Starting phenix.real_space_refine on Tue Aug 4 19:12:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11zw_76233/08_2026/11zw_76233.cif Found real_map, /net/cci-nas-00/data/ceres_data/11zw_76233/08_2026/11zw_76233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11zw_76233/08_2026/11zw_76233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11zw_76233/08_2026/11zw_76233.map" model { file = "/net/cci-nas-00/data/ceres_data/11zw_76233/08_2026/11zw_76233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11zw_76233/08_2026/11zw_76233.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3763 2.51 5 N 995 2.21 5 O 1328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6116 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 862 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 111} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 884 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 15, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "H" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1584 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1599 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 200} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "N" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 882 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "L" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Time building chain proxies: 1.44, per 1000 atoms: 0.24 Number of scatterers: 6116 At special positions: 0 Unit cell: (79.237, 81.243, 116.348, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1328 8.00 N 995 7.00 C 3763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.04 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.02 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.04 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 311 " " NAG D 1 " - " ASN A 331 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 259.6 milliseconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 15 sheets defined 19.2% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.806A pdb=" N VAL A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'B' and resid 8 through 14 removed outlier: 3.619A pdb=" N GLY B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 31 removed outlier: 3.880A pdb=" N PHE B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 57 through 80 removed outlier: 4.579A pdb=" N LEU B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 105 removed outlier: 3.963A pdb=" N LEU B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 126 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 194 through 198 removed outlier: 3.899A pdb=" N GLY H 197 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 211 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.989A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.610A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'N' and resid 29 through 33 removed outlier: 4.334A pdb=" N ARG N 32 " --> pdb=" O THR N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 328 removed outlier: 6.561A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU A 306 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU A 344 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL A 308 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN A 346 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 310 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N MET A 348 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 312 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 10.756A pdb=" N ALA A 408 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 11.932A pdb=" N SER A 380 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N GLU A 410 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 11.454A pdb=" N CYS A 378 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLN A 412 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N GLN A 376 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 328 removed outlier: 6.561A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU A 306 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU A 344 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL A 308 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN A 346 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 310 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N MET A 348 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 312 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 400 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL A 392 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN A 402 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE A 390 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.035A pdb=" N GLY