sigma weight residual -180.00 -151.60 -28.40 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 6861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1219 0.044 - 0.088: 364 0.088 - 0.132: 125 0.132 - 0.176: 21 0.176 - 0.220: 1 Chirality restraints: 1730 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 251 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1 NAG B 801 " pdb=" ND2 ASN B 251 " pdb=" C2 NAG B 801 " pdb=" O5 NAG B 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CB THR B 310 " pdb=" CA THR B 310 " pdb=" OG1 THR B 310 " pdb=" CG2 THR B 310 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 1727 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 446 " 0.353 9.50e-02 1.11e+02 1.59e-01 1.93e+01 pdb=" NE ARG A 446 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 446 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 446 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 446 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 446 " -0.335 9.50e-02 1.11e+02 1.51e-01 1.75e+01 pdb=" NE ARG B 446 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG B 446 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG B 446 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 446 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 719 " -0.314 9.50e-02 1.11e+02 1.42e-01 1.62e+01 pdb=" NE ARG A 719 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 719 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG A 719 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 719 " 0.000 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1908 2.77 - 3.30: 10818 3.30 - 3.84: 18279 3.84 - 4.37: 22905 4.37 - 4.90: 38419 Nonbonded interactions: 92329 Sorted by model distance: nonbonded pdb=" OD1 ASN B 626 " pdb=" OH TYR B 643 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASN A 626 " pdb=" OH TYR A 643 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR A 239 " pdb=" OD2 ASP A 242 " model vdw 2.356 3.040 nonbonded pdb=" OG1 THR B 536 " pdb=" OD1 ASP B 538 " model vdw 2.377 3.040 nonbonded pdb=" OG1 THR A 536 " pdb=" OD1 ASP A 538 " model vdw 2.380 3.040 ... (remaining 92324 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'X' selection = chain 'Y' } 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: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.070 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 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 0.024 11472 Z= 0.133 Angle : 0.671 6.991 15572 Z= 0.398 Chirality : 0.048 0.220 1730 Planarity : 0.009 0.159 1992 Dihedral : 13.813 89.074 4240 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.24 % Favored : 96.62 % Rotamer: Outliers : 1.00 % Allowed : 4.06 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.12 (0.22), residues: 1390 helix: -0.36 (0.19), residues: 596 sheet: 0.75 (0.34), residues: 190 loop : 0.17 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.004 ARG A 719 TYR 0.019 0.004 TYR A 503 PHE 0.019 0.002 PHE A 297 TRP 0.043 0.003 TRP A 740 HIS 0.008 0.001 HIS B 699 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (11466) covalent geometry : angle 0.66229 / 0.40 (15554) hydrogen bonds : bond 0.18050 / 11.55 ( 517) hydrogen bonds : angle 6.56665 / 4.65 ( 1470) link_NAG-ASN : bond 0.00438 / 0.22 ( 6) link_NAG-ASN : angle 3.19895 / 1.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.350 Fit side-chains REVERT: A 241 LYS cc_start: 0.8766 (tptt) cc_final: 0.8516 (tmtm) REVERT: A 261 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8609 (mttm) REVERT: A 398 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8101 (mt-10) REVERT: A 520 GLN cc_start: 0.8223 (mt0) cc_final: 0.7645 (mm110) REVERT: A 578 GLU cc_start: 0.8674 (tt0) cc_final: 0.8461 (tm-30) REVERT: B 241 LYS cc_start: 0.8744 (tptt) cc_final: 0.8401 (tmtm) REVERT: B 514 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8612 (mttp) REVERT: B 520 GLN cc_start: 0.8312 (mt0) cc_final: 0.7736 (mm110) REVERT: B 582 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7571 (mp0) REVERT: X 49 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8477 (tm) REVERT: Y 34 ASP cc_start: 0.8018 (t0) cc_final: 0.7349 (p0) outliers start: 12 outliers final: 3 residues processed: 179 average time/residue: 0.6209 time to fit residues: 117.9196 Evaluate side-chains 96 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain X residue 49 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 ASN A 512 ASN A 721 GLN B 372 ASN B 512 ASN B 721 GLN X 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.097896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.074777 