Starting phenix.real_space_refine on Wed Mar 4 00:46:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rxc_24728/03_2026/7rxc_24728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxc_24728/03_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_24728/03_2026/7rxc_24728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxc_24728/03_2026/7rxc_24728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rxc_24728/03_2026/7rxc_24728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxc_24728/03_2026/7rxc_24728.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-dev-5986/lib/python3.9/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 dihedrals: 3 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: 123 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: 2.07, per 1000 atoms: 0.22 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: 0.62 Conformation dependent library (CDL) restraints added in 325.1 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: 0.36 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: 1.42 Time building geometry restraints manager: 0.83 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: 12946 3.73 - 7.46: 47 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: 5128 17.95 - 35.91: 428 35.91 - 53.86: 92 53.86 - 71.82: 17 71.82 - 89.77: 10 Dihedral angle restraints: 5675 sinusoidal: 2250 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 5672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1243 0.059 - 0.118: 181 0.118 - 0.177: 14 0.177 - 0.236: 1 0.236 - 0.294: 1 Chirality restraints: 1440 Sorted by residual: 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=" 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 -2.04 -2.33 0.29 2.00e-01 2.50e+01 2.17e+00 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: 0.750 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.830 Find NCS groups from input model: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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= 0.266 Angle : 0.782 18.648 13018 Z= 0.349 Chirality : 0.042 0.294 1440 Planarity : 0.011 0.279 1630 Dihedral : 14.270 89.769 3466 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 covalent geometry : bond 0.00553 ( 9590) covalent geometry : angle 0.77722 (13005) SS BOND : bond 0.00254 ( 5) SS BOND : angle 1.26536 ( 10) hydrogen bonds : bond 0.12327 ( 477) hydrogen bonds : angle 6.23942 ( 1368) link_ALPHA1-4 : bond 0.02914 ( 1) link_ALPHA1-4 : angle 5.61296 ( 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 : 0.342 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: 0.1144 time to fit residues: 22.5721 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 : 0.331 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.171573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121939 restraints weight = 12484.951| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.99 r_work: 0.3237 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9596 Z= 0.160 Angle : 0.549 7.662 13018 Z= 0.284 Chirality : 0.041 0.150 1440 Planarity : 0.005 0.125 1630 Dihedral : 7.285 70.978 1352 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.60 % Allowed : 6.71 % Favored : 92.69 % 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: 1.28 (0.25), residues: 1152 helix: 1.94 (0.25), residues: 389 sheet: 0.71 (0.29), residues: 305 loop : 0.08 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 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 L 95 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9590) covalent geometry : angle 0.54835 (13005) SS BOND : bond 0.00160 ( 5) SS BOND : angle 0.91443 ( 10) hydrogen bonds : bond 0.03917 ( 477) hydrogen bonds : angle 5.15079 ( 1368) link_ALPHA1-4 : bond 0.00272 ( 1) link_ALPHA1-4 : angle 1.78445 ( 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 138 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: H 153 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7874 (ttmt) REVERT: N 46 GLU cc_start: 0.8311 (pt0) cc_final: 0.8084 (pt0) REVERT: B 178 ASP cc_start: 0.7158 (t0) cc_final: 0.6123 (p0) REVERT: B 323 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8063 (tt0) REVERT: K 201 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7557 (ttpt) outliers start: 6 outliers final: 4 residues processed: 135 average time/residue: 0.0967 time to fit residues: 18.2281 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 : 0.268 ------------------------------------------------------------------------------- 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: 1.9990 chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3998 r_free = 0.3998 target = 0.171654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130752 restraints weight = 12445.752| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.00 