Starting phenix.real_space_refine on Sat Jul 4 20:37:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tal_41137/07_2026/8tal_41137_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tal_41137/07_2026/8tal_41137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tal_41137/07_2026/8tal_41137_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tal_41137/07_2026/8tal_41137_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tal_41137/07_2026/8tal_41137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tal_41137/07_2026/8tal_41137.map" } resolution = 3.2 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= 0.004 sd= 0.682 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 S 71 5.16 5 C 7824 2.51 5 N 1906 2.21 5 O 2105 1.98 5 H 11607 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23516 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 11239 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 32, 'TRANS': 672} Chain breaks: 6 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 12190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 12190 Classifications: {'peptide': 743} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 709} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.21, per 1000 atoms: 0.14 Number of scatterers: 23516 At special positions: 0 Unit cell: (135.079, 88.095, 119.977, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 71 16.00 O 2105 8.00 N 1906 7.00 C 7824 6.00 H 11607 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 362 " " NAG A 902 " - " ASN A 785 " " NAG A 903 " - " ASN A 778 " " NAG B 901 " - " ASN B 362 " Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 558.3 milliseconds 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 64.0% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.625A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 326 removed outlier: 3.740A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.836A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.684A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 486 removed outlier: 3.759A pdb=" N PHE A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.881A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 573 removed outlier: 5.604A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 620 Processing helix chain 'A' and resid 620 through 637 removed outlier: 3.717A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 656 Processing helix chain 'A' and resid 662 through 681 removed outlier: 4.065A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 4.119A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 4.156A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 856 Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'B' and resid 87 through 109 removed outlier: 3.726A pdb=" N ASN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 188 through 195 removed outlier: 5.528A pdb=" N ASN B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE B 195 " --> pdb=" O MET B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.522A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.957A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 360 through 363 Processing helix chain 'B' and resid 364 through 375 Processing helix chain 'B' and resid 376 through 408 removed outlier: 3.797A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 456 through 487 Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.952A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.114A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.972A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.962A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 710 removed outlier: 4.454A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 4.052A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 868 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 116 removed outlier: 3.559A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 removed outlier: 3.541A pdb=" N TRP A 359 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.692A pdb=" N VAL B 124 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR B 77 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 74 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA B 245 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 76 " --> pdb=" O LYS B 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 225 removed outlier: 3.502A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 784 through 785 694 hydrogen bonds defined for protein. 