Starting phenix.real_space_refine on Fri Jun 20 05:37:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tal_41137/06_2025/8tal_41137_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tal_41137/06_2025/8tal_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tal_41137/06_2025/8tal_41137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tal_41137/06_2025/8tal_41137.map" model { file = "/net/cci-nas-00/data/ceres_data/8tal_41137/06_2025/8tal_41137_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tal_41137/06_2025/8tal_41137_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG: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: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.88, per 1000 atoms: 0.46 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: 6.71 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.69 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: 8.33 Time building geometry restraints manager: 8.08 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: 0.880 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: 0.430 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 49.800 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 10.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP A 273 HIS 0.005 0.001 HIS B 275 PHE 0.023 0.001 PHE A 558 TYR 0.021 0.001 TYR A 827 ARG 0.005 0.001 ARG B 200 Details of bonding type rmsd link_NAG-ASN : bond 0.37601 ( 4) link_NAG-ASN : angle 24.14452 ( 12) hydrogen bonds : bond 0.11874 ( 694) hydrogen bonds : angle 5.60325 ( 2034) SS BOND : bond 0.00234 ( 10) SS BOND : angle 1.93144 ( 20) covalent geometry : bond 0.00398 (12236) covalent geometry : angle 0.60271 (16607) *********************** 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 : 1.937 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: 0.7090 (mt0) cc_final: 0.6698 (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: 0.5105 time to fit residues: 133.7218 Evaluate side-chains 154 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.182927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143411 restraints weight = 46462.544| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.83 r_work: 0.3583 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12250 Z= 0.134 Angle : 0.543 7.277 16639 Z= 0.294 Chirality : 0.046 0.404 1823 Planarity : 0.005 0.051 2064 Dihedral : 5.853 58.341 1721 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.14 % Favored : 95.72 % Rotamer: Outliers : 0.71 % Allowed : 4.68 % Favored : 94.60 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1426 helix: 2.06 (0.17), residues: 831 sheet: -1.35 (0.61), residues: 71 loop : -1.35 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.004 0.001 HIS B 275 PHE 0.016 0.001 PHE A 461 TYR 0.014 0.001 TYR A 306 ARG 0.004 0.000 ARG A 209 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 4) link_NAG-ASN : angle 3.19593 ( 12) hydrogen bonds : bond 0.05136 ( 694) hydrogen bonds : angle 4.80333 ( 2034) SS BOND : bond 0.00237 ( 10) SS BOND : angle 0.93280 ( 20) covalent geometry : bond 0.00290 (12236) covalent geometry : angle 0.53550 (16607) *********************** 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 174 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 1.989 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: 0.7530 (mt0) cc_final: 0.6938 (mp10) REVERT: A 309 MET cc_start: 0.8327 (mtp) cc_final: 0.7857 (mtp) REVERT: A 323 TYR cc_start: 0.8629 (t80) cc_final: 0.8305 (t80) REVERT: B 506 GLN cc_start: 0.6797 (mm110) cc_final: 0.6502 (tp40) outliers start: 9 outliers final: 8 residues processed: 171 average time/residue: 0.4640 time to fit residues: 119.5507 Evaluate side-chains 166 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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 B residue 221 LYS Chi-restraints excluded: chain B residue 590 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 107 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4331 r_free = 0.4331 target = 0.188480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.149068 restraints weight = 46668.959| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.86 r_work: 0.3623 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12250 Z= 0.177 Angle : 0.538 6.830 16639 Z= 0.294 Chirality : 0.045 0.403 1823 Planarity : 0.005 0.053 2064 Dihedral : 5.412 54.733 1721 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.95 % Allowed : 7.30 % Favored : 91.75 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1426 helix: 1.93 (0.17), residues: 834 sheet: -1.67 (0.62), residues: 69 loop : -1.36 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.006 0.001 HIS B 275 PHE 0.012 0.001 PHE B 393 TYR 0.015 0.001 TYR A 306 ARG 0.003 0.000 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 4) link_NAG-ASN : angle 2.31561 ( 12) hydrogen bonds : bond 0.04999 ( 694) hydrogen bonds : angle 4.61070 ( 2034) SS BOND : bond 0.00239 ( 10) SS BOND : angle 0.73924 ( 20) covalent geometry : bond 0.00394 (12236) covalent geometry : angle 0.53402 (16607) *********************** 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 179 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7622 (mt0) cc_final: 0.7012 (mp10) REVERT: B 739 THR cc_start: 0.8085 (m) cc_final: 0.7697 (p) REVERT: B 750 MET cc_start: 0.7877 (tpp) cc_final: 0.7590 (ttp) outliers start: 12 outliers final: 9 residues processed: 