Starting phenix.real_space_refine on Fri Sep 11 13:42:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rxc_24728/09_2026/7rxc_24728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxc_24728/09_2026/7rxc_24728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rxc_24728/09_2026/7rxc_24728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxc_24728/09_2026/7rxc_24728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rxc_24728/09_2026/7rxc_24728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxc_24728/09_2026/7rxc_24728.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rxc_24728/09_2026/7rxc_24728.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rxc_24728/09_2026/7rxc_24728.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 32 5.16 5 C 6056 2.51 5 N 1510 2.21 5 O 1762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9360 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1582 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 192} Chain breaks: 2 Chain: "L" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1588 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 194} Chain breaks: 2 Chain: "N" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 24, 'TRANS': 414} Chain breaks: 4 Chain: "K" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1661 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 3, 'TRANS': 198} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'POV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-2': 4, 'POV:plan-3': 4} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 1.72, per 1000 atoms: 0.18 Number of scatterers: 9360 At special positions: 0 Unit cell: (128.26, 125.08, 108.12, 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 32 16.00 O 1762 8.00 N 1510 7.00 C 6056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " 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 ALPHA1-4 " GLC A 1 " - " GLC A 2 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 340.0 milliseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 19 sheets defined 36.9% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.550A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.649A pdb=" N LEU L 89 " --> pdb=" O PRO L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.984A pdb=" N HIS L 194 " --> pdb=" O ASP L 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 43 through 52 Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.631A pdb=" N GLY B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.712A pdb=" N THR B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 231 through 240 removed outlier: 4.545A pdb=" N ASN B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.868A pdb=" N ASP B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 336 through 353 Processing helix chain 'B' and resid 357 through 370 Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 502 through 517 Processing helix chain 'K' and resid 3 through 27 Processing helix chain 'K' and resid 33 through 48 Processing helix chain 'K' and resid 49 through 52 removed outlier: 4.196A pdb=" N PHE K 52 " --> pdb=" O LEU K 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 49 through 52' Processing helix chain 'K' and resid 57 through 80 Processing helix chain 'K' and resid 95 through 110 Proline residue: K 101 - end of helix removed outlier: 3.702A pdb=" N ASN K 110 " --> pdb=" O SER K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 129 Processing helix chain 'K' and resid 131 through 142 Processing helix chain 'K' and resid 148 through 173 Processing helix chain 'K' and resid 177 through 202 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.740A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.344A pdb=" N TYR H 112 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.891A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY H 149 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL H 192 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU H 151 " --> pdb=" O SER H 190 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER H 190 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS H 153 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU H 188 " --> pdb=" O LYS H 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.891A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY H 149 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL H 192 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU H 151 " --> pdb=" O SER H 190 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER H 190 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS H 153 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU H 188 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER H 187 " --> pdb=" O VAL H 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 161 through 164 removed outlier: 6.586A pdb=" N LYS B 484 " --> pdb=" O PHE B 532 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 534 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B 486 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.921A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA L 90 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.921A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA L 90 " --> pdb=" O LEU L 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.766A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 150 through 154 Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.719A pdb=" N TRP N 32 " --> pdb=" O ARG N 52 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ARG N 52 " --> pdb=" O TRP N 32 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N MET N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 11 through 13 Processing sheet with id=AB6, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.931A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ALA B 64 " --> pdb=" O TRP B 11 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 261 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL B 111 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 263 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.931A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ALA B 64 " --> pdb=" O TRP B 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AB9, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 173 removed outlier: 4.059A pdb=" N LYS B 171 " --> pdb=" O ASP B 178 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1509 1.31 - 1.44: 2699 1.44 - 1.56: 5330 1.56 - 1.69: 1 1.69 - 1.81: 51 Bond restraints: 9590 Sorted by residual: bond pdb=" C29 POV K 304 " pdb="C210 POV K 304 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.46e+01 bond pdb=" C29 POV K 302 " pdb="C210 POV K 302 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C29 POV K 303 " pdb="C210 POV K 303 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.37e+01 bond pdb=" C29 POV K 301 " pdb="C210 POV K 301 " ideal model delta sigma weight residual 1.333 1.526 -0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" C21 POV K 302 " pdb=" O21 POV K 302 " ideal model delta sigma weight residual 1.330 1.185 0.145 2.00e-02 2.50e+03 5.24e+01 ... (remaining 9585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 12950 3.73 - 7.46: 43 7.46 - 11.19: 3 11.19 - 14.92: 1 14.92 - 18.65: 8 Bond angle restraints: 13005 Sorted by residual: angle pdb=" C29 POV K 301 " pdb="C210 POV K 301 " pdb="C211 POV K 301 " ideal model delta sigma weight residual 127.67 109.02 18.65 3.00e+00 1.11e-01 3.86e+01 angle pdb=" C28 POV K 303 " pdb=" C29 POV K 303 " pdb="C210 POV K 303 " ideal model delta sigma weight residual 127.79 109.29 18.50 3.00e+00 1.11e-01 3.80e+01 angle pdb=" C28 POV K 302 " pdb=" C29 POV K 302 " pdb="C210 POV K 302 " ideal model delta sigma weight residual 127.79 109.32 18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C29 POV K 303 " pdb="C210 POV K 303 " pdb="C211 POV K 303 " ideal model delta sigma weight residual 127.67 109.31 18.36 3.00e+00 1.11e-01 3.75e+01 angle pdb=" C28 POV K 301 " pdb=" C29 POV K 301 " pdb="C210 POV K 301 " ideal model delta sigma weight residual 127.79 109.48 18.31 3.00e+00 1.11e-01 3.73e+01 ... (remaining 13000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5102 17.95 - 35.91: 427 35.91 - 53.86: 92 53.86 - 71.82: 17 71.82 - 89.77: 10 Dihedral angle restraints: 5648 sinusoidal: 2223 harmonic: 3425 Sorted by residual: dihedral pdb=" CA GLU H 158 " pdb=" C GLU H 158 " pdb=" N PRO H 159 " pdb=" CA PRO H 159 " ideal model delta harmonic sigma weight residual 180.00 148.16 31.84 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.49 45.51 1 1.00e+01 1.00e-02 2.87e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.52 34.48 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 5645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.933: 1439 0.933 - 1.867: 0 1.867 - 2.800: 0 2.800 - 3.734: 0 3.734 - 4.667: 1 Chirality restraints: 1440 Sorted by residual: chirality pdb=" C1 GLC A 1 " pdb=" C2 GLC A 1 " pdb=" O1 GLC A 1 " pdb=" O5 GLC A 1 " both_signs ideal model delta