2034 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: 5.39 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11595 1.03 - 1.23: 42 1.23 - 1.42: 5276 1.42 - 1.62: 6818 1.62 - 1.81: 112 Bond restraints: 23843 Sorted by residual: bond pdb=" ND2 ASN A 620 " pdb="HD21 ASN A 620 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN A 620 " pdb="HD22 ASN A 620 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN A 621 " pdb="HD22 ASN A 621 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN A 621 " pdb="HD21 ASN A 621 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" N PHE B 52 " pdb=" H1 PHE B 52 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 23838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.19: 42921 7.19 - 14.38: 3 14.38 - 21.56: 0 21.56 - 28.75: 0 28.75 - 35.94: 24 Bond angle restraints: 42948 Sorted by residual: angle pdb=" CB GLN A 94 " pdb=" CA GLN A 94 " pdb=" HA GLN A 94 " ideal model delta sigma weight residual 109.00 73.06 35.94 3.00e+00 1.11e-01 1.44e+02 angle pdb=" N ILE B 141 " pdb=" CA ILE B 141 " pdb=" HA ILE B 141 " ideal model delta sigma weight residual 110.00 74.40 35.60 3.00e+00 1.11e-01 1.41e+02 angle pdb=" CB PHE B 215 " pdb=" CA PHE B 215 " pdb=" HA PHE B 215 " ideal model delta sigma weight residual 109.00 73.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N PHE B 215 " pdb=" CA PHE B 215 " pdb=" HA PHE B 215 " ideal model delta sigma weight residual 110.00 74.83 35.17 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 110.00 74.98 35.02 3.00e+00 1.11e-01 1.36e+02 ... (remaining 42943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 10187 17.82 - 35.65: 916 35.65 - 53.47: 232 53.47 - 71.30: 67 71.30 - 89.12: 19 Dihedral angle restraints: 11421 sinusoidal: 6017 harmonic: 5404 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual -86.00 -173.72 87.72 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 352 " pdb=" SG CYS A 352 " pdb=" SG CYS A 356 " pdb=" CB CYS A 356 " ideal model delta sinusoidal sigma weight residual -86.00 -151.96 65.96 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS B 352 " pdb=" SG CYS B 352 " pdb=" SG CYS B 356 " pdb=" CB CYS B 356 " ideal model delta sinusoidal sigma weight residual -86.00 -126.81 40.81 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 11418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.668: 1820 0.668 - 1.335: 0 1.335 - 2.003: 1 2.003 - 2.670: 1 2.670 - 3.338: 1 Chirality restraints: 1823 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 785 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 0.94 -3.34 2.00e-01 2.50e+01 2.79e+02 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 778 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -0.31 -2.09 2.00e-01 2.50e+01 1.09e+02 chirality pdb=" C4 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C5 NAG A 901 " pdb=" O4 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.53 -0.99 -1.54 2.00e-01 2.50e+01 5.92e+01 ... (remaining 1820 not shown) Planarity restraints: 3439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 362 " 0.364 2.00e-02 2.50e+03 2.81e-01 1.18e+03 pdb=" CG ASN B 362 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 362 " -0.143 2.00e-02 2.50e+03 pdb=" ND2 ASN B 362 " -0.320 2.00e-02 2.50e+03 pdb="HD21 ASN B 362 " -0.247 2.00e-02 2.50e+03 pdb=" C1 NAG B 901 " 0.394 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 785 " -0.261 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" CG ASN A 785 " 0.094 2.00e-02 2.50e+03 pdb=" OD1 ASN A 785 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 785 " 0.509 2.00e-02 2.50e+03 pdb=" C1 NAG A 902 " -0.335 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 778 " -0.258 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" CG ASN A 778 " 0.094 2.00e-02 2.50e+03 pdb=" OD1 ASN A 778 " 0.266 2.00e-02 2.50e+03 pdb=" ND2 