restraints weight = 16914.659| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.06 r_work: 0.2852 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11472 Z= 0.153 Angle : 0.594 8.340 15572 Z= 0.323 Chirality : 0.046 0.174 1730 Planarity : 0.004 0.052 1992 Dihedral : 6.352 70.157 1634 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.07 % Allowed : 6.63 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.28 (0.23), residues: 1390 helix: 1.58 (0.21), residues: 588 sheet: 0.72 (0.34), residues: 206 loop : 0.28 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 651 TYR 0.014 0.001 TYR A 470 PHE 0.019 0.002 PHE A 297 TRP 0.031 0.002 TRP B 740 HIS 0.004 0.001 HIS A 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (11466) covalent geometry : angle 0.58846 / 0.32 (15554) hydrogen bonds : bond 0.05048 / 3.30 ( 517) hydrogen bonds : angle 4.34396 / 3.10 ( 1470) link_NAG-ASN : bond 0.00152 / 0.08 ( 6) link_NAG-ASN : angle 2.40781 / 1.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.288 Fit side-chains REVERT: A 369 GLU cc_start: 0.8486 (tp30) cc_final: 0.8119 (tp30) REVERT: A 398 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8260 (mt-10) REVERT: A 514 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8650 (mttp) REVERT: A 520 GLN cc_start: 0.8393 (mt0) cc_final: 0.7808 (mm110) REVERT: A 578 GLU cc_start: 0.8759 (tt0) cc_final: 0.8499 (tm-30) REVERT: B 514 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8580 (mttp) REVERT: B 520 GLN cc_start: 0.8448 (mt0) cc_final: 0.7857 (mm110) REVERT: B 668 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8062 (mtp-110) REVERT: X 49 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8622 (tm) REVERT: Y 37 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8568 (tt) outliers start: 25 outliers final: 7 residues processed: 114 average time/residue: 0.5333 time to fit residues: 65.7385 Evaluate side-chains 95 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 668 ARG Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 112 optimal weight: 0.0000 chunk 95 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN A 275 ASN B 191 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.074357 restraints weight = 17135.585| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.05 r_work: 0.2860 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11472 Z= 0.158 Angle : 0.563 7.519 15572 Z= 0.305 Chirality : 0.046 0.164 1730 Planarity : 0.004 0.049 1992 Dihedral : 5.846 57.474 1631 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.32 % Allowed : 7.55 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.23), residues: 1390 helix: 1.99 (0.21), residues: 588 sheet: 0.72 (0.35), residues: 202 loop : 0.13 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 719 TYR 0.013 0.001 TYR A 309 PHE 0.018 0.002 PHE A 297 TRP 0.025 0.002 TRP B 740 HIS 0.003 0.001 HIS A 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (11466) covalent geometry : angle 0.55764 / 0.30 (15554) hydrogen bonds : bond 0.04920 / 3.20 ( 517) hydrogen bonds : angle 4.14995 / 2.95 ( 1470) link_NAG-ASN : bond 0.00147 / 0.07 ( 6) link_NAG-ASN : angle 2.27039 / 1.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.374 Fit side-chains REVERT: A 369 GLU cc_start: 0.8667 (tp30) cc_final: 0.8167 (tp30) REVERT: A 398 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8234 (mt-10) REVERT: A 514 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8687 (mttp) REVERT: A 520 GLN cc_start: 0.8464 (mt0) cc_final: 0.7892 (mm110) REVERT: A 578 GLU cc_start: 0.8779 (tt0) cc_final: 0.8523 (tm-30) REVERT: B 514 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8618 (mttp) REVERT: B 520 GLN cc_start: 0.8512 (mt0) cc_final: 0.7935 (mm110) REVERT: B 623 ARG cc_start: 0.8411 (ttp-110) cc_final: 0.8209 (ttp-110) REVERT: B 668 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7910 (mtp-110) REVERT: X 49 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8680 (tm) REVERT: X 54 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: Y 37 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8614 (tt) outliers start: 28 outliers final: 13 residues processed: 101 average time/residue: 0.5561 time to fit residues: 60.4277 Evaluate side-chains 95 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 668 ARG Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 54 GLU Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 57 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075076 restraints weight = 17190.103| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.03 