sigma weight residual False 2.33 -2.33 4.67 2.00e-01 2.50e+01 5.45e+02 chirality pdb=" C1 GLC A 2 " pdb=" O4 GLC A 1 " pdb=" C2 GLC A 2 " pdb=" O5 GLC A 2 " both_signs ideal model delta sigma weight residual False 2.40 2.33 0.07 2.00e-02 2.50e+03 1.28e+01 chirality pdb=" CA ASN B 283 " pdb=" N ASN B 283 " pdb=" C ASN B 283 " pdb=" CB ASN B 283 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1437 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV K 303 " -0.278 2.00e-02 2.50e+03 2.79e-01 7.76e+02 pdb=" C29 POV K 303 " 0.278 2.00e-02 2.50e+03 pdb="C210 POV K 303 " 0.279 2.00e-02 2.50e+03 pdb="C211 POV K 303 " -0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV K 304 " 0.172 2.00e-02 2.50e+03 1.72e-01 2.96e+02 pdb=" C29 POV K 304 " -0.173 2.00e-02 2.50e+03 pdb="C210 POV K 304 " -0.171 2.00e-02 2.50e+03 pdb="C211 POV K 304 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV K 302 " -0.147 2.00e-02 2.50e+03 1.47e-01 2.16e+02 pdb=" C29 POV K 302 " 0.146 2.00e-02 2.50e+03 pdb="C210 POV K 302 " 0.148 2.00e-02 2.50e+03 pdb="C211 POV K 302 " -0.147 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 111 2.65 - 3.21: 8507 3.21 - 3.78: 14725 3.78 - 4.34: 20837 4.34 - 4.90: 34383 Nonbonded interactions: 78563 Sorted by model distance: nonbonded pdb=" OD1 ASP K 9 " pdb=" OH TYR K 162 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR N 106 " pdb=" OD2 ASP K 9 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR K 45 " pdb=" OH TYR K 72 " model vdw 2.157 3.040 nonbonded pdb=" O ASN B 235 " pdb=" OG1 THR B 238 " model vdw 2.173 3.040 nonbonded pdb=" O PRO H 129 " pdb=" OH TYR B 513 " model vdw 2.182 3.040 ... (remaining 78558 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: 0.700 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: 0.030 Set scattering table: 0.030 Process input model: 8.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.006 0.195 9596 Z= 0.265 Angle : 0.774 18.648 13018 Z= 0.347 Chirality : 0.130 4.667 1440 Planarity : 0.011 0.279 1630 Dihedral : 14.322 89.769 3439 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 1.92 % 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 (0.24), residues: 1152 helix: 1.83 (0.26), residues: 381 sheet: 0.63 (0.28), residues: 305 loop : 0.12 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 99 TYR 0.048 0.001 TYR K 162 PHE 0.030 0.001 PHE B 259 TRP 0.013 0.001 TRP N 107 HIS 0.004 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.26 ( 9590) covalent geometry : angle 0.76907 / 0.35 (13005) SS BOND : bond 0.00254 / 0.16 ( 5) SS BOND : angle 1.26536 / 0.77 ( 10) hydrogen bonds : bond 0.12327 / 7.90 ( 477) hydrogen bonds : angle 6.23942 / 4.42 ( 1368) link_ALPHA1-4 : bond 0.02914 / 1.53 ( 1) link_ALPHA1-4 : angle 5.61296 / 2.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.285 Fit side-chains REVERT: N 46 GLU cc_start: 0.7803 (pt0) cc_final: 0.7590 (pt0) REVERT: K 201 LYS cc_start: 0.7743 (ttmt) cc_final: 0.7519 (ttpt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1068 time to fit residues: 21.3829 Evaluate side-chains 118 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128695 restraints weight = 12486.703| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.87 r_work: 0.3272 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9596 Z= 0.161 Angle : 0.556 7.654 13018 Z= 0.286 Chirality : 0.041 0.148 1440 Planarity : 0.005 0.124 1630 Dihedral : 7.297 69.127 1325 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.60 % Allowed : 6.61 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 1.92 % 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: 1.29 (0.25), residues: 1152 helix: 1.94 (0.25), residues: 389 sheet: 0.72 (0.29), residues: 305 loop : 0.09 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 113 TYR 0.030 0.001 TYR K 162 PHE 0.019 0.001 PHE B 259 TRP 0.009 0.001 TRP B 523 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 9590) covalent geometry : angle 0.55493 / 0.29 (13005) SS BOND : bond 0.00178 / 0.09 ( 5) SS BOND : angle 0.91435 / 0.53 ( 10) hydrogen bonds : bond 0.03880 / 2.52 ( 477) hydrogen bonds : angle 5.12564 / 3.62 ( 1368) link_ALPHA1-4 : bond 0.00047 / 0.02 ( 1) link_ALPHA1-4 : angle 1.50361 / 1.