ASN A 778 " 0.217 2.00e-02 2.50e+03 pdb=" C1 NAG A 903 " -0.318 2.00e-02 2.50e+03 ... (remaining 3436 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1153 2.17 - 2.78: 45336 2.78 - 3.39: 64735 3.39 - 3.99: 79694 3.99 - 4.60: 124803 Nonbonded interactions: 315721 Sorted by model distance: nonbonded pdb=" OD1 ASN B 56 " pdb=" H GLY B 57 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASN B 205 " pdb=" HG1 THR B 208 " model vdw 1.582 2.450 nonbonded pdb=" HA PHE B 215 " pdb=" HB3 PHE B 215 " model vdw 1.589 1.952 nonbonded pdb="HH11 ARG B 69 " pdb=" OE1 GLN B 111 " model vdw 1.590 2.450 nonbonded pdb=" HA ASP A 286 " pdb=" HB2 ASP A 286 " model vdw 1.605 1.952 ... (remaining 315716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 59 through 868 or resid 901 through 902 or resid 904)) selection = (chain 'B' and (resid 59 through 82 or resid 91 through 93 or (resid 94 through \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 100 or (resid 101 through 107 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 108 throug \ h 115 or (resid 116 through 126 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 127 through 128 or (resid 129 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 130 \ through 134 or (resid 135 through 137 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 138 through 140 or (resid 141 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 142 or (resid 143 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 144 through 147 or resid 185 through 222 or resid 232 \ through 235 or (resid 236 through 239 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 240 or (resid 241 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 242 throu \ gh 423 or resid 457 through 487 or resid 503 through 589 or (resid 590 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 59 \ 1 through 638 or resid 645 through 660 or (resid 661 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 662 through 777 or ( \ resid 778 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 779 t \ hrough 784 or (resid 785 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) \ or resid 786 through 857 or (resid 858 and (name N or name CA or name C or name \ O or name CB or name CG or name CD )) or (resid 859 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name OD2)) or resid 860 thr \ ough 868 or resid 902 through 903 or resid 905)) } 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: 1.010 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: 0.130 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 20.630 Find NCS groups from input model: 0.350 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 : 0.008 0.604 12250 Z= 0.387 Angle : 0.887 45.709 16639 Z= 0.401 Chirality : 0.109 3.338 1823 Planarity : 0.005 0.075 2064 Dihedral : 14.461 89.119 4502 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.49 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1426 helix: 2.05 (0.17), residues: 816 sheet: -1.18 (0.64), residues: 71 loop : -1.47 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 200 TYR 0.021 0.001 TYR A 827 PHE 0.023 0.001 PHE A 558 TRP 0.012 0.001 TRP A 273 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (12236) covalent geometry : angle 0.60271 / 0.34 (16607) SS BOND : bond 0.00234 / 0.14 ( 10) SS BOND : angle 1.93144 / 1.19 ( 20) hydrogen bonds : bond 0.11874 / 8.39 ( 694) hydrogen bonds : angle 5.60325 / 4.02 ( 2034) link_NAG-ASN : bond 0.37601 / 24.20 ( 4) link_NAG-ASN : angle 24.14452 / 13.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7090 (mt0) cc_final: 0.6702 (mp10) REVERT: B 524 LEU cc_start: 0.8980 (tp) cc_final: 0.8687 (tp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1866 time to fit residues: 48.8739 Evaluate side-chains 155 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN B 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.180938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141300 restraints weight = 46909.234| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.85 r_work: 0.3550 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12250 Z= 0.182 Angle : 0.568 7.324 16639 Z= 0.310 Chirality : 