r_work: 0.3240 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9596 Z= 0.177 Angle : 0.541 6.314 13018 Z= 0.280 Chirality : 0.041 0.187 1440 Planarity : 0.004 0.103 1630 Dihedral : 6.995 56.263 1352 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.70 % Allowed : 8.61 % Favored : 89.69 % 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: 1.35 (0.25), residues: 1152 helix: 2.05 (0.26), residues: 386 sheet: 0.73 (0.29), residues: 305 loop : 0.12 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 355 TYR 0.021 0.001 TYR K 162 PHE 0.017 0.001 PHE B 259 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9590) covalent geometry : angle 0.54054 (13005) SS BOND : bond 0.00151 ( 5) SS BOND : angle 0.79297 ( 10) hydrogen bonds : bond 0.03705 ( 477) hydrogen bonds : angle 4.91834 ( 1368) link_ALPHA1-4 : bond 0.00379 ( 1) link_ALPHA1-4 : angle 1.72026 ( 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 150 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: H 153 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8107 (ttpt) REVERT: L 172 ASP cc_start: 0.6499 (p0) cc_final: 0.6269 (p0) REVERT: L 175 ASP cc_start: 0.8042 (t0) cc_final: 0.7616 (t0) REVERT: B 23 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: B 178 ASP cc_start: 0.7199 (t0) cc_final: 0.6240 (p0) REVERT: B 323 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8145 (tt0) REVERT: B 366 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8262 (mm-40) REVERT: K 33 SER cc_start: 0.8891 (t) cc_final: 0.8554 (m) REVERT: K 134 GLN cc_start: 0.8748 (tp40) cc_final: 0.8253 (tp-100) outliers start: 17 outliers final: 8 residues processed: 142 average time/residue: 0.0955 time to fit residues: 18.9224 Evaluate side-chains 134 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 181 SER Chi-restraints excluded: chain B residue 23 GLU 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: 0.0570 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4009 r_free = 0.4009 target = 0.172917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130219 restraints weight = 12674.811| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.20 r_work: 0.3258 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9596 Z= 0.130 Angle : 0.509 6.645 13018 Z= 0.263 Chirality : 0.040 0.185 1440 Planarity : 0.004 0.084 1630 Dihedral : 6.699 53.876 1352 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.10 % Allowed : 10.61 % Favored : 88.29 % 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: 1.46 (0.25), residues: 1152 helix: 2.16 (0.26), residues: 386 sheet: 0.71 (0.28), residues: 322 loop : 0.19 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 113 TYR 0.012 0.001 TYR H 95 PHE 0.010 0.001 PHE B 259 TRP 0.009 0.001 TRP H 47 HIS 0.006 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9590) covalent geometry : angle 0.50834 (13005) SS BOND : bond 0.00111 ( 5) SS BOND : angle 0.67317 ( 10) hydrogen bonds : bond 0.03434 ( 477) hydrogen bonds : angle 4.75853 ( 1368) link_ALPHA1-4 : bond 0.00229 ( 1) link_ALPHA1-4 : angle 1.57513 ( 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 145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: H 153 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8116 (ttpt) REVERT: L 172 ASP cc_start: 0.6361 (p0) cc_final: 0.6139 (p0) REVERT: L 175 ASP cc_start: 0.7770 (t0) cc_final: 0.7508 (t0) REVERT: L 193 LYS cc_start: 0.6933 (pptt) cc_final: 0.6669 (pptt) REVERT: B 23 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: B 178 ASP cc_start: 0.7164 (t0) cc_final: 0.6114 (p0) REVERT: B 323 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8136 (tt0) REVERT: K 33 SER cc_start: 0.8906 (t) cc_final: 0.8586 (m) REVERT: K 134 GLN cc_start: 0.8721 (tp40) cc_final: 0.8283 (tp-100) outliers start: 11 outliers final: 8 residues processed: 140 average time/residue: 0.0903 time to fit residues: 17.6141 Evaluate side-chains 137 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 LEU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 23 GLU 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: 1.9990 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 0.0270 chunk 34 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3899 r_free = 0.3899 target = 0.163117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108136 restraints weight = 12353.137| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.11 r_work: 0.3102 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9596 Z= 0.189 Angle : 0.542 7.205 13018 Z= 0.279 Chirality : 0.041 0.208 1440 Planarity : 0.004 0.064 1630 Dihedral : 6.741 56.766 1352 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.80 % Allowed : 12.01 % Favored : 86.19 % 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: 1.37 (0.25), residues: 1152 helix: 2.13 (0.26), residues: 