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: H 153 LYS cc_start: 0.8337 (ttpt) cc_final: 0.7870 (ttmt) REVERT: N 46 GLU cc_start: 0.8219 (pt0) cc_final: 0.7991 (pt0) REVERT: B 178 ASP cc_start: 0.7178 (t0) cc_final: 0.6228 (p0) REVERT: B 323 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8069 (tt0) outliers start: 6 outliers final: 4 residues processed: 135 average time/residue: 0.0926 time to fit residues: 17.4768 Evaluate side-chains 126 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 356 GLN B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.161640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106119 restraints weight = 12220.309| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.11 r_work: 0.3074 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 9596 Z= 0.256 Angle : 0.605 6.014 13018 Z= 0.311 Chirality : 0.043 0.189 1440 Planarity : 0.005 0.106 1630 Dihedral : 7.394 57.136 1325 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.70 % Allowed : 9.01 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1152 helix: 1.91 (0.26), residues: 385 sheet: 0.63 (0.29), residues: 305 loop : 0.09 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.025 0.002 TYR K 162 PHE 0.021 0.002 PHE B 259 TRP 0.014 0.002 TRP N 32 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 ( 9590) covalent geometry : angle 0.60381 / 0.31 (13005) SS BOND : bond 0.00168 / 0.09 ( 5) SS BOND : angle 0.87249 / 0.49 ( 10) hydrogen bonds : bond 0.04069 / 2.65 ( 477) hydrogen bonds : angle 5.11353 / 3.61 ( 1368) link_ALPHA1-4 : bond 0.00690 / 0.36 ( 1) link_ALPHA1-4 : angle 2.23646 / 1.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: H 153 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7886 (ttpt) REVERT: L 175 ASP cc_start: 0.7934 (t0) cc_final: 0.7416 (t0) REVERT: N 46 GLU cc_start: 0.8488 (pt0) cc_final: 0.8287 (pt0) REVERT: B 23 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6467 (mp0) REVERT: B 178 ASP cc_start: 0.7149 (t0) cc_final: 0.5980 (p0) REVERT: B 312 LEU cc_start: 0.6712 (tp) cc_final: 0.6497 (tp) REVERT: B 323 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7944 (tt0) REVERT: B 366 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8124 (mm-40) REVERT: K 33 SER cc_start: 0.8917 (t) cc_final: 0.8463 (m) REVERT: K 134 GLN cc_start: 0.8718 (tp40) cc_final: 0.7991 (tp-100) outliers start: 17 outliers final: 10 residues processed: 144 average time/residue: 0.0862 time to fit residues: 17.5195 Evaluate side-chains 137 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107439 restraints weight = 12411.856| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.12 r_work: 0.3087 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9596 Z= 0.198 Angle : 0.561 6.691 13018 Z= 0.289 Chirality : 0.041 0.184 1440 Planarity : 0.004 0.085 1630 Dihedral : 7.231 56.760 1325 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.80 % Allowed : 11.21 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.20 (0.25), residues: 1152 helix: 1.92 (0.26), residues: 384 sheet: 0.55 (0.28), residues: 322 loop : 0.10 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.015 0.001 TYR K 162 PHE 0.014 0.001 PHE B 259 TRP 0.012 0.001 TRP H 47 HIS 0.008 0.001 HIS L 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 ( 9590) covalent geometry : angle 0.55967 / 0.29 (13005) SS BOND : bond 0.00305 / 0.15 ( 5) SS BOND : angle 0.76095 / 0.43 ( 10) hydrogen bonds : bond 0.03772 / 2.47 ( 477) hydrogen bonds : angle 4.97737 / 3.51 ( 1368) link_ALPHA1-4 : bond 0.00502 / 0.26 ( 1) link_ALPHA1-4 : angle 2.14263 / 1.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: H 153 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7840 (ttpt) REVERT: L 175 ASP cc_start: 0.7711 (t0) cc_final: 0.7501 (t0) REVERT: L 193 LYS cc_start: 0.6612 (pptt) cc_final: 0.6069 (pttt) REVERT: B 23 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: B 178 ASP cc_start: 0.7113 (t0) cc_final: 0.5926 (p0) REVERT: B 323 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7915 (tt0) REVERT: K 33 SER cc_start: 0.8972 (t) cc_final: 0.8483 (m) REVERT: K 134 GLN cc_start: 0.8699 (tp40) cc_final: 0.7981 (tp-100) outliers start: 18 outliers final: 12 residues processed: 142 average time/residue: 0.0909 time to fit residues: 18.2740 Evaluate side-chains 140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 100 optimal weight: 0.0060 chunk 85 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 356 GLN B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.165647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111040 restraints weight = 12334.975| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.17 r_work: 0.3138 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9596 Z= 0.108 Angle : 0.503 8.020 13018 Z= 0.258 