H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.035A pdb=" N GLY H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 127 through 131 removed outlier: 6.119A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 127 through 131 removed outlier: 6.119A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 158 through 161 Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.683A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.603A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.677A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AB4, first strand: chain 'N' and resid 4 through 8 Processing sheet with id=AB5, first strand: chain 'N' and resid 59 through 61 removed outlier: 5.465A pdb=" N PHE N 48 " --> pdb=" O ARG N 39 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG N 39 " --> pdb=" O PHE N 48 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA N 34 " --> pdb=" O ASP N 100 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR N 111 " --> pdb=" O ILE N 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 59 through 61 removed outlier: 5.465A pdb=" N PHE N 48 " --> pdb=" O ARG N 39 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG N 39 " --> pdb=" O PHE N 48 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA N 34 " --> pdb=" O ASP N 100 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.63 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1866 1.34 - 1.47: 1498 1.47 - 1.59: 2618 1.59 - 1.71: 0 1.71 - 1.83: 43 Bond restraints: 6025 Sorted by residual: bond pdb=" CB CYS N 97 " pdb=" SG CYS N 97 " ideal model delta sigma weight residual 1.808 1.713 0.095 3.30e-02 9.18e+02 8.31e+00 bond pdb=" N VAL A 395 " pdb=" CA VAL A 395 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.89e+00 bond pdb=" N VAL A 392 " pdb=" CA VAL A 392 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.49e+00 bond pdb=" CD1 TYR L 36 " pdb=" CE1 TYR L 36 " ideal model delta sigma weight residual 1.382 1.312 0.070 3.00e-02 1.11e+03 5.40e+00 bond pdb=" CA TYR L 87 " pdb=" CB TYR L 87 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.82e-02 3.02e+03 5.37e+00 ... (remaining 6020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 8059 4.15 - 8.31: 120 8.31 - 12.46: 10 12.46 - 16.61: 4 16.61 - 20.77: 1 Bond angle restraints: 8194 Sorted by residual: angle pdb=" CA LEU H 18 " pdb=" CB LEU H 18 " pdb=" CG LEU H 18 " ideal model delta sigma weight residual 116.30 137.07 -20.77 3.50e+00 8.16e-02 3.52e+01 angle pdb=" C VAL N 13 " pdb=" N GLN N 14 " pdb=" CA GLN N 14 " ideal model delta sigma weight residual 120.68 129.18 -8.50 1.52e+00 4.33e-01 3.13e+01 angle pdb=" CE1 TYR H 183 " pdb=" CZ TYR H 183 " pdb=" OH TYR H 183 " ideal model delta sigma weight residual 119.90 105.42 14.48 3.00e+00 1.11e-01 2.33e+01 angle pdb=" CE2 TYR H 183 " pdb=" CZ TYR H 183 " pdb=" OH TYR H 183 " ideal model delta sigma weight residual 119.90 134.31 -14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" N ALA H 97 " pdb=" CA ALA H 97 " pdb=" CB ALA H 97 " ideal model delta sigma weight residual 111.52 103.08 8.44 1.86e+00 2.89e-01 2.06e+01 ... (remaining 8189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.39: 3453 20.39 - 40.79: 148 40.79 - 61.18: 27 61.18 - 81.58: 16 81.58 - 101.97: 8 Dihedral angle restraints: 3652 sinusoidal: 1403 harmonic: 2249 Sorted by residual: dihedral pdb=" CA PHE L 49 " pdb=" C PHE L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta harmonic sigma weight residual 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA PRO H 156 " pdb=" C PRO H 156 " pdb=" N VAL H 157 " pdb=" CA VAL H 157 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA SER A 325 " pdb=" C SER A 325 " pdb=" N VAL A 326 " pdb=" CA VAL A 326 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 3649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 809 0.094 - 0.189: 112 0.189 - 0.283: 20 0.283 - 0.377: 5 0.377 - 0.471: 6 Chirality restraints: 952 Sorted by residual: chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" CG LEU B 123 " pdb=" CB LEU B 123 " pdb=" CD1 LEU B 123 " pdb=" CD2 LEU B 123 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CB ILE B 11 " pdb=" CA ILE B 11 " pdb=" CG1 ILE B 11 " pdb=" CG2 ILE B 11 " both_signs ideal model delta sigma weight residual False 2.64 3.07 -0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 949 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 42 " -0.045 2.00e-02 2.50e+03 9.06e-02 8.21e+01 pdb=" C LYS L 42 " 0.157 2.00e-02 2.50e+03 pdb=" O LYS L 42 " -0.059 2.00e-02 2.50e+03 pdb=" N ALA L 43 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 169 " 0.039 2.00e-02 2.50e+03 7.83e-02 6.13e+01 pdb=" C GLY H 169 " -0.135 2.00e-02 2.50e+03 pdb=" O GLY H 169 " 0.050 2.00e-02 2.50e+03 pdb=" N