r_work: 0.2877 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11472 Z= 0.124 Angle : 0.512 5.170 15572 Z= 0.280 Chirality : 0.044 0.160 1730 Planarity : 0.004 0.048 1992 Dihedral : 5.636 56.891 1631 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.16 % Allowed : 8.54 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.45 (0.22), residues: 1390 helix: 2.05 (0.21), residues: 602 sheet: 0.82 (0.35), residues: 202 loop : -0.08 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 719 TYR 0.011 0.001 TYR B 309 PHE 0.015 0.001 PHE A 297 TRP 0.022 0.002 TRP B 740 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (11466) covalent geometry : angle 0.50761 / 0.28 (15554) hydrogen bonds : bond 0.04370 / 2.86 ( 517) hydrogen bonds : angle 4.02315 / 2.85 ( 1470) link_NAG-ASN : bond 0.00189 / 0.10 ( 6) link_NAG-ASN : angle 2.07054 / 1.22 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.435 Fit side-chains REVERT: A 205 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8353 (mtpt) REVERT: A 369 GLU cc_start: 0.8672 (tp30) cc_final: 0.8335 (tp30) REVERT: A 398 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8224 (mt-10) REVERT: A 514 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8685 (mttp) REVERT: A 520 GLN cc_start: 0.8465 (mt0) cc_final: 0.7894 (mm110) REVERT: A 578 GLU cc_start: 0.8778 (tt0) cc_final: 0.8525 (tm-30) REVERT: A 714 GLU cc_start: 0.8679 (tp30) cc_final: 0.8469 (mm-30) REVERT: B 514 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8610 (mttp) REVERT: B 520 GLN cc_start: 0.8503 (mt0) cc_final: 0.7944 (mm110) REVERT: B 623 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.8203 (ttm-80) REVERT: B 668 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7913 (mtp-110) outliers start: 26 outliers final: 13 residues processed: 96 average time/residue: 0.5839 time to fit residues: 60.5888 Evaluate side-chains 93 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 668 ARG Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain Y residue 57 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.077011 restraints weight = 16957.016| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.07 r_work: 0.2901 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11472 Z= 0.102 Angle : 0.479 6.660 15572 Z= 0.260 Chirality : 0.043 0.157 1730 Planarity : 0.004 0.046 1992 Dihedral : 5.334 55.689 1629 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.66 % Allowed : 9.62 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.59 (0.23), residues: 1390 helix: 2.22 (0.21), residues: 602 sheet: 0.88 (0.36), residues: 202 loop : -0.06 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 719 TYR 0.010 0.001 TYR B 309 PHE 0.014 0.001 PHE B 313 TRP 0.021 0.002 TRP B 740 HIS 0.002 0.001 HIS A 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (11466) covalent geometry : angle 0.47508 / 0.26 (15554) hydrogen bonds : bond 0.03863 / 2.54 ( 517) hydrogen bonds : angle 3.90400 / 2.76 ( 1470) link_NAG-ASN : bond 0.00225 / 0.12 ( 6) link_NAG-ASN : angle 1.76874 / 1.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.443 Fit side-chains REVERT: A 205 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8360 (mtpt) REVERT: A 369 GLU cc_start: 0.8735 (tp30) cc_final: 0.8391 (tp30) REVERT: A 398 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 435 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8552 (t0) REVERT: A 514 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8693 (mtpp) REVERT: A 520 GLN cc_start: 0.8472 (mt0) cc_final: 0.7928 (mm110) REVERT: A 578 GLU cc_start: 0.8774 (tt0) cc_final: 0.8522 (tm-30) REVERT: B 514 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8627 (mtpp) REVERT: B 520 GLN cc_start: 0.8500 (mt0) cc_final: 0.7980 (mm110) REVERT: B 623 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.8124 (ttm-80) REVERT: B 668 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7973 (mtp-110) REVERT: X 54 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: Y 29 LYS cc_start: 0.8996 (tppp) cc_final: 0.8788 (ttmm) outliers start: 20 outliers final: 14 residues processed: 94 average time/residue: 0.5986 time to fit residues: 60.7334 Evaluate side-chains 96 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 668 ARG Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 54 GLU Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain Y residue 57 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.075698 restraints weight = 16947.351| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.07 r_work: 0.2883 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11472 