173 average time/residue: 0.4222 time to fit residues: 111.5435 Evaluate side-chains 168 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 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 738 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4330 r_free = 0.4330 target = 0.188281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.148674 restraints weight = 47427.215| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.91 r_work: 0.3621 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12250 Z= 0.166 Angle : 0.521 7.232 16639 Z= 0.285 Chirality : 0.045 0.417 1823 Planarity : 0.005 0.053 2064 Dihedral : 5.274 52.927 1721 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.35 % Allowed : 8.49 % Favored : 90.16 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1426 helix: 1.97 (0.17), residues: 828 sheet: -1.82 (0.61), residues: 69 loop : -1.38 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.005 0.001 HIS B 275 PHE 0.014 0.001 PHE A 461 TYR 0.010 0.001 TYR A 306 ARG 0.002 0.000 ARG B 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 4) link_NAG-ASN : angle 2.07604 ( 12) hydrogen bonds : bond 0.04784 ( 694) hydrogen bonds : angle 4.50030 ( 2034) SS BOND : bond 0.00207 ( 10) SS BOND : angle 0.62331 ( 20) covalent geometry : bond 0.00371 (12236) covalent geometry : angle 0.51793 (16607) *********************** 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 183 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 1.818 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: 0.9061 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: A 308 GLN cc_start: 0.7632 (mt0) cc_final: 0.7011 (mp10) REVERT: A 323 TYR cc_start: 0.8725 (t80) cc_final: 0.8452 (t80) REVERT: A 401 GLN cc_start: 0.7822 (tt0) cc_final: 0.7554 (tt0) REVERT: B 739 THR cc_start: 0.8086 (m) cc_final: 0.7684 (p) outliers start: 17 outliers final: 10 residues processed: 176 average time/residue: 0.4485 time to fit residues: 120.6125 Evaluate side-chains 172 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE 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 A residue 780 THR 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 659 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.186165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146669 restraints weight = 47204.595| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.91 r_work: 0.3626 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12250 Z= 0.207 Angle : 0.543 6.970 16639 Z= 0.300 Chirality : 0.046 0.412 1823 Planarity : 0.005 0.054 2064 Dihedral : 5.274 48.493 1721 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.51 % Allowed : 9.76 % Favored : 88.73 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1426 helix: 1.84 (0.17), residues: 831 sheet: -2.13 (0.59), residues: 71 loop : -1.49 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 397 HIS 0.006 0.001 HIS B 275 PHE 0.013 0.001 PHE B 393 TYR 0.012 0.001 TYR B 291 ARG 0.003 0.000 ARG A 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 4) link_NAG-ASN : angle 2.07202 ( 12) hydrogen bonds : bond 0.04968 ( 694) hydrogen bonds : angle 4.55682 ( 2034) SS BOND : bond 0.00259 ( 10) SS BOND : angle 0.62427 ( 20) covalent geometry : bond 0.00466 (12236) covalent geometry : angle 0.54070 (16607) *********************** 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 183 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 2.459 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: 0.9136 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: A 308 GLN cc_start: 0.7654 (mt0) cc_final: 0.7036 (mp10) REVERT: B 739 THR cc_start: 0.8112 (m) cc_final: 0.7697 (p) outliers start: 19 outliers final: 14 residues processed: 176 average time/residue: 0.6185 time to fit residues: 167.3646 Evaluate side-chains 176 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 2.495 ------------------------------------------------------------------------------- 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 613 MET Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 780 THR 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 659 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 143 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4266 r_free = 0.4266 target = 0.182739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144202 restraints weight = 46476.077| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.73 r_work: 0.3597 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12250 Z= 0.139 Angle : 0.503 7.245 16639 Z= 0.275 Chirality : 0.044 0.416 1823 Planarity : 0.005 0.054 2064 Dihedral : 5.113 49.055 1721 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.43 % Allowed : 10.32 % Favored : 88.25 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1426 helix: 2.02 (0.17), residues: 833 sheet: -2.15 (0.57), residues: 71 loop : -1.41 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 397 HIS 0.004 0.001 HIS B 275 PHE 0.012 0.001 PHE B 393 TYR 0.010 0.001 TYR B 214 ARG 0.006 0.000 ARG B 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 4) link_NAG-ASN : angle 1.87365 ( 12) hydrogen bonds : bond 0.04606 ( 694) hydrogen bonds : angle 4.39963 ( 2034) SS BOND : bond 0.00165 ( 10) SS BOND : angle 0.52884 ( 20) covalent geometry : bond 0.00309 (12236) covalent geometry : angle 0.50038 (16607) *********************** 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 