VAL H 170 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 108 " -0.033 2.00e-02 2.50e+03 6.98e-02 4.87e+01 pdb=" CG ASP H 108 " 0.121 2.00e-02 2.50e+03 pdb=" OD1 ASP H 108 " -0.045 2.00e-02 2.50e+03 pdb=" OD2 ASP H 108 " -0.043 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 2295 2.88 - 3.38: 5162 3.38 - 3.89: 10453 3.89 - 4.39: 12704 4.39 - 4.90: 21419 Nonbonded interactions: 52033 Sorted by model distance: nonbonded pdb=" OE1 GLU A 382 " pdb=" O HOH A 501 " model vdw 2.372 3.040 nonbonded pdb=" O GLN L 124 " pdb=" OG SER L 127 " model vdw 2.480 3.040 nonbonded pdb=" OE1 GLN H 3 " pdb=" O HOH H 301 " model vdw 2.487 3.040 nonbonded pdb=" OD2 ASP N 57 " pdb=" OH TYR N 105 " model vdw 2.488 3.040 nonbonded pdb=" OE2 GLU A 306 " pdb=" OH TYR A 334 " model vdw 2.495 3.040 ... (remaining 52028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.730 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 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 : 0.007 0.095 6040 Z= 0.315 Angle : 1.335 20.765 8231 Z= 0.714 Chirality : 0.078 0.471 952 Planarity : 0.015 0.150 1038 Dihedral : 14.341 101.969 2184 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.87 % Allowed : 1.74 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.29), residues: 763 helix: -0.59 (0.46), residues: 104 sheet: 0.70 (0.30), residues: 274 loop : -0.04 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.007 ARG N 39 TYR 0.089 0.009 TYR L 87 PHE 0.052 0.006 PHE H 173 TRP 0.049 0.008 TRP H 110 HIS 0.021 0.005 HIS H 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.31 ( 6025) covalent geometry : angle 1.31788 / 0.71 ( 8194) SS BOND : bond 0.01073 / 0.52 ( 8) SS BOND : angle 1.57884 / 0.80 ( 16) hydrogen bonds : bond 0.15217 / 10.15 ( 257) hydrogen bonds : angle 8.45170 / 5.84 ( 765) link_ALPHA1-3 : bond 0.01883 / 0.99 ( 1) link_ALPHA1-3 : angle 6.04978 / 3.16 ( 3) link_ALPHA1-6 : bond 0.01752 / 0.92 ( 1) link_ALPHA1-6 : angle 1.00190 / 0.57 ( 3) link_BETA1-4 : bond 0.01653 / 0.84 ( 3) link_BETA1-4 : angle 4.05495 / 1.74 ( 9) link_NAG-ASN : bond 0.01300 / 0.68 ( 2) link_NAG-ASN : angle 4.70882 / 2.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 167 ASP cc_start: 0.7947 (t70) cc_final: 0.7663 (t0) outliers start: 5 outliers final: 1 residues processed: 128 average time/residue: 0.6274 time to fit residues: 83.0200 Evaluate side-chains 94 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 HIS A 355 ASN L 152 ASN L 198 HIS N 66 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.068667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.051394 restraints weight = 14480.696| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 3.14 r_work: 0.2512 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6040 Z= 0.165 Angle : 0.634 7.473 8231 Z= 0.332 Chirality : 0.045 0.267 952 Planarity : 0.004 0.057 1038 Dihedral : 8.397 72.358 978 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.04 % Allowed : 9.57 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.30), residues: 763 helix: 1.06 (0.46), residues: 104 sheet: 0.74 (0.28), residues: 302 loop : 0.17 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 24 TYR 0.010 0.001 TYR A 398 PHE 0.029 0.002 PHE B 63 TRP 0.007 0.001 TRP H 33 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 6025) covalent geometry : angle 0.61979 / 0.33 ( 8194) SS BOND : bond 0.00638 / 0.32 ( 8) SS BOND : angle 1.07681 / 0.57 ( 16) hydrogen bonds : bond 0.04182 / 2.75 ( 257) hydrogen bonds : angle 5.74175 / 3.94 ( 765) link_ALPHA1-3 : bond 0.00809 / 0.43 ( 1) link_ALPHA1-3 : angle 4.61549 / 2.32 ( 3) link_ALPHA1-6 : bond 0.00634 / 0.33 ( 1) link_ALPHA1-6 : angle 1.56331 / 0.83 ( 3) link_BETA1-4 : bond 0.00437 / 0.21 ( 3) link_BETA1-4 : angle 2.21153 / 0.92 ( 9) link_NAG-ASN : bond 0.00344 / 0.18 ( 2) link_NAG-ASN : angle 2.21463 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.8460 (t0) cc_final: 0.7546 (t0) REVERT: A 320 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8289 (mt-10) REVERT: A 334 TYR cc_start: 0.8652 (t80) cc_final: 0.8315 (t80) REVERT: A 344 GLU cc_start: 0.8266 (tt0) cc_final: 0.7880 (tt0) REVERT: B 18 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7428 (tm-30) REVERT: B 58 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8005 (mtm-85) REVERT: H 83 MET cc_start: 0.9615 (mtp) cc_final: 0.9362 (mtp) REVERT: H 208 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8743 (mmmt) REVERT: H 213 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8746 (mtmm) REVERT: L 70 GLU cc_start: 0.8083 (tt0) cc_final: 0.7622 (tt0) REVERT: N 28 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8087 (mtm180) REVERT: N 106 SER cc_start: 0.8985 (OUTLIER) cc_final: 0.8609 (p) REVERT: N 114 