Z= 0.126 Angle : 0.500 5.579 15572 Z= 0.272 Chirality : 0.044 0.162 1730 Planarity : 0.004 0.044 1992 Dihedral : 5.359 55.603 1629 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.32 % Allowed : 9.04 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.22), residues: 1390 helix: 2.23 (0.21), residues: 602 sheet: 0.87 (0.36), residues: 202 loop : -0.10 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 719 TYR 0.012 0.001 TYR B 309 PHE 0.015 0.001 PHE A 297 TRP 0.020 0.002 TRP B 740 HIS 0.002 0.001 HIS A 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (11466) covalent geometry : angle 0.49648 / 0.27 (15554) hydrogen bonds : bond 0.04182 / 2.74 ( 517) hydrogen bonds : angle 3.92818 / 2.78 ( 1470) link_NAG-ASN : bond 0.00175 / 0.09 ( 6) link_NAG-ASN : angle 1.86856 / 1.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.432 Fit side-chains REVERT: A 204 ASP cc_start: 0.8970 (t0) cc_final: 0.8665 (t0) REVERT: A 266 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8318 (mt-10) REVERT: A 369 GLU cc_start: 0.8747 (tp30) cc_final: 0.8400 (tp30) REVERT: A 398 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8248 (mt-10) REVERT: A 435 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8550 (t0) REVERT: A 514 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8686 (mtpp) REVERT: A 520 GLN cc_start: 0.8476 (mt0) cc_final: 0.7906 (mm110) REVERT: A 578 GLU cc_start: 0.8788 (tt0) cc_final: 0.8528 (tm-30) REVERT: A 757 ASP cc_start: 0.8133 (t0) cc_final: 0.7663 (p0) REVERT: B 376 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8544 (p) REVERT: B 514 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8624 (mtpp) REVERT: B 520 GLN cc_start: 0.8513 (mt0) cc_final: 0.7965 (mm110) REVERT: B 623 ARG cc_start: 0.8407 (ttp-110) cc_final: 0.8116 (ttm-80) REVERT: B 668 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7979 (mtp-110) REVERT: X 54 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: Y 29 LYS cc_start: 0.9029 (tppp) cc_final: 0.8822 (ttmm) outliers start: 28 outliers final: 16 residues processed: 97 average time/residue: 0.5248 time to fit residues: 55.1267 Evaluate side-chains 101 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 668 ARG Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 54 GLU Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain Y residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.099305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.076584 restraints weight = 17073.910| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.07 r_work: 0.2897 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11472 Z= 0.106 Angle : 0.476 6.214 15572 Z= 0.258 Chirality : 0.043 0.158 1730 Planarity : 0.003 0.044 1992 Dihedral : 5.246 55.452 1629 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.99 % Allowed : 9.54 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.63 (0.22), residues: 1390 helix: 2.31 (0.21), residues: 602 sheet: 0.88 (0.36), residues: 202 loop : -0.12 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 668 TYR 0.012 0.001 TYR Y 20 PHE 0.013 0.001 PHE A 313 TRP 0.020 0.001 TRP A 740 HIS 0.002 0.001 HIS A 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11466) covalent geometry : angle 0.47274 / 0.26 (15554) hydrogen bonds : bond 0.03860 / 2.54 ( 517) hydrogen bonds : angle 3.85144 / 2.72 ( 1470) link_NAG-ASN : bond 0.00211 / 0.11 ( 6) link_NAG-ASN : angle 1.72902 / 1.00 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.361 Fit side-chains REVERT: A 266 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8317 (mt-10) REVERT: A 369 GLU cc_start: 0.8748 (tp30) cc_final: 0.8366 (tp30) REVERT: A 398 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8266 (mt-10) REVERT: A 435 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8558 (t0) REVERT: A 514 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8678 (mtpp) REVERT: A 520 GLN cc_start: 0.8485 (mt0) cc_final: 0.7981 (mm110) REVERT: A 578 GLU cc_start: 0.8787 (tt0) cc_final: 0.8531 (tm-30) REVERT: A 757 ASP cc_start: 0.8152 (t0) cc_final: 0.7651 (p0) REVERT: B 514 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8624 (mtpp) REVERT: B 520 GLN cc_start: 0.8506 (mt0) cc_final: 0.7973 (mm110) REVERT: B 623 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.8130 (ttm-80) REVERT: B 668 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7994 (mtp-110) REVERT: X 51 ASN cc_start: 0.8233 (m-40) cc_final: 0.7982 (m-40) REVERT: X 54 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: Y 29 LYS cc_start: 0.8981 (tppp) cc_final: 0.8779 (ttmm) outliers start: 