186 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.801 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: symmetry clash REVERT: A 73 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: A 308 GLN cc_start: 0.7625 (mt0) cc_final: 0.6994 (mp10) REVERT: A 401 GLN cc_start: 0.7763 (tt0) cc_final: 0.7480 (tt0) REVERT: B 221 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7560 (pmtt) REVERT: B 739 THR cc_start: 0.8011 (m) cc_final: 0.7569 (p) outliers start: 18 outliers final: 13 residues processed: 179 average time/residue: 0.4935 time to fit residues: 136.7182 Evaluate side-chains 178 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 1.986 ------------------------------------------------------------------------------- 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 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 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 646 ILE Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4247 r_free = 0.4247 target = 0.180588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142375 restraints weight = 47064.903| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.70 r_work: 0.3563 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12250 Z= 0.204 Angle : 0.537 7.029 16639 Z= 0.297 Chirality : 0.046 0.415 1823 Planarity : 0.005 0.053 2064 Dihedral : 5.158 48.281 1721 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.27 % Allowed : 11.43 % Favored : 87.30 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1426 helix: 1.87 (0.17), residues: 833 sheet: -2.27 (0.58), residues: 71 loop : -1.46 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.005 0.001 HIS B 275 PHE 0.013 0.001 PHE B 393 TYR 0.012 0.001 TYR B 291 ARG 0.005 0.000 ARG B 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 4) link_NAG-ASN : angle 1.99377 ( 12) hydrogen bonds : bond 0.04901 ( 694) hydrogen bonds : angle 4.52167 ( 2034) SS BOND : bond 0.00259 ( 10) SS BOND : angle 0.61291 ( 20) covalent geometry : bond 0.00461 (12236) covalent geometry : angle 0.53419 (16607) *********************** 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 182 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.766 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: symmetry clash REVERT: A 73 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: A 308 GLN cc_start: 0.7637 (mt0) cc_final: 0.6999 (mp10) REVERT: B 221 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7499 (pmtt) REVERT: B 739 THR cc_start: 0.8053 (m) cc_final: 0.7612 (p) outliers start: 16 outliers final: 12 residues processed: 175 average time/residue: 0.4494 time to fit residues: 119.3161 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 : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS 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 524 LEU Chi-restraints excluded: chain B residue 659 MET 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 14 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4259 r_free = 0.4259 target = 0.181885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.143626 restraints weight = 46793.801| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.71 r_work: 0.3577 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12250 Z= 0.155 Angle : 0.511 7.225 16639 Z= 0.281 Chirality : 0.045 0.417 1823 Planarity : 0.005 0.057 2064 Dihedral : 5.058 48.093 1721 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.35 % Allowed : 11.43 % Favored : 87.22 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1426 helix: 1.98 (0.17), residues: 833 sheet: -2.25 (0.57), residues: 71 loop : -1.40 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 397 HIS 0.004 0.001 HIS B 275 PHE 0.012 0.001 PHE B 393 TYR 0.010 0.001 TYR A 528 ARG 0.004 0.000 ARG B 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 4) link_NAG-ASN : angle 1.85876 ( 12) hydrogen bonds : bond 0.04683 ( 694) hydrogen bonds : angle 4.42196 ( 2034) SS BOND : bond 0.00177 ( 10) SS BOND : angle 0.55034 ( 20) covalent geometry : bond 0.00347 (12236) covalent geometry : angle 0.50885 (16607) *********************** 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 185 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 2.025 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: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: A 308 GLN cc_start: 0.7616 (mt0) cc_final: 0.6976 (mp10) REVERT: A 401 GLN cc_start: 0.7774 (tt0) cc_final: 0.7497 (tt0) REVERT: B 221 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7541 (pmtt) REVERT: B 739 THR cc_start: 0.8015 (m) cc_final: 0.7561 (p) outliers start: 17 outliers final: 12 residues processed: 179 average time/residue: 0.4525 time to fit residues: 123.1326 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 : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP 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 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 524 LEU Chi-restraints excluded: chain B residue 659 MET 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 109 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 102 optimal weight: 0.0060 chunk 89 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4256 r_free = 0.4256 target = 0.181456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143312 restraints weight = 46523.081| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.67 r_work: 0.3574 