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8835 (pm20) outliers start: 6 outliers final: 0 residues processed: 102 average time/residue: 0.6229 time to fit residues: 65.7600 Evaluate side-chains 91 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain N residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 51 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.1906 > 50:) chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN N 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.066672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.049960 restraints weight = 14517.067| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 3.08 r_work: 0.2465 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 6040 Z= 0.240 Angle : 0.619 6.658 8231 Z= 0.323 Chirality : 0.045 0.274 952 Planarity : 0.004 0.051 1038 Dihedral : 7.480 61.227 977 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.91 % Allowed : 11.65 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.30), residues: 763 helix: 1.52 (0.46), residues: 106 sheet: 0.83 (0.29), residues: 309 loop : 0.15 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 30 TYR 0.012 0.001 TYR B 31 PHE 0.037 0.002 PHE B 63 TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 ( 6025) covalent geometry : angle 0.60726 / 0.32 ( 8194) SS BOND : bond 0.00794 / 0.39 ( 8) SS BOND : angle 1.31183 / 0.70 ( 16) hydrogen bonds : bond 0.04078 / 2.66 ( 257) hydrogen bonds : angle 5.42728 / 3.75 ( 765) link_ALPHA1-3 : bond 0.00437 / 0.23 ( 1) link_ALPHA1-3 : angle 4.21469 / 2.08 ( 3) link_ALPHA1-6 : bond 0.00302 / 0.16 ( 1) link_ALPHA1-6 : angle 1.58231 / 0.85 ( 3) link_BETA1-4 : bond 0.00346 / 0.17 ( 3) link_BETA1-4 : angle 1.88602 / 0.78 ( 9) link_NAG-ASN : bond 0.00257 / 0.12 ( 2) link_NAG-ASN : angle 1.50691 / 0.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 306 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8570 (mt-10) REVERT: A 317 ASP cc_start: 0.8504 (t0) cc_final: 0.7973 (OUTLIER) REVERT: A 320 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8588 (mt-10) REVERT: A 344 GLU cc_start: 0.8339 (tt0) cc_final: 0.7881 (tt0) REVERT: B 18 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7291 (tm-30) REVERT: B 58 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8335 (mtm-85) REVERT: B 97 GLU cc_start: 0.8560 (pt0) cc_final: 0.8226 (pm20) REVERT: B 119 LYS cc_start: 0.9315 (ttmm) cc_final: 0.9110 (ttmt) REVERT: H 208 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8910 (mmpt) REVERT: L 70 GLU cc_start: 0.8220 (tt0) cc_final: 0.7680 (tt0) REVERT: L 81 GLU cc_start: 0.9344 (pm20) cc_final: 0.8969 (pm20) REVERT: N 74 ASP cc_start: 0.8458 (t0) cc_final: 0.8175 (t70) REVERT: N 106 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8646 (p) outliers start: 11 outliers final: 4 residues processed: 100 average time/residue: 0.6392 time to fit residues: 65.9975 Evaluate side-chains 92 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 106 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN N 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.067686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.051367 restraints weight = 14480.130| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.09 r_work: 0.2496 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6040 Z= 0.145 Angle : 0.550 6.692 8231 Z= 0.286 Chirality : 0.044 0.295 952 Planarity : 0.004 0.051 1038 Dihedral : 6.640 55.430 977 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.39 % Allowed : 12.52 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.31), residues: 763 helix: 1.96 (0.47), residues: 106 sheet: 0.81 (0.29), residues: 316 loop : 0.25 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 217 TYR 0.012 0.001 TYR L 94 PHE 0.034 0.002 PHE B 63 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 6025) covalent geometry : angle 0.53829 / 0.28 ( 8194) SS BOND : bond 0.00481 / 0.23 ( 8) SS BOND : angle 1.01844 / 0.56 ( 16) hydrogen bonds : bond 0.03414 / 2.22 ( 257) hydrogen bonds : angle 5.03794 / 3.50 ( 765) link_ALPHA1-3 : bond 0.00345 / 0.18 ( 1) link_ALPHA1-3 : angle 4.27557 / 2.10 ( 3) link_ALPHA1-6 : bond 0.00445 / 0.23 ( 1) link_ALPHA1-6 : angle 1.61232 / 0.87 ( 3) link_BETA1-4 : bond 0.00386 / 0.19 ( 3) link_BETA1-4 : angle 1.65584 / 0.68 ( 9) link_NAG-ASN : bond 0.00153 / 0.08 ( 2) link_NAG-ASN : angle 1.21529 / 0.