0.046 0.412 1823 Planarity : 0.005 0.054 2064 Dihedral : 5.983 59.595 1721 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 0.71 % Allowed : 5.32 % Favored : 93.97 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.22), residues: 1426 helix: 1.88 (0.17), residues: 831 sheet: -1.50 (0.61), residues: 71 loop : -1.42 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 200 TYR 0.014 0.001 TYR A 306 PHE 0.013 0.001 PHE A 461 TRP 0.013 0.001 TRP A 397 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (12236) covalent geometry : angle 0.56152 / 0.31 (16607) SS BOND : bond 0.00253 / 0.15 ( 10) SS BOND : angle 0.97818 / 0.50 ( 20) hydrogen bonds : bond 0.05269 / 3.68 ( 694) hydrogen bonds : angle 4.89731 / 3.50 ( 2034) link_NAG-ASN : bond 0.00383 / 0.19 ( 4) link_NAG-ASN : angle 3.13998 / 1.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7602 (mt0) cc_final: 0.6995 (mp10) REVERT: A 309 MET cc_start: 0.8338 (mtp) cc_final: 0.7837 (mtp) REVERT: A 323 TYR cc_start: 0.8674 (t80) cc_final: 0.8396 (t80) REVERT: A 742 MET cc_start: 0.7823 (mmm) cc_final: 0.7487 (mmt) REVERT: B 506 GLN cc_start: 0.6916 (mm110) cc_final: 0.6581 (tp40) REVERT: B 524 LEU cc_start: 0.8931 (tp) cc_final: 0.8561 (tp) outliers start: 9 outliers final: 7 residues processed: 170 average time/residue: 0.1777 time to fit residues: 46.2199 Evaluate side-chains 163 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 806 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 24 optimal weight: 0.1980 chunk 125 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.189899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.149969 restraints weight = 46874.902| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.85 r_work: 0.3670 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12250 Z= 0.137 Angle : 0.513 7.207 16639 Z= 0.280 Chirality : 0.045 0.408 1823 Planarity : 0.005 0.055 2064 Dihedral : 5.432 57.056 1721 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.07 % Favored : 95.86 % Rotamer: Outliers : 0.87 % Allowed : 6.90 % Favored : 92.22 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1426 helix: 2.00 (0.17), residues: 832 sheet: -1.60 (0.62), residues: 69 loop : -1.35 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.013 0.001 TYR A 306 PHE 0.012 0.001 PHE B 215 TRP 0.014 0.001 TRP A 397 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (12236) covalent geometry : angle 0.50975 / 0.28 (16607) SS BOND : bond 0.00195 / 0.12 ( 10) SS BOND : angle 0.67590 / 0.35 ( 20) hydrogen bonds : bond 0.04816 / 3.37 ( 694) hydrogen bonds : angle 4.57367 / 3.27 ( 2034) link_NAG-ASN : bond 0.00325 / 0.22 ( 4) link_NAG-ASN : angle 2.27845 / 1.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7619 (mt0) cc_final: 0.6999 (mp10) REVERT: A 323 TYR cc_start: 0.8671 (t80) cc_final: 0.8371 (t80) REVERT: A 339 ASP cc_start: 0.7698 (t0) cc_final: 0.7479 (t0) REVERT: B 699 GLU cc_start: 0.7499 (tp30) cc_final: 0.7294 (tp30) REVERT: B 750 MET cc_start: 0.7859 (tpp) cc_final: 0.7560 (ttp) outliers start: 11 outliers final: 8 residues processed: 173 average time/residue: 0.1763 time to fit residues: 47.2539 Evaluate side-chains 170 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 806 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 HIS ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.190221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.145841 restraints weight = 46824.375| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.01 r_work: 0.3700 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12250 Z= 0.124 Angle : 0.496 7.212 16639 Z= 0.271 Chirality : 0.044 0.408 1823 Planarity : 0.005 0.052 2064 Dihedral : 5.239 56.612 1721 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.27 % Allowed : 7.78 % Favored : 90.95 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.22), residues: 1426 helix: 2.13 (0.17), residues: 830 sheet: -1.73 (0.61), residues: 69 loop : -1.38 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.010 0.001 TYR A 305 PHE 0.012 0.001 PHE A 461 TRP 0.013 0.001 TRP A 397 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (12236) covalent geometry : angle 0.49263 / 0.27 (16607) SS BOND : bond 0.00169 / 0.11 ( 10) SS BOND : angle 0.56554 / 0.29 ( 20) hydrogen bonds : bond 0.04549 / 3.16 ( 694) hydrogen bonds : angle 4.43518 / 3.16 ( 2034) link_NAG-ASN : bond 0.00251 / 0.17 ( 4) link_NAG-ASN : angle 2.05974 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: A 308 GLN cc_start: 0.7629 (mt0) cc_final: 0.6951 (mp10) REVERT: A 323 TYR cc_start: 0.8669 (t80) cc_final: 0.8378 (t80) REVERT: A 401 GLN cc_start: 0.7775 (tt0) cc_final: 0.7515 (tt0) REVERT: B 699 GLU cc_start: 0.7475 (tp30) cc_final: 0.7153 (tp30) REVERT: B 739 THR cc_start: 0.8017 (m) cc_final: 0.7600 (p) outliers start: 16 outliers final: 10 residues processed: 175 average time/residue: 0.1772 time to fit residues: 47.7121 Evaluate side-chains 174 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 0.0040 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.190208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.150756 restraints weight = 46635.191| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.80 r_work: 0.3648 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12250 Z= 0.121 Angle : 0.484 7.279 16639 Z= 0.263 Chirality : 0.044 0.411 1823 Planarity : 0.005 0.051 2064 Dihedral : 5.047 53.712 1721 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.27 % Allowed : 8.65 % Favored : 90.08 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.22), residues: 1426 helix: 2.17 (0.17), residues: 832 sheet: -1.73 (0.61), residues: 69 loop : -1.34 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.010 0.001 TYR A 306 PHE 0.010 0.001 PHE B 393 TRP 0.013 0.001 TRP A 397 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (12236) covalent geometry : angle 0.48154 / 0.26 (16607) SS BOND : bond 0.00133 / 0.08 ( 10) SS BOND : angle 0.48173 / 0.27 ( 20) hydrogen bonds : bond 0.04349 / 3.03 ( 694) hydrogen bonds : angle 4.32364 / 3.09 ( 2034) link_NAG-ASN : bond 0.00253 / 0.17 ( 4) link_NAG-ASN : angle 1.92457 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: A 308 GLN cc_start: 0.7654 (mt0) cc_final: 0.6989 (mp10) REVERT: A 323 TYR cc_start: 0.8662 (t80) cc_final: 0.8420 (t80) REVERT: A 401 GLN cc_start: 0.7833 (tt0) cc_final: 0.7568 (tt0) REVERT: B 221 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7514 (pmtt) REVERT: B 699 GLU cc_start: 0.7580 (tp30) cc_final: 0.7275 (tp30) REVERT: B 739 THR cc_start: 0.8029 (m) cc_final: 0.7640 (p) outliers start: 16 outliers final: 10 residues processed: 178 average time/residue: 0.1738 time to fit residues: 48.0863 Evaluate side-chains 174 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 123 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.191077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.151699 restraints weight = 46630.453| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.79 r_work: 0.3694 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12250 Z= 0.107 Angle : 0.474 7.266 16639 Z= 0.257 Chirality : 0.044 0.409 1823 Planarity : 0.004 0.052 2064 Dihedral : 4.948 52.939 1721 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.27 % Allowed : 9.05 % Favored : 89.68 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.22), residues: 1426 helix: 2.27 (0.17), residues: 832 sheet: -1.80 (0.60), residues: 69 loop : -1.32 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.010 0.001 TYR A 306 PHE 0.010 0.001 PHE B 393 TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (12236) covalent geometry : angle 0.47133 / 0.26 (16607) SS BOND : bond 0.00126 / 0.08 ( 10) SS BOND : angle 0.48960 / 0.27 ( 20) hydrogen bonds : bond 0.04234 / 2.94 ( 694) hydrogen bonds : angle 4.25630 / 3.03 ( 2034) link_NAG-ASN : bond 0.00244 / 0.16 ( 4) link_NAG-ASN : angle 1.82429 / 0.