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12250 Z= 0.161 Angle : 0.513 7.145 16639 Z= 0.282 Chirality : 0.045 0.415 1823 Planarity : 0.005 0.054 2064 Dihedral : 5.010 47.724 1721 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.43 % Allowed : 11.67 % Favored : 86.90 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1426 helix: 2.00 (0.17), residues: 833 sheet: -2.25 (0.57), residues: 71 loop : -1.42 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 397 HIS 0.004 0.001 HIS B 275 PHE 0.012 0.001 PHE B 393 TYR 0.011 0.001 TYR A 528 ARG 0.004 0.000 ARG B 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 4) link_NAG-ASN : angle 1.86458 ( 12) hydrogen bonds : bond 0.04662 ( 694) hydrogen bonds : angle 4.41742 ( 2034) SS BOND : bond 0.00178 ( 10) SS BOND : angle 0.54901 ( 20) covalent geometry : bond 0.00361 (12236) covalent geometry : angle 0.51034 (16607) *********************** 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 182 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.914 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: symmetry clash REVERT: A 73 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: A 308 GLN cc_start: 0.7620 (mt0) cc_final: 0.6969 (mp10) REVERT: A 401 GLN cc_start: 0.7770 (tt0) cc_final: 0.7487 (tt0) REVERT: B 221 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7493 (pmtt) REVERT: B 739 THR cc_start: 0.8005 (m) cc_final: 0.7535 (p) outliers start: 18 outliers final: 12 residues processed: 175 average time/residue: 0.4333 time to fit residues: 116.9653 Evaluate side-chains 177 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP 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 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 524 LEU Chi-restraints excluded: chain B residue 659 MET 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 105 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 29 optimal weight: 0.0170 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.182298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144110 restraints weight = 46669.687| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.68 r_work: 0.3599 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2207 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= 0.139 Angle : 0.504 7.233 16639 Z= 0.275 Chirality : 0.045 0.416 1823 Planarity : 0.005 0.053 2064 Dihedral : 4.923 47.371 1721 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.03 % Allowed : 11.98 % Favored : 86.98 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.22), residues: 1426 helix: 2.09 (0.17), residues: 833 sheet: -2.24 (0.57), residues: 71 loop : -1.40 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 397 HIS 0.003 0.001 HIS B 275 PHE 0.011 0.001 PHE B 393 TYR 0.010 0.001 TYR B 101 ARG 0.003 0.000 ARG B 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 4) link_NAG-ASN : angle 1.79376 ( 12) hydrogen bonds : bond 0.04510 ( 694) hydrogen bonds : angle 4.35042 ( 2034) SS BOND : bond 0.00163 ( 10) SS BOND : angle 0.55753 ( 20) covalent geometry : bond 0.00309 (12236) covalent geometry : angle 0.50166 (16607) ********************** 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 180 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 1.771 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: symmetry clash REVERT: A 73 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: A 308 GLN cc_start: 0.7623 (mt0) cc_final: 0.6964 (mp10) REVERT: A 339 ASP cc_start: 0.7756 (t0) cc_final: 0.7512 (t0) REVERT: B 221 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7550 (pmtt) REVERT: B 739 THR cc_start: 0.7993 (m) cc_final: 0.7522 (p) outliers start: 13 outliers final: 11 residues processed: 175 average time/residue: 0.4349 time to fit residues: 116.9138 Evaluate side-chains 178 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 1.889 ------------------------------------------------------------------------------- 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 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 524 LEU Chi-restraints excluded: chain B residue 659 MET 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 88 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.182863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.144609 restraints weight = 46548.715| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.69 r_work: 0.3594 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12250 Z= 0.128 Angle : 0.498 7.219 16639 Z= 0.272 Chirality : 0.045 0.414 1823 Planarity : 0.005 0.051 2064 Dihedral : 4.837 46.780 1721 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.19 % Allowed : 11.90 % Favored : 86.90 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1426 helix: 2.16 (0.17), residues: 833 sheet: -2.21 (0.57), residues: 71 loop : -1.36 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 397 HIS 0.003 0.001 HIS B 275 PHE 0.011 0.001 PHE B 393 TYR 0.009 0.001 TYR A 528 ARG 0.005 0.000 ARG A 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 4) link_NAG-ASN : angle 1.75767 ( 12) hydrogen bonds : bond 0.04420 ( 694) hydrogen bonds : angle 4.30562 ( 2034) SS BOND : bond 0.00137 ( 10) SS BOND : angle 0.53164 ( 20) covalent geometry : bond 0.00284 (12236) covalent geometry : angle 0.49616 (16607) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10988.81 seconds wall clock time: 189 minutes 12.21 seconds (11352.21 seconds total)