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 306 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8532 (mt-10) REVERT: A 317 ASP cc_start: 0.8486 (t0) cc_final: 0.7975 (t0) REVERT: A 320 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8363 (mt-10) REVERT: A 344 GLU cc_start: 0.8365 (tt0) cc_final: 0.7885 (tt0) REVERT: B 18 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7499 (tm-30) REVERT: B 58 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8107 (mtm-85) REVERT: B 74 MET cc_start: 0.8790 (mmp) cc_final: 0.8505 (mmm) REVERT: B 89 LYS cc_start: 0.8897 (tppp) cc_final: 0.8660 (tmmm) REVERT: B 119 LYS cc_start: 0.9287 (ttmm) cc_final: 0.9051 (ttmt) REVERT: L 70 GLU cc_start: 0.8154 (tt0) cc_final: 0.7569 (tt0) REVERT: L 81 GLU cc_start: 0.9417 (pm20) cc_final: 0.9044 (pm20) REVERT: L 161 GLU cc_start: 0.8453 (mp0) cc_final: 0.8231 (mp0) REVERT: N 74 ASP cc_start: 0.8453 (t0) cc_final: 0.8103 (t0) outliers start: 8 outliers final: 1 residues processed: 94 average time/residue: 0.6750 time to fit residues: 65.4894 Evaluate side-chains 86 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain H residue 150 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 48 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN N 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.067328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.051178 restraints weight = 14670.005| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 3.09 r_work: 0.2482 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6040 Z= 0.174 Angle : 0.551 6.488 8231 Z= 0.286 Chirality : 0.044 0.298 952 Planarity : 0.004 0.049 1038 Dihedral : 6.050 50.227 977 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.57 % Allowed : 13.22 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.31), residues: 763 helix: 2.16 (0.47), residues: 106 sheet: 0.87 (0.29), residues: 315 loop : 0.24 (0.37), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 217 TYR 0.012 0.001 TYR L 94 PHE 0.025 0.002 PHE B 63 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 6025) covalent geometry : angle 0.53952 / 0.28 ( 8194) SS BOND : bond 0.00471 / 0.22 ( 8) SS BOND : angle 1.10612 / 0.59 ( 16) hydrogen bonds : bond 0.03413 / 2.21 ( 257) hydrogen bonds : angle 4.96769 / 3.45 ( 765) link_ALPHA1-3 : bond 0.00302 / 0.16 ( 1) link_ALPHA1-3 : angle 4.18953 / 2.05 ( 3) link_ALPHA1-6 : bond 0.00497 / 0.26 ( 1) link_ALPHA1-6 : angle 1.56080 / 0.85 ( 3) link_BETA1-4 : bond 0.00327 / 0.16 ( 3) link_BETA1-4 : angle 1.67856 / 0.70 ( 9) link_NAG-ASN : bond 0.00209 / 0.10 ( 2) link_NAG-ASN : angle 1.13897 / 0.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.8545 (t0) cc_final: 0.8004 (t0) REVERT: A 320 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8456 (mt-10) REVERT: A 344 GLU cc_start: 0.8379 (tt0) cc_final: 0.7916 (tt0) REVERT: B 18 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 58 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8128 (mtm-85) REVERT: B 89 LYS cc_start: 0.9018 (tppp) cc_final: 0.8695 (tmmm) REVERT: B 97 GLU cc_start: 0.8736 (pt0) cc_final: 0.8351 (pm20) REVERT: B 119 LYS cc_start: 0.9297 (ttmm) cc_final: 0.9096 (ttmt) REVERT: H 199 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: L 70 GLU cc_start: 0.8261 (tt0) cc_final: 0.7687 (tt0) REVERT: L 81 GLU cc_start: 0.9433 (pm20) cc_final: 0.9035 (pm20) REVERT: L 161 GLU cc_start: 0.8430 (mp0) cc_final: 0.8155 (mp0) REVERT: N 74 ASP cc_start: 0.8385 (t0) cc_final: 0.8017 (t0) REVERT: N 90 GLU cc_start: 0.9118 (mp0) cc_final: 0.8863 (mp0) REVERT: N 106 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8608 (p) REVERT: N 114 GLN cc_start: 0.9251 (mm-40) cc_final: 0.8989 (mp10) outliers start: 9 outliers final: 1 residues processed: 94 average time/residue: 0.6760 time to fit residues: 65.6139 Evaluate side-chains 91 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 106 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN N 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.051546 restraints weight = 14355.547| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 3.09 r_work: 0.2501 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6040 Z= 0.135 Angle : 0.540 7.567 8231 Z= 0.279 Chirality : 0.043 0.294 952 Planarity : 0.004 0.049 1038 Dihedral : 5.642 46.418 977 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.91 % Allowed : 14.09 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.32), residues: 763 helix: 2.39 (0.49), residues: 106 sheet: 0.87 (0.29), residues: 319 loop : 0.28 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 217 TYR 0.011 0.001 TYR L 94 PHE 0.023 0.002 PHE B 63 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 6025) covalent geometry : angle 0.52942 / 0.28 ( 8194) SS BOND : bond 0.00459 / 0.22 ( 8) SS BOND : angle 1.01754 / 0.56 ( 16) hydrogen bonds : bond 0.03140 / 2.02 ( 257) hydrogen bonds : angle 4.79125 / 3.33 ( 765) link_ALPHA1-3 : bond 0.00270 / 0.14 ( 1) link_ALPHA1-3 : angle 4.18432 / 2.04 ( 3) link_ALPHA1-6 : bond 0.00521 / 0.27 ( 1) link_ALPHA1-6 : angle 1.47901 / 0.81 ( 3) link_BETA1-4 : bond 0.00369 / 0.18 ( 3) link_BETA1-4 : angle 1.61647 / 0.65 ( 9) link_NAG-ASN : bond 0.00091 / 0.04 ( 2) link_NAG-ASN : angle 0.98339 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.8576 (t0) cc_final: 0.8051 (OUTLIER) REVERT: A 320 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8431 (mt-10) REVERT: A 344 GLU cc_start: 0.8413 (tt0) cc_final: 0.7957 (tt0) REVERT: B 18 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7402 (tm-30) REVERT: B 58 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8013 (mtm-85) REVERT: B 89 LYS cc_start: 0.9040 (tppp) cc_final: 0.8726 (tmmm) REVERT: B 96 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8273 (mtpm) REVERT: B 97 GLU cc_start: 0.8722 (pt0) cc_final: 0.8506 (pt0) REVERT: H 199 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: L 70 GLU cc_start: 0.8197 (tt0) cc_final: 0.7636 (tt0) REVERT: L 81 GLU cc_start: 0.9444 (pm20) cc_final: 0.9052 (pm20) REVERT: N 74 ASP cc_start: 0.8385 (t0) cc_final: 0.8007 (t0) REVERT: N 90 GLU cc_start: 0.9150 (mp0) cc_final: 0.8880 (mp0) REVERT: N 106 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8597 (p) REVERT: N 114 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8985 (mp10) outliers start: 11 outliers final: 2 residues processed: 94 average time/residue: 0.6017 time to fit residues: 58.5660 Evaluate side-chains 90 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 106 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN H 35 ASN N 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.050689 restraints weight = 14544.315| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.07 r_work: 0.2475 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6040 Z= 0.203 Angle : 0.571 7.984 8231 Z= 0.295 Chirality : 0.044 0.290 952 Planarity : 0.004 0.049 1038 Dihedral : 5.459 42.582 977 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.74 % Allowed : 13.91 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.32), residues: 763 helix: 2.53 (0.49), residues: 106 sheet: 0.80 (0.29), residues: 318 loop : 0.23 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 217 TYR 0.013 0.001 TYR L 94 PHE 0.039 0.002 PHE B 63 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 ( 6025) covalent geometry : angle 0.55953 / 0.29 ( 8194) SS BOND : bond 0.00599 / 0.29 ( 8) SS BOND : angle 1.29576 / 0.71 ( 16) hydrogen bonds : bond 0.03464 / 2.24 ( 257) hydrogen bonds : angle 4.90906 / 3.41 ( 765) link_ALPHA1-3 : bond 0.00343 / 0.18 ( 1) link_ALPHA1-3 : angle 4.08029 / 1.98 ( 3) link_ALPHA1-6 : bond 0.00491 / 0.26 ( 1) link_ALPHA1-6 : angle 1.45273 / 0.80 ( 3) link_BETA1-4 : bond 0.00258 / 0.12 ( 3) link_BETA1-4 : angle 1.68667 / 0.69 ( 9) link_NAG-ASN : bond 0.00206 / 0.10 ( 2) link_NAG-ASN : angle 1.07465 / 0.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.191 Fit side-chains REVERT: A 317 ASP cc_start: 0.8581 (t0) cc_final: 0.8085 (t0) REVERT: A 320 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8447 (mt-10) REVERT: A 334 TYR cc_start: 0.8777 (t80) cc_final: 0.8120 (t80) REVERT: A 344 GLU cc_start: 0.8442 (tt0) cc_final: 0.7986 (tt0) REVERT: B 18 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 58 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8030 (mtm-85) REVERT: B 89 LYS cc_start: 0.9063 (tppp) cc_final: 0.8715 (tmmm) REVERT: H 199 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: H 216 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7953 (tppt) REVERT: L 70 GLU cc_start: 0.8280 (tt0) cc_final: 0.7711 (tt0) REVERT: L 81 GLU cc_start: 0.9429 (pm20) cc_final: 0.8983 (pm20) REVERT: N 74 ASP cc_start: 0.8380 (t0) cc_final: 0.7989 (t0) REVERT: N 90 GLU cc_start: 0.9172 (mp0) cc_final: 0.8920 (mp0) REVERT: N 106 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8616 (p) REVERT: N 114 GLN cc_start: 0.9256 (mm-40) cc_final: 0.9007 (mp10) outliers start: 10 outliers final: 2 residues processed: 98 average time/residue: 0.6531 time to fit residues: 66.0993 Evaluate side-chains 91 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 106 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN H 35 ASN N 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.051354 restraints weight = 14565.954| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.09 r_work: 0.2494 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6040 Z= 0.142 Angle : 0.550 9.060 8231 Z= 0.283 Chirality : 0.043 0.283 952 Planarity : 0.004 0.048 1038 Dihedral : 5.212 39.560 977 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.39 % Allowed : 14.26 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.32), residues: 763 helix: 2.54 (0.50), residues: 106 sheet: 0.85 (0.29), residues: 323 loop : 0.26 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 217 TYR 0.014 0.001 TYR L 94 PHE 0.032 0.002 PHE