Chirality : 0.040 0.191 1440 Planarity : 0.004 0.063 1630 Dihedral : 6.579 59.651 1325 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.40 % Allowed : 12.71 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.25), residues: 1152 helix: 2.20 (0.26), residues: 385 sheet: 0.63 (0.28), residues: 323 loop : 0.14 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 67 TYR 0.011 0.001 TYR B 525 PHE 0.012 0.001 PHE N 104 TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS L 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9590) covalent geometry : angle 0.50221 / 0.26 (13005) SS BOND : bond 0.00195 / 0.11 ( 5) SS BOND : angle 0.67019 / 0.39 ( 10) hydrogen bonds : bond 0.03186 / 2.06 ( 477) hydrogen bonds : angle 4.64959 / 3.29 ( 1368) link_ALPHA1-4 : bond 0.00023 / 0.01 ( 1) link_ALPHA1-4 : angle 1.98773 / 1.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: L 193 LYS cc_start: 0.7407 (pptt) cc_final: 0.7002 (pttt) REVERT: N 101 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8335 (mm-30) REVERT: B 23 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: B 178 ASP cc_start: 0.6983 (t0) cc_final: 0.5732 (p0) REVERT: B 323 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7914 (tt0) REVERT: K 33 SER cc_start: 0.8933 (t) cc_final: 0.8402 (m) REVERT: K 134 GLN cc_start: 0.8699 (tp40) cc_final: 0.8073 (tp-100) outliers start: 14 outliers final: 8 residues processed: 144 average time/residue: 0.1037 time to fit residues: 20.8889 Evaluate side-chains 134 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 194 HIS B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.162299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106886 restraints weight = 12383.727| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.15 r_work: 0.3081 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9596 Z= 0.220 Angle : 0.573 8.252 13018 Z= 0.291 Chirality : 0.042 0.214 1440 Planarity : 0.004 0.053 1630 Dihedral : 6.768 58.613 1325 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.20 % Allowed : 13.11 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1152 helix: 2.12 (0.26), residues: 385 sheet: 0.50 (0.28), residues: 324 loop : 0.08 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 38 TYR 0.015 0.001 TYR K 158 PHE 0.013 0.001 PHE B 259 TRP 0.012 0.002 TRP N 32 HIS 0.005 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 ( 9590) covalent geometry : angle 0.57185 / 0.29 (13005) SS BOND : bond 0.00130 / 0.07 ( 5) SS BOND : angle 0.81977 / 0.42 ( 10) hydrogen bonds : bond 0.03664 / 2.40 ( 477) hydrogen bonds : angle 4.84622 / 3.44 ( 1368) link_ALPHA1-4 : bond 0.00545 / 0.29 ( 1) link_ALPHA1-4 : angle 2.10427 / 1.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: L 175 ASP cc_start: 0.7846 (t0) cc_final: 0.7642 (t0) REVERT: L 192 GLU cc_start: 0.6362 (mm-30) cc_final: 0.5668 (tm-30) REVERT: L 193 LYS cc_start: 0.7213 (pptt) cc_final: 0.6900 (pptt) REVERT: B 23 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: B 178 ASP cc_start: 0.6961 (t0) cc_final: 0.5750 (p0) REVERT: B 285 LEU cc_start: 0.7191 (tp) cc_final: 0.6910 (tt) REVERT: B 323 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7892 (tt0) REVERT: B 366 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7999 (mm-40) REVERT: K 33 SER cc_start: 0.8927 (t) cc_final: 0.8520 (m) REVERT: K 134 GLN cc_start: 0.8713 (tp40) cc_final: 0.8274 (tp-100) outliers start: 22 outliers final: 17 residues processed: 138 average time/residue: 0.1000 time to fit residues: 19.3576 Evaluate side-chains 139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 91 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 26 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.164666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110410 restraints weight = 12325.373| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.98 r_work: 0.3143 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9596 Z= 0.114 Angle : 0.509 8.885 13018 Z= 0.260 Chirality : 0.040 0.210 1440 Planarity : 0.003 0.042 1630 Dihedral : 6.303 57.173 1325 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.40 % Allowed : 14.01 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.25), residues: 1152 helix: 2.27 (0.26), residues: 385 sheet: 0.60 (0.28), residues: 324 loop : 0.08 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 67 TYR 0.011 0.001 TYR B 525 PHE 0.017 0.001 PHE K 97 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS L 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 9590) covalent geometry : angle 0.50849 / 0.26 (13005) SS BOND : bond 0.00168 / 0.09 ( 5) SS BOND : angle 0.65656 / 0.36 ( 10) hydrogen bonds : bond 0.03189 / 2.08 ( 477) hydrogen bonds : angle 4.63298 / 3.28 ( 1368) link_ALPHA1-4 : bond 0.00150 / 0.08 ( 1) link_ALPHA1-4 : angle 1.89930 / 1.