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: A 308 GLN cc_start: 0.7615 (mt0) cc_final: 0.6989 (mp10) REVERT: A 323 TYR cc_start: 0.8633 (t80) cc_final: 0.8418 (t80) REVERT: B 221 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7520 (pmtt) REVERT: B 699 GLU cc_start: 0.7633 (tp30) cc_final: 0.7255 (tp30) REVERT: B 739 THR cc_start: 0.8006 (m) cc_final: 0.7606 (p) outliers start: 16 outliers final: 12 residues processed: 178 average time/residue: 0.1724 time to fit residues: 47.9303 Evaluate side-chains 179 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.188526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.149142 restraints weight = 46779.078| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.84 r_work: 0.3622 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12250 Z= 0.178 Angle : 0.515 7.238 16639 Z= 0.281 Chirality : 0.045 0.417 1823 Planarity : 0.005 0.055 2064 Dihedral : 4.989 49.088 1721 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.27 % Allowed : 9.68 % Favored : 89.05 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1426 helix: 2.13 (0.17), residues: 832 sheet: -1.92 (0.60), residues: 69 loop : -1.35 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.014 0.001 TYR B 214 PHE 0.012 0.001 PHE B 393 TRP 0.011 0.001 TRP A 397 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (12236) covalent geometry : angle 0.51263 / 0.28 (16607) SS BOND : bond 0.00198 / 0.11 ( 10) SS BOND : angle 0.51370 / 0.31 ( 20) hydrogen bonds : bond 0.04533 / 3.16 ( 694) hydrogen bonds : angle 4.36541 / 3.12 ( 2034) link_NAG-ASN : bond 0.00170 / 0.11 ( 4) link_NAG-ASN : angle 1.93532 / 0.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: A 308 GLN cc_start: 0.7670 (mt0) cc_final: 0.7049 (mp10) REVERT: A 323 TYR cc_start: 0.8717 (t80) cc_final: 0.8456 (t80) REVERT: B 221 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7514 (pmtt) REVERT: B 739 THR cc_start: 0.8057 (m) cc_final: 0.7660 (p) outliers start: 16 outliers final: 11 residues processed: 178 average time/residue: 0.1852 time to fit residues: 50.6517 Evaluate side-chains 174 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.184610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.145624 restraints weight = 46614.654| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.73 r_work: 0.3623 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12250 Z= 0.126 Angle : 0.497 7.295 16639 Z= 0.270 Chirality : 0.045 0.413 1823 Planarity : 0.005 0.051 2064 Dihedral : 4.925 48.900 1721 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.35 % Allowed : 9.84 % Favored : 88.81 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.22), residues: 1426 helix: 2.20 (0.17), residues: 833 sheet: -1.89 (0.59), residues: 69 loop : -1.30 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 753 TYR 0.009 0.001 TYR A 306 PHE 0.016 0.001 PHE A 461 TRP 0.012 0.001 TRP A 397 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (12236) covalent geometry : angle 0.49451 / 0.27 (16607) SS BOND : bond 0.00132 / 0.08 ( 10) SS BOND : angle 0.49063 / 0.27 ( 20) hydrogen bonds : bond 0.04355 / 3.02 ( 694) hydrogen bonds : angle 4.28560 / 3.05 ( 2034) link_NAG-ASN : bond 0.00231 / 0.16 ( 4) link_NAG-ASN : angle 1.81868 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: A 308 GLN cc_start: 0.7685 (mt0) cc_final: 0.7037 (mp10) REVERT: A 323 TYR cc_start: 0.8666 (t80) cc_final: 0.8424 (t80) REVERT: A 401 GLN cc_start: 0.7765 (tt0) cc_final: 0.7550 (tt0) REVERT: B 221 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7543 (pmtt) REVERT: B 739 THR cc_start: 0.8003 (m) cc_final: 0.7584 (p) outliers start: 17 outliers final: 14 residues processed: 179 average time/residue: 0.1797 time to fit residues: 50.3114 Evaluate side-chains 182 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.0570 chunk 119 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 134 optimal weight: 0.0170 chunk 108 optimal weight: 4.9990 overall best weight: 0.9538 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.185669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.146453 restraints weight = 46431.220| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.74 r_work: 0.3637 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12250 Z= 0.107 Angle : 0.484 7.318 16639 Z= 0.262 Chirality : 0.045 0.412 1823 Planarity : 0.004 0.049 2064 Dihedral : 4.819 48.281 1721 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.51 % Allowed : 10.08 % Favored : 88.41 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.22), residues: 1426 helix: 2.30 (0.17), residues: 833 sheet: -1.88 (0.59), residues: 69 loop : -1.28 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 753 TYR 0.014 0.001 TYR A 528 PHE 0.015 0.001 PHE B 215 TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (12236) covalent geometry : angle 0.48204 / 0.26 (16607) SS BOND : bond 0.00112 / 0.07 ( 10) SS BOND : angle 0.47171 / 0.26 ( 20) hydrogen bonds : bond 0.04180 / 2.91 ( 694) hydrogen bonds : angle 4.22218 / 3.01 ( 2034) link_NAG-ASN : bond 0.00245 / 0.17 ( 4) link_NAG-ASN : angle 1.73488 / 0.