386 sheet: 0.61 (0.28), residues: 324 loop : 0.16 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 113 TYR 0.014 0.001 TYR K 158 PHE 0.014 0.001 PHE B 259 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 9590) covalent geometry : angle 0.54147 (13005) SS BOND : bond 0.00188 ( 5) SS BOND : angle 0.75934 ( 10) hydrogen bonds : bond 0.03584 ( 477) hydrogen bonds : angle 4.82546 ( 1368) link_ALPHA1-4 : bond 0.00486 ( 1) link_ALPHA1-4 : angle 1.56715 ( 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 148 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: H 153 LYS cc_start: 0.8080 (ttpt) cc_final: 0.7873 (ttpt) REVERT: L 175 ASP cc_start: 0.7521 (t0) cc_final: 0.7269 (t0) REVERT: L 193 LYS cc_start: 0.7115 (pptt) cc_final: 0.6288 (pptt) REVERT: N 101 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8410 (mm-30) REVERT: B 23 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: B 178 ASP cc_start: 0.7018 (t0) cc_final: 0.5871 (p0) REVERT: B 251 PHE cc_start: 0.7045 (t80) cc_final: 0.6781 (t80) REVERT: B 323 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7921 (tt0) REVERT: K 33 SER cc_start: 0.8997 (t) cc_final: 0.8496 (m) REVERT: K 134 GLN cc_start: 0.8681 (tp40) cc_final: 0.7958 (tp-100) outliers start: 18 outliers final: 13 residues processed: 142 average time/residue: 0.1046 time to fit residues: 20.3511 Evaluate side-chains 139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 29 ILE Chi-restraints excluded: chain L residue 181 SER 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 74 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain K residue 53 THR 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: 10.0000 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 0.0870 chunk 103 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.173649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131029 restraints weight = 12628.881| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.07 r_work: 0.3282 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9596 Z= 0.109 Angle : 0.490 7.669 13018 Z= 0.252 Chirality : 0.039 0.206 1440 Planarity : 0.003 0.051 1630 Dihedral : 6.262 58.141 1352 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.10 % Allowed : 13.51 % Favored : 85.39 % 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: 1.51 (0.25), residues: 1152 helix: 2.31 (0.26), residues: 386 sheet: 0.67 (0.28), residues: 324 loop : 0.17 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 113 TYR 0.011 0.001 TYR H 95 PHE 0.011 0.001 PHE N 104 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9590) covalent geometry : angle 0.48893 (13005) SS BOND : bond 0.00121 ( 5) SS BOND : angle 0.63475 ( 10) hydrogen bonds : bond 0.03160 ( 477) hydrogen bonds : angle 4.59445 ( 1368) link_ALPHA1-4 : bond 0.00020 ( 1) link_ALPHA1-4 : angle 1.46323 ( 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 141 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: L 193 LYS cc_start: 0.7475 (pptt) cc_final: 0.6679 (pptt) REVERT: B 23 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: B 39 GLU cc_start: 0.6921 (mp0) cc_final: 0.6388 (pm20) REVERT: B 178 ASP cc_start: 0.7133 (t0) cc_final: 0.6083 (p0) REVERT: B 285 LEU cc_start: 0.7401 (tp) cc_final: 0.7151 (tt) REVERT: B 323 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8114 (tt0) REVERT: K 33 SER cc_start: 0.8900 (t) cc_final: 0.8560 (m) REVERT: K 134 GLN cc_start: 0.8744 (tp40) cc_final: 0.8328 (tp-100) outliers start: 11 outliers final: 8 residues processed: 137 average time/residue: 0.0943 time to fit residues: 18.0307 Evaluate side-chains 133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 91 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 72 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3991 r_free = 0.3991 target = 0.170666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130425 restraints weight = 12469.867| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.11 r_work: 0.3258 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9596 Z= 0.129 Angle : 0.509 8.923 13018 Z= 0.260 Chirality : 0.040 0.209 1440 Planarity : 0.003 0.044 1630 Dihedral : 6.162 59.153 1352 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.70 % Allowed : 13.31 % Favored : 84.98 % 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: 2.37 (0.26), residues: 386 sheet: 0.69 (0.28), residues: 324 loop : 0.17 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 113 TYR 0.011 0.001 TYR H 95 PHE 0.010 0.001 PHE B 259 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS L 95 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9590) covalent geometry : angle 0.50824 (13005) SS BOND : bond 0.00243 ( 5) SS BOND : angle 0.68317 ( 10) hydrogen bonds : bond 0.03191 ( 477) hydrogen bonds : angle 4.56278 ( 1368) link_ALPHA1-4 : bond 0.00049 ( 1) link_ALPHA1-4 : angle 1.45297 ( 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 143 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: L 172 ASP cc_start: 0.6568 (p0) cc_final: 0.6354 (p0) REVERT: L 175 ASP cc_start: 0.7843 (t0) cc_final: 0.7589 (t0) REVERT: L 193 LYS cc_start: 0.7561 (pptt) cc_final: 0.7155 (pptt) REVERT: B 23 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: B 178 ASP cc_start: 0.7077 (t0) cc_final: 0.6040 (p0) REVERT: B 285 LEU cc_start: 0.7466 (tp) cc_final: 0.7222 (tt) REVERT: B 323 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8144 (tt0) REVERT: K 33 SER cc_start: 0.8903 (t) cc_final: 0.8556 (m) REVERT: K 134 GLN cc_start: 0.8754 (tp40) cc_final: 0.8303 (tp-100) outliers start: 17 outliers final: 12 residues processed: 137 average time/residue: 0.0959 time to fit residues: 18.1468 Evaluate side-chains 135 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 366 GLN 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: 0.8980 chunk 96 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4026 r_free = 0.4026 target = 0.174392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123234 restraints weight = 12554.941| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.92 r_work: 0.3269 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9596 Z= 0.106 Angle : 0.496 9.602 13018 Z= 0.253 Chirality : 0.040 0.201 1440 Planarity : 0.003 0.041 1630 Dihedral : 6.007 57.341 1352 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.20 % Allowed : 14.01 % Favored : 84.78 % 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: 1.63 (0.25), residues: 1152 helix: 2.43 (0.26), residues: 386 sheet: 0.77 (0.28), residues: 323 loop : 0.19 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 99 TYR 0.016 0.001 TYR K 196 PHE 0.011 0.001 PHE B 364 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9590) covalent geometry : angle 0.49526 (13005) SS BOND : bond 0.00121 ( 5) SS BOND : angle 0.67840 ( 10) hydrogen bonds : bond 0.03053 ( 477) hydrogen bonds : angle 4.47437 ( 1368) link_ALPHA1-4 : bond 0.00009 ( 1) link_ALPHA1-4 : angle 1.37719 ( 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 139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: L 172 ASP cc_start: 0.6465 (p0) cc_final: 0.6147 (p0) REVERT: L 175 ASP cc_start: 0.7793 (t0) cc_final: 0.7497 (t0) REVERT: L 193 LYS cc_start: 0.7504 (pptt) cc_final: 0.7128 (pptt) REVERT: B 23 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: B 39 GLU cc_start: 0.7007 (mp0) cc_final: 0.6456 (pm20) REVERT: B 178 ASP cc_start: 0.6977 (t0) cc_final: 0.5904 (p0) REVERT: B 285 LEU cc_start: 0.7334 (tp) cc_final: 0.7109 (tt) REVERT: B 323 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8012 (tt0) REVERT: K 33 SER cc_start: 0.8912 (t) cc_final: 0.8522 (m) REVERT: K 134 GLN cc_start: 0.8733 (tp40) cc_final: 0.8243 (tp-100) outliers start: 12 outliers final: 10 residues processed: 135 average time/residue: 0.1022 time to fit residues: 19.0478 Evaluate side-chains 136 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain H residue 192 VAL 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 8 LEU Chi-restraints excluded: chain B residue 23 GLU 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: 8.9990 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.161431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105765 restraints weight = 12272.150| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.19 r_work: 0.3058 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 9596 Z= 0.279 Angle : 0.622 10.197 13018 Z= 0.318 Chirality : 0.044 0.216 1440 Planarity : 0.004 0.040 1630 Dihedral : 6.705 59.577 1352 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.80 % Allowed : 14.11 % 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: 1.25 (0.25), residues: 1152 helix: 2.04 (0.25), residues: 388 sheet: 0.48 (0.28), residues: 324 loop : 0.11 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 99 TYR 0.019 0.002 TYR K 158 PHE 0.020 0.002 PHE B 259 TRP 0.016 0.002 TRP N 32 HIS 0.005 0.001 HIS L 95 Details of bonding type rmsd covalent geometry : bond 0.00661 ( 9590) covalent geometry : angle 0.62154 (13005) SS BOND : bond 0.00142 ( 5) SS BOND : angle 0.79323 ( 10) hydrogen bonds : bond 0.03892 ( 477) hydrogen bonds : angle 4.91988 ( 1368) link_ALPHA1-4 : bond 0.00802 ( 1) link_ALPHA1-4 : angle 1.68149 ( 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 148 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: H 214 ASN cc_start: 0.8462 (t0) cc_final: 0.7565 (m-40) REVERT: L 113 ARG cc_start: 0.7448 (ptt180) cc_final: 0.7211 (ptt90) REVERT: L 175 ASP cc_start: 0.7672 (t0) cc_final: 0.7189 (t0) REVERT: L 192 GLU cc_start: 0.6397 (mm-30) cc_final: 0.5671 (tm-30) REVERT: L 193 LYS cc_start: 