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: L 192 GLU cc_start: 0.6411 (mm-30) cc_final: 0.5654 (tm-30) REVERT: L 193 LYS cc_start: 0.7514 (pptt) cc_final: 0.6939 (pptt) REVERT: N 101 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8331 (mm-30) REVERT: B 23 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6482 (mp0) REVERT: B 178 ASP cc_start: 0.6999 (t0) cc_final: 0.5801 (p0) REVERT: B 285 LEU cc_start: 0.7237 (tp) cc_final: 0.6982 (tt) REVERT: B 323 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7903 (tt0) REVERT: K 33 SER cc_start: 0.8911 (t) cc_final: 0.8409 (m) REVERT: K 134 GLN cc_start: 0.8714 (tp40) cc_final: 0.8098 (tp-100) outliers start: 14 outliers final: 10 residues processed: 136 average time/residue: 0.1051 time to fit residues: 19.8120 Evaluate side-chains 134 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 366 GLN ** 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 = 0.3918 r_free = 0.3918 target = 0.164826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110891 restraints weight = 12280.745| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.94 r_work: 0.3146 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9596 Z= 0.118 Angle : 0.511 9.432 13018 Z= 0.259 Chirality : 0.040 0.201 1440 Planarity : 0.003 0.041 1630 Dihedral : 6.032 54.321 1325 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.50 % Allowed : 13.91 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.52 (0.25), residues: 1152 helix: 2.40 (0.26), residues: 385 sheet: 0.67 (0.28), residues: 323 loop : 0.09 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.010 0.001 TYR H 95 PHE 0.021 0.001 PHE K 97 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9590) covalent geometry : angle 0.50984 / 0.26 (13005) SS BOND : bond 0.00135 / 0.07 ( 5) SS BOND : angle 0.66402 / 0.35 ( 10) hydrogen bonds : bond 0.03127 / 2.04 ( 477) hydrogen bonds : angle 4.53302 / 3.21 ( 1368) link_ALPHA1-4 : bond 0.00012 / 0.01 ( 1) link_ALPHA1-4 : angle 1.81749 / 1.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: L 192 GLU cc_start: 0.6403 (mm-30) cc_final: 0.5716 (pp20) REVERT: L 193 LYS cc_start: 0.7546 (pptt) cc_final: 0.6658 (pptt) REVERT: N 101 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8267 (mm-30) REVERT: B 23 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: B 178 ASP cc_start: 0.6986 (t0) cc_final: 0.5776 (p0) REVERT: B 285 LEU cc_start: 0.7189 (tp) cc_final: 0.6937 (tt) REVERT: B 323 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7867 (tt0) REVERT: K 33 SER cc_start: 0.8908 (t) cc_final: 0.8407 (m) REVERT: K 127 GLU cc_start: 0.8626 (tt0) cc_final: 0.8419 (tt0) REVERT: K 134 GLN cc_start: 0.8712 (tp40) cc_final: 0.8088 (tp-100) outliers start: 15 outliers final: 13 residues processed: 138 average time/residue: 0.0994 time to fit residues: 19.4167 Evaluate side-chains 141 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 93 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 44 optimal weight: 0.0010 chunk 58 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** 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 = 0.3923 r_free = 0.3923 target = 0.165356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111559 restraints weight = 12224.739| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.04 r_work: 0.3152 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9596 Z= 0.116 Angle : 0.517 10.218 13018 Z= 0.261 Chirality : 0.040 0.184 1440 Planarity : 0.003 0.042 1630 Dihedral : 5.884 50.526 1325 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.70 % Allowed : 14.21 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.55 (0.25), residues: 1152 helix: 2.45 (0.26), residues: 385 sheet: 0.71 (0.28), residues: 323 loop : 0.08 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 99 TYR 0.020 0.001 TYR K 76 PHE 0.020 0.001 PHE K 97 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9590) covalent geometry : angle 0.51581 / 0.26 (13005) SS BOND : bond 0.00122 / 0.06 ( 5) SS BOND : angle 0.64376 / 0.35 ( 10) hydrogen bonds : bond 0.03071 / 2.00 ( 477) hydrogen bonds : angle 4.48858 / 3.18 ( 1368) link_ALPHA1-4 : bond 0.00078 / 0.04 ( 1) link_ALPHA1-4 : angle 1.72851 / 1.