24 outliers final: 14 residues processed: 98 average time/residue: 0.5422 time to fit residues: 57.2565 Evaluate side-chains 98 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 668 ARG Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 54 GLU Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain Y residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 56 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.076396 restraints weight = 17002.613| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.04 r_work: 0.2896 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11472 Z= 0.108 Angle : 0.486 7.057 15572 Z= 0.260 Chirality : 0.043 0.160 1730 Planarity : 0.004 0.047 1992 Dihedral : 5.220 55.326 1629 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.74 % Allowed : 10.20 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.61 (0.22), residues: 1390 helix: 2.34 (0.21), residues: 602 sheet: 0.87 (0.36), residues: 202 loop : -0.18 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 208 TYR 0.013 0.001 TYR Y 20 PHE 0.013 0.001 PHE A 297 TRP 0.020 0.002 TRP B 740 HIS 0.002 0.001 HIS A 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11466) covalent geometry : angle 0.48244 / 0.26 (15554) hydrogen bonds : bond 0.03875 / 2.55 ( 517) hydrogen bonds : angle 3.84183 / 2.72 ( 1470) link_NAG-ASN : bond 0.00200 / 0.10 ( 6) link_NAG-ASN : angle 1.70904 / 0.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.355 Fit side-chains REVERT: A 266 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: A 369 GLU cc_start: 0.8747 (tp30) cc_final: 0.8384 (tp30) REVERT: A 398 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8237 (mt-10) REVERT: A 435 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8552 (t0) REVERT: A 514 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8669 (mtpp) REVERT: A 520 GLN cc_start: 0.8486 (mt0) cc_final: 0.7973 (mm110) REVERT: A 578 GLU cc_start: 0.8779 (tt0) cc_final: 0.8517 (tm-30) REVERT: A 757 ASP cc_start: 0.8159 (t0) cc_final: 0.7643 (p0) REVERT: B 376 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8536 (p) REVERT: B 514 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8615 (mtpp) REVERT: B 520 GLN cc_start: 0.8517 (mt0) cc_final: 0.7968 (mm110) REVERT: B 623 ARG cc_start: 0.8398 (ttp-110) cc_final: 0.8124 (ttm-80) REVERT: B 668 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7982 (mtp180) REVERT: X 51 ASN cc_start: 0.8241 (m-40) cc_final: 0.8007 (m-40) REVERT: X 54 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: Y 29 LYS cc_start: 0.9000 (tppp) cc_final: 0.8795 (ttmm) outliers start: 21 outliers final: 12 residues processed: 93 average time/residue: 0.5283 time to fit residues: 53.0471 Evaluate side-chains 96 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 668 ARG Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 54 GLU Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain Y residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 50 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.097560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.075145 restraints weight = 17022.803| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.04 r_work: 0.2874 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11472 Z= 0.134 Angle : 0.519 6.973 15572 Z= 0.277 Chirality : 0.044 0.162 1730 Planarity : 0.004 0.042 1992 Dihedral : 5.349 55.501 1629 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.99 % Allowed : 10.03 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.57 (0.22), residues: 1390 helix: 2.32 (0.21), residues: 600 sheet: 0.86 (0.36), residues: 202 loop : -0.22 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 208 TYR 0.014 0.001 TYR Y 20 PHE 0.015 0.001 PHE A 297 TRP 0.019 0.002 TRP B 740 HIS 0.003 0.001 HIS A 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (11466) covalent geometry : angle 0.51564 / 0.28 (15554) hydrogen bonds : bond 0.04241 / 2.78 ( 517) hydrogen bonds : angle 3.90578 / 2.77 ( 1470) link_NAG-ASN : bond 0.00160 / 0.08 ( 6) link_NAG-ASN : angle 1.86842 / 1.