0.7190 (pptt) cc_final: 0.6679 (pptt) REVERT: B 11 TRP cc_start: 0.7364 (m-10) cc_final: 0.7017 (m-10) REVERT: B 23 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: B 39 GLU cc_start: 0.7001 (mp0) cc_final: 0.6393 (pm20) REVERT: B 178 ASP cc_start: 0.7089 (t0) cc_final: 0.5942 (p0) REVERT: B 285 LEU cc_start: 0.7288 (tp) cc_final: 0.6980 (tt) REVERT: B 323 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7919 (tt0) REVERT: K 33 SER cc_start: 0.8949 (t) cc_final: 0.8482 (m) REVERT: K 134 GLN cc_start: 0.8741 (tp40) cc_final: 0.7978 (tp-100) outliers start: 18 outliers final: 14 residues processed: 141 average time/residue: 0.1007 time to fit residues: 19.5841 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 : 0.308 ------------------------------------------------------------------------------- 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 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 75 THR 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 107 TYR Chi-restraints excluded: chain B residue 487 ILE 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: 3.9990 chunk 54 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3914 r_free = 0.3914 target = 0.164472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110215 restraints weight = 12243.237| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.96 r_work: 0.3143 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9596 Z= 0.128 Angle : 0.526 10.519 13018 Z= 0.268 Chirality : 0.040 0.196 1440 Planarity : 0.003 0.040 1630 Dihedral : 6.129 57.983 1352 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.20 % Allowed : 14.61 % Favored : 84.18 % 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: 1.44 (0.25), residues: 1152 helix: 2.32 (0.26), residues: 385 sheet: 0.57 (0.28), residues: 323 loop : 0.12 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.016 0.001 TYR K 196 PHE 0.023 0.001 PHE K 97 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 95 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9590) covalent geometry : angle 0.52582 (13005) SS BOND : bond 0.00173 ( 5) SS BOND : angle 0.70594 ( 10) hydrogen bonds : bond 0.03216 ( 477) hydrogen bonds : angle 4.63465 ( 1368) link_ALPHA1-4 : bond 0.00157 ( 1) link_ALPHA1-4 : angle 1.46823 ( 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 142 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: H 214 ASN cc_start: 0.8424 (t0) cc_final: 0.7464 (m-40) REVERT: L 192 GLU cc_start: 0.6325 (mm-30) cc_final: 0.5633 (pp20) REVERT: L 193 LYS cc_start: 0.7468 (pptt) cc_final: 0.6597 (pptt) REVERT: B 8 LEU cc_start: 0.5198 (OUTLIER) cc_final: 0.4827 (tp) REVERT: B 23 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: B 39 GLU cc_start: 0.6849 (mp0) cc_final: 0.6312 (pm20) REVERT: B 178 ASP cc_start: 0.7033 (t0) cc_final: 0.5812 (p0) REVERT: B 312 LEU cc_start: 0.7036 (tp) cc_final: 0.6606 (pp) REVERT: B 323 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7873 (tt0) REVERT: K 33 SER cc_start: 0.8888 (t) cc_final: 0.8421 (m) REVERT: K 134 GLN cc_start: 0.8711 (tp40) cc_final: 0.8089 (tp-100) outliers start: 12 outliers final: 10 residues processed: 138 average time/residue: 0.0969 time to fit residues: 18.5832 Evaluate side-chains 140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 THR 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 29 ILE 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 23 GLU Chi-restraints excluded: chain K residue 42 LEU 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: 4.9990 chunk 102 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 109 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.164113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109985 restraints weight = 12146.419| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.12 r_work: 0.3117 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9596 Z= 0.142 Angle : 0.535 10.789 13018 Z= 0.273 Chirality : 0.040 0.184 1440 Planarity : 0.003 0.040 1630 Dihedral : 6.027 57.869 1352 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.50 % Allowed : 14.31 % Favored : 84.18 % 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: 1.50 (0.25), residues: 1152 helix: 2.39 (0.26), residues: 384 sheet: 0.60 (0.28), residues: 323 loop : 0.13 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.016 0.001 TYR K 196 PHE 0.020 0.001 PHE K 97 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9590) covalent geometry : angle 0.53436 (13005) SS BOND : bond 0.00150 ( 5) SS BOND : angle 0.65486 ( 10) hydrogen bonds : bond 0.03229 ( 477) hydrogen bonds : angle 4.57519 ( 1368) link_ALPHA1-4 : bond 0.00169 ( 1) link_ALPHA1-4 : angle 1.43964 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.24 seconds wall clock time: 50 minutes 38.12 seconds (3038.12 seconds total)