B 63 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6025) covalent geometry : angle 0.54040 / 0.28 ( 8194) SS BOND : bond 0.00394 / 0.18 ( 8) SS BOND : angle 1.04472 / 0.56 ( 16) hydrogen bonds : bond 0.03186 / 2.05 ( 257) hydrogen bonds : angle 4.76301 / 3.32 ( 765) link_ALPHA1-3 : bond 0.00358 / 0.19 ( 1) link_ALPHA1-3 : angle 4.01072 / 1.94 ( 3) link_ALPHA1-6 : bond 0.00563 / 0.30 ( 1) link_ALPHA1-6 : angle 1.42097 / 0.77 ( 3) link_BETA1-4 : bond 0.00285 / 0.14 ( 3) link_BETA1-4 : angle 1.61552 / 0.65 ( 9) link_NAG-ASN : bond 0.00100 / 0.05 ( 2) link_NAG-ASN : angle 0.95909 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.140 Fit side-chains REVERT: A 317 ASP cc_start: 0.8580 (t0) cc_final: 0.8087 (t0) REVERT: A 320 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8395 (mt-10) REVERT: A 334 TYR cc_start: 0.8738 (t80) cc_final: 0.8292 (t80) REVERT: A 344 GLU cc_start: 0.8439 (tt0) cc_final: 0.7985 (tt0) REVERT: B 58 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7933 (mtm-85) REVERT: B 89 LYS cc_start: 0.9053 (tppp) cc_final: 0.8737 (tmmm) REVERT: B 97 GLU cc_start: 0.8736 (pt0) cc_final: 0.8366 (pm20) REVERT: B 100 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8636 (mm-30) REVERT: H 199 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: L 70 GLU cc_start: 0.8276 (tt0) cc_final: 0.7711 (tt0) REVERT: L 81 GLU cc_start: 0.9436 (pm20) cc_final: 0.8995 (pm20) REVERT: L 161 GLU cc_start: 0.8472 (mp0) cc_final: 0.8232 (mp0) REVERT: N 28 ARG cc_start: 0.8860 (mtm180) cc_final: 0.8389 (mtm180) REVERT: N 74 ASP cc_start: 0.8389 (t0) cc_final: 0.8006 (t0) REVERT: N 90 GLU cc_start: 0.9174 (mp0) cc_final: 0.8942 (mp0) REVERT: N 106 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8593 (p) REVERT: N 114 GLN cc_start: 0.9245 (mm-40) cc_final: 0.9001 (mp10) outliers start: 8 outliers final: 3 residues processed: 96 average time/residue: 0.6624 time to fit residues: 65.6229 Evaluate side-chains 92 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 106 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 69 optimal weight: 0.0050 chunk 9 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN H 77 ASN N 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.067386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.051262 restraints weight = 14474.104| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.11 r_work: 0.2497 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6040 Z= 0.143 Angle : 0.580 10.377 8231 Z= 0.298 Chirality : 0.044 0.277 952 Planarity : 0.004 0.048 1038 Dihedral : 5.086 37.308 977 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.39 % Allowed : 15.13 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.32), residues: 763 helix: 2.36 (0.51), residues: 106 sheet: 0.88 (0.29), residues: 323 loop : 0.29 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 217 TYR 0.014 0.001 TYR L 94 PHE 0.029 0.002 PHE B 63 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 6025) covalent geometry : angle 0.56683 / 0.29 ( 8194) SS BOND : bond 0.00570 / 0.28 ( 8) SS BOND : angle 1.77210 / 0.94 ( 16) hydrogen bonds : bond 0.03189 / 2.05 ( 257) hydrogen bonds : angle 4.71880 / 3.29 ( 765) link_ALPHA1-3 : bond 0.00419 / 0.22 ( 1) link_ALPHA1-3 : angle 3.92804 / 1.90 ( 3) link_ALPHA1-6 : bond 0.00528 / 0.28 ( 1) link_ALPHA1-6 : angle 1.39265 / 0.75 ( 3) link_BETA1-4 : bond 0.00275 / 0.13 ( 3) link_BETA1-4 : angle 1.61681 / 0.66 ( 9) link_NAG-ASN : bond 0.00143 / 0.07 ( 2) link_NAG-ASN : angle 0.96789 / 0.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.233 Fit side-chains REVERT: A 317 ASP cc_start: 0.8604 (t0) cc_final: 0.8114 (t0) REVERT: A 320 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8387 (mt-10) REVERT: A 334 TYR cc_start: 0.8750 (t80) cc_final: 0.8142 (t80) REVERT: A 344 GLU cc_start: 0.8437 (tt0) cc_final: 0.7985 (tt0) REVERT: B 58 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7878 (mtm-85) REVERT: B 89 LYS cc_start: 0.9042 (tppp) cc_final: 0.8715 (tmmm) REVERT: B 96 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8235 (mtpm) REVERT: B 97 GLU cc_start: 0.8694 (pt0) cc_final: 0.8319 (pm20) REVERT: H 199 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: H 213 LYS cc_start: 0.9233 (ttmm) cc_final: 0.9016 (ttmm) REVERT: L 70 GLU cc_start: 0.8282 (tt0) cc_final: 0.7760 (tt0) REVERT: L 81 GLU cc_start: 0.9436 (pm20) cc_final: 0.8994 (pm20) REVERT: L 161 GLU cc_start: 0.8471 (mp0) cc_final: 0.8225 (mp0) REVERT: N 28 ARG cc_start: 0.8859 (mtm180) cc_final: 0.8420 (mtm180) REVERT: N 74 ASP cc_start: 0.8393 (t0) cc_final: 0.7989 (t0) REVERT: N 90 GLU cc_start: 0.9181 (mp0) cc_final: 0.8939 (mp0) REVERT: N 106 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8599 (p) REVERT: N 