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.393 Fit side-chains REVERT: A 266 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8316 (mt-10) REVERT: A 369 GLU cc_start: 0.8791 (tp30) cc_final: 0.8399 (tp30) REVERT: A 398 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8254 (mt-10) REVERT: A 435 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8513 (t0) REVERT: A 520 GLN cc_start: 0.8495 (mt0) cc_final: 0.7955 (mm110) REVERT: A 578 GLU cc_start: 0.8785 (tt0) cc_final: 0.8521 (tm-30) REVERT: A 666 THR cc_start: 0.8674 (m) cc_final: 0.8222 (p) REVERT: A 757 ASP cc_start: 0.8194 (t0) cc_final: 0.7667 (p0) REVERT: B 376 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8545 (p) REVERT: B 514 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8597 (mttp) REVERT: B 520 GLN cc_start: 0.8533 (mt0) cc_final: 0.7986 (mm110) REVERT: B 623 ARG cc_start: 0.8399 (ttp-110) cc_final: 0.8132 (ttm-80) REVERT: B 668 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7981 (mtp180) REVERT: X 54 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: Y 29 LYS cc_start: 0.9002 (tppp) cc_final: 0.8799 (ttmm) outliers start: 24 outliers final: 15 residues processed: 93 average time/residue: 0.5267 time to fit residues: 52.9843 Evaluate side-chains 99 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 668 ARG Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 54 GLU Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain Y residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.075673 restraints weight = 17037.714| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.06 r_work: 0.2879 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11472 Z= 0.123 Angle : 0.511 7.141 15572 Z= 0.273 Chirality : 0.043 0.160 1730 Planarity : 0.004 0.042 1992 Dihedral : 5.329 55.611 1629 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.66 % Allowed : 10.36 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.56 (0.22), residues: 1390 helix: 2.32 (0.21), residues: 602 sheet: 0.84 (0.36), residues: 202 loop : -0.23 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 208 TYR 0.015 0.001 TYR Y 20 PHE 0.015 0.001 PHE B 297 TRP 0.019 0.002 TRP B 740 HIS 0.002 0.001 HIS A 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (11466) covalent geometry : angle 0.50761 / 0.27 (15554) hydrogen bonds : bond 0.04118 / 2.70 ( 517) hydrogen bonds : angle 3.88544 / 2.75 ( 1470) link_NAG-ASN : bond 0.00170 / 0.09 ( 6) link_NAG-ASN : angle 1.82850 / 1.04 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.323 Fit side-chains REVERT: A 266 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: A 369 GLU cc_start: 0.8796 (tp30) cc_final: 0.8404 (tp30) REVERT: A 398 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8264 (mt-10) REVERT: A 435 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8520 (t0) REVERT: A 520 GLN cc_start: 0.8500 (mt0) cc_final: 0.7949 (mm110) REVERT: A 578 GLU cc_start: 0.8781 (tt0) cc_final: 0.8525 (tm-30) REVERT: A 666 THR cc_start: 0.8664 (m) cc_final: 0.8212 (p) REVERT: A 720 LYS cc_start: 0.8331 (pptt) cc_final: 0.7416 (mtmm) REVERT: A 757 ASP cc_start: 0.8205 (t0) cc_final: 0.7659 (p0) REVERT: B 376 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8547 (p) REVERT: B 514 LYS cc_start: 0.8850 (mtmt) cc_final: 0.8596 (mttp) REVERT: B 520 GLN cc_start: 0.8541 (mt0) cc_final: 0.7992 (mm110) REVERT: B 623 ARG cc_start: 0.8401 (ttp-110) cc_final: 0.8135 (ttm-80) REVERT: B 668 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7985 (mtp180) REVERT: X 54 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: Y 29 LYS cc_start: 0.8997 (tppp) cc_final: 0.8795 (ttmm) outliers start: 20 outliers final: 15 residues processed: 91 average time/residue: 0.5213 time to fit residues: 51.1719 Evaluate side-chains 99 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 668 ARG Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 54 GLU Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain Y residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.075750 restraints weight = 17180.124| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.04 r_work: 0.2884 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11472 Z= 0.116 Angle : 0.503 6.860 15572 Z= 0.269 Chirality : 0.043 0.159 1730 Planarity : 0.004 0.042 1992 Dihedral : 5.299 55.506 1629 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.41 % Allowed : 10.53 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.22), residues: 1390 helix: 2.34 (0.21), residues: 602 sheet: 0.84 (0.36), residues: 202 loop : -0.23 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 208 TYR 0.013 0.001 TYR Y 20 PHE 0.014 0.001 PHE A 297 TRP 0.020 0.002 TRP B 740 HIS 0.002 0.001 HIS A 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (11466) covalent geometry : angle 0.50006 / 0.27 (15554) hydrogen bonds : bond 0.04021 / 2.64 ( 517) hydrogen bonds : angle 3.86544 / 2.73 ( 1470) link_NAG-ASN : bond 0.00181 / 0.09 ( 6) link_NAG-ASN : angle 1.77867 / 1.01 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3496.75 seconds wall clock time: 60 minutes 10.42 seconds (3610.42 seconds total)