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: A 308 GLN cc_start: 0.7641 (mt0) cc_final: 0.6994 (mp10) REVERT: A 323 TYR cc_start: 0.8629 (t80) cc_final: 0.8364 (t80) REVERT: A 401 GLN cc_start: 0.7626 (tt0) cc_final: 0.7373 (tt0) REVERT: A 465 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8156 (mm) REVERT: B 142 MET cc_start: 0.7521 (mmp) cc_final: 0.6732 (mtt) REVERT: B 739 THR cc_start: 0.7961 (m) cc_final: 0.7517 (p) outliers start: 19 outliers final: 15 residues processed: 183 average time/residue: 0.1805 time to fit residues: 50.7506 Evaluate side-chains 185 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 806 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 = 0.4279 r_free = 0.4279 target = 0.183763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144531 restraints weight = 46840.949| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.75 r_work: 0.3635 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12250 Z= 0.163 Angle : 0.515 7.224 16639 Z= 0.282 Chirality : 0.046 0.416 1823 Planarity : 0.005 0.055 2064 Dihedral : 4.871 47.411 1721 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.27 % Allowed : 10.95 % Favored : 87.78 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.22), residues: 1426 helix: 2.20 (0.17), residues: 830 sheet: -1.95 (0.59), residues: 69 loop : -1.24 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 753 TYR 0.011 0.001 TYR A 528 PHE 0.013 0.001 PHE B 215 TRP 0.011 0.001 TRP A 397 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (12236) covalent geometry : angle 0.51230 / 0.28 (16607) SS BOND : bond 0.00186 / 0.10 ( 10) SS BOND : angle 0.54012 / 0.32 ( 20) hydrogen bonds : bond 0.04487 / 3.11 ( 694) hydrogen bonds : angle 4.33694 / 3.09 ( 2034) link_NAG-ASN : bond 0.00176 / 0.12 ( 4) link_NAG-ASN : angle 1.88113 / 0.80 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: A 308 GLN cc_start: 0.7659 (mt0) cc_final: 0.7031 (mp10) REVERT: A 323 TYR cc_start: 0.8713 (t80) cc_final: 0.8477 (t80) REVERT: A 401 GLN cc_start: 0.7671 (tt0) cc_final: 0.7382 (tt0) REVERT: A 465 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8212 (mm) REVERT: B 142 MET cc_start: 0.7495 (mmp) cc_final: 0.6922 (mtt) REVERT: B 739 THR cc_start: 0.8008 (m) cc_final: 0.7570 (p) outliers start: 16 outliers final: 11 residues processed: 175 average time/residue: 0.1756 time to fit residues: 47.9191 Evaluate side-chains 179 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.184926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.145535 restraints weight = 46514.646| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.75 r_work: 0.3621 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12250 Z= 0.129 Angle : 0.495 7.281 16639 Z= 0.269 Chirality : 0.045 0.413 1823 Planarity : 0.005 0.054 2064 Dihedral : 4.797 46.832 1721 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.03 % Allowed : 11.19 % Favored : 87.78 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.22), residues: 1426 helix: 2.24 (0.17), residues: 830 sheet: -1.96 (0.59), residues: 69 loop : -1.20 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 753 TYR 0.012 0.001 TYR A 528 PHE 0.012 0.001 PHE B 215 TRP 0.012 0.001 TRP A 397 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (12236) covalent geometry : angle 0.49283 / 0.27 (16607) SS BOND : bond 0.00129 / 0.08 ( 10) SS BOND : angle 0.49223 / 0.27 ( 20) hydrogen bonds : bond 0.04313 / 3.00 ( 694) hydrogen bonds : angle 4.26436 / 3.04 ( 2034) link_NAG-ASN : bond 0.00224 / 0.15 ( 4) link_NAG-ASN : angle 1.76253 / 0.77 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4519.33 seconds wall clock time: 77 minutes 23.11 seconds (4643.11 seconds total)