114 GLN cc_start: 0.9253 (mm-40) cc_final: 0.9015 (mp10) outliers start: 8 outliers final: 3 residues processed: 97 average time/residue: 0.6706 time to fit residues: 67.2290 Evaluate side-chains 96 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 106 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 43 optimal weight: 0.0050 chunk 40 optimal weight: 0.0010 chunk 36 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN N 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.051736 restraints weight = 14587.766| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.18 r_work: 0.2521 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6040 Z= 0.111 Angle : 0.563 11.018 8231 Z= 0.289 Chirality : 0.043 0.266 952 Planarity : 0.004 0.046 1038 Dihedral : 4.769 33.366 977 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.87 % Allowed : 15.65 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.32), residues: 763 helix: 2.26 (0.52), residues: 106 sheet: 0.99 (0.29), residues: 323 loop : 0.31 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 217 TYR 0.014 0.001 TYR L 94 PHE 0.013 0.001 PHE B 27 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6025) covalent geometry : angle 0.55088 / 0.29 ( 8194) SS BOND : bond 0.00529 / 0.27 ( 8) SS BOND : angle 1.64985 / 0.87 ( 16) hydrogen bonds : bond 0.02990 / 1.95 ( 257) hydrogen bonds : angle 4.59346 / 3.22 ( 765) link_ALPHA1-3 : bond 0.00477 / 0.25 ( 1) link_ALPHA1-3 : angle 3.79968 / 1.83 ( 3) link_ALPHA1-6 : bond 0.00597 / 0.31 ( 1) link_ALPHA1-6 : angle 1.37714 / 0.74 ( 3) link_BETA1-4 : bond 0.00288 / 0.14 ( 3) link_BETA1-4 : angle 1.55293 / 0.63 ( 9) link_NAG-ASN : bond 0.00058 / 0.03 ( 2) link_NAG-ASN : angle 0.87028 / 0.28 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.150 Fit side-chains REVERT: A 317 ASP cc_start: 0.8609 (t0) cc_final: 0.8104 (t0) REVERT: A 320 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8417 (mt-10) REVERT: A 344 GLU cc_start: 0.8444 (tt0) cc_final: 0.8000 (tt0) REVERT: B 58 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7813 (mtm-85) REVERT: B 64 MET cc_start: 0.8976 (mmp) cc_final: 0.8574 (mmm) REVERT: B 89 LYS cc_start: 0.9039 (tppp) cc_final: 0.8702 (tmmm) REVERT: B 97 GLU cc_start: 0.8699 (pt0) cc_final: 0.8403 (pm20) REVERT: H 52 LYS cc_start: 0.8872 (tttt) cc_final: 0.8527 (tttm) REVERT: H 199 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8568 (tp40) REVERT: L 70 GLU cc_start: 0.8206 (tt0) cc_final: 0.7743 (tt0) REVERT: L 81 GLU cc_start: 0.9442 (pm20) cc_final: 0.9010 (pm20) REVERT: L 161 GLU cc_start: 0.8484 (mp0) cc_final: 0.8236 (mp0) REVERT: N 28 ARG cc_start: 0.8833 (mtm180) cc_final: 0.8390 (mtm180) REVERT: N 74 ASP cc_start: 0.8404 (t0) cc_final: 0.7987 (t0) REVERT: N 90 GLU cc_start: 0.9186 (mp0) cc_final: 0.8942 (mp0) REVERT: N 106 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8616 (p) REVERT: N 114 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8977 (mp10) outliers start: 5 outliers final: 2 residues processed: 98 average time/residue: 0.6268 time to fit residues: 63.5121 Evaluate side-chains 91 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 106 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.0770 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN N 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.068079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.051863 restraints weight = 14413.954| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.14 r_work: 0.2524 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6040 Z= 0.129 Angle : 0.623 14.918 8231 Z= 0.317 Chirality : 0.044 0.339 952 Planarity : 0.004 0.047 1038 Dihedral : 4.685 31.153 977 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.39 % Allowed : 15.48 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.32), residues: 763 helix: 2.16 (0.51), residues: 106 sheet: 1.02 (0.29), residues: 323 loop : 0.30 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 217 TYR 0.014 0.001 TYR L 94 PHE 0.015 0.001 PHE L 49 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 6025) covalent geometry : angle 0.59755 / 0.31 ( 8194) SS BOND : bond 0.00726 / 0.37 ( 8) SS BOND : angle 3.46037 / 1.96 ( 16) hydrogen bonds : bond 0.03082 / 2.00 ( 257) hydrogen bonds : angle 4.62834 / 3.24 ( 765) link_ALPHA1-3 : bond 0.00400 / 0.21 ( 1) link_ALPHA1-3 : angle 3.74109 / 1.81 ( 3) link_ALPHA1-6 : bond 0.00615 / 0.32 ( 1) link_ALPHA1-6 : angle 1.39978 / 0.75 ( 3) link_BETA1-4 : bond 0.00259 / 0.13 ( 3) link_BETA1-4 : angle 1.58111 / 0.65 ( 9) link_NAG-ASN : bond 0.00065 / 0.03 ( 2) link_NAG-ASN : angle 0.98670 / 0.32 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.40 seconds wall clock time: 30 minutes 5.59 seconds (1805.59 seconds total)