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: H 108 TYR cc_start: 0.7523 (m-80) cc_final: 0.7119 (m-10) REVERT: L 192 GLU cc_start: 0.6385 (mm-30) cc_final: 0.5710 (pp20) REVERT: L 193 LYS cc_start: 0.7527 (pptt) cc_final: 0.6649 (pptt) REVERT: N 101 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8234 (mm-30) REVERT: B 23 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: B 178 ASP cc_start: 0.6883 (t0) cc_final: 0.5680 (p0) REVERT: B 312 LEU cc_start: 0.7035 (tp) cc_final: 0.6616 (pp) REVERT: B 323 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7844 (tt0) REVERT: K 33 SER cc_start: 0.8922 (t) cc_final: 0.8382 (m) REVERT: K 127 GLU cc_start: 0.8627 (tt0) cc_final: 0.8406 (tt0) REVERT: K 134 GLN cc_start: 0.8694 (tp40) cc_final: 0.8031 (tp-100) outliers start: 17 outliers final: 14 residues processed: 138 average time/residue: 0.0968 time to fit residues: 18.8610 Evaluate side-chains 139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 23 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 30 optimal weight: 0.0470 chunk 14 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** 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 = 0.3929 r_free = 0.3929 target = 0.165787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112384 restraints weight = 12239.414| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.19 r_work: 0.3147 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9596 Z= 0.110 Angle : 0.511 10.045 13018 Z= 0.258 Chirality : 0.039 0.151 1440 Planarity : 0.003 0.042 1630 Dihedral : 5.678 48.771 1325 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.50 % Allowed : 14.61 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.64 (0.25), residues: 1152 helix: 2.50 (0.26), residues: 385 sheet: 0.81 (0.28), residues: 323 loop : 0.10 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.015 0.001 TYR K 196 PHE 0.019 0.001 PHE K 97 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9590) covalent geometry : angle 0.51002 / 0.26 (13005) SS BOND : bond 0.00120 / 0.07 ( 5) SS BOND : angle 0.64249 / 0.35 ( 10) hydrogen bonds : bond 0.02967 / 1.93 ( 477) hydrogen bonds : angle 4.40416 / 3.12 ( 1368) link_ALPHA1-4 : bond 0.00043 / 0.02 ( 1) link_ALPHA1-4 : angle 1.62963 / 1.36 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: L 192 GLU cc_start: 0.6327 (mm-30) cc_final: 0.5646 (pp20) REVERT: L 193 LYS cc_start: 0.7467 (pptt) cc_final: 0.6590 (pptt) REVERT: N 101 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 23 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: B 178 ASP cc_start: 0.6884 (t0) cc_final: 0.5673 (p0) REVERT: B 284 TYR cc_start: 0.7216 (m-80) cc_final: 0.6996 (m-80) REVERT: B 312 LEU cc_start: 0.7274 (tp) cc_final: 0.6896 (pp) REVERT: B 323 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7861 (tt0) REVERT: K 33 SER cc_start: 0.8929 (t) cc_final: 0.8379 (m) REVERT: K 127 GLU cc_start: 0.8640 (tt0) cc_final: 0.8430 (tt0) REVERT: K 134 GLN cc_start: 0.8704 (tp40) cc_final: 0.8051 (tp-100) outliers start: 15 outliers final: 14 residues processed: 139 average time/residue: 0.0982 time to fit residues: 19.2932 Evaluate side-chains 140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 366 GLN ** 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 = 0.3909 r_free = 0.3909 target = 0.163892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109647 restraints weight = 12190.154| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.96 r_work: 0.3130 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9596 Z= 0.160 Angle : 0.545 10.556 13018 Z= 0.275 Chirality : 0.041 0.157 1440 Planarity : 0.004 0.045 1630 Dihedral : 5.831 47.568 1325 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.70 % Allowed : 14.71 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.52 (0.25), residues: 1152 helix: 2.39 (0.26), residues: 386 sheet: 0.73 (0.28), residues: 323 loop : 0.06 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 99 TYR 0.015 0.001 TYR K 196 PHE 0.018 0.001 PHE K 97 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9590) covalent geometry : angle 0.54405 / 0.27 (13005) SS BOND : bond 0.00113 / 0.06 ( 5) SS BOND : angle 0.64491 / 0.33 ( 10) hydrogen bonds : bond 0.03231 / 2.11 ( 477) hydrogen bonds : angle 4.54400 / 3.23 ( 1368) link_ALPHA1-4 : bond 0.00133 / 0.07 ( 1) link_ALPHA1-4 : angle 1.70589 / 1.47 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.21 seconds wall clock time: 51 minutes 19.10 seconds (3079.10 seconds total)