Starting phenix.real_space_refine on Tue Feb 3 18:02:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lof_63247/02_2026/9lof_63247.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lof_63247/02_2026/9lof_63247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lof_63247/02_2026/9lof_63247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lof_63247/02_2026/9lof_63247.map" model { file = "/net/cci-nas-00/data/ceres_data/9lof_63247/02_2026/9lof_63247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lof_63247/02_2026/9lof_63247.cif" } resolution = 3.03 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= 0.168 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 38 5.16 5 C 3680 2.51 5 N 971 2.21 5 O 1168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5857 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2444 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 300} Chain: "B" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1696 Classifications: {'peptide': 226} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain: "C" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1617 Classifications: {'peptide': 210} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 198} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.16, per 1000 atoms: 0.20 Number of scatterers: 5857 At special positions: 0 Unit cell: (68.481, 80.438, 143.484, 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 38 16.00 O 1168 8.00 N 971 7.00 C 3680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 49 " distance=2.03 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 156 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 258 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 305 " distance=2.04 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " 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 ALPHA1-3 " MAN E 3 " - " MAN E 6 " " MAN E 4 " - " MAN E 5 " ALPHA1-4 " NAG E 2 " - " MAN E 3 " ALPHA1-6 " MAN E 3 " - " MAN E 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG D 1 " - " ASN A 33 " " NAG E 1 " - " ASN A 63 " Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 331.0 milliseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 16 sheets defined 13.7% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.767A pdb=" N LYS A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 removed outlier: 3.616A pdb=" N SER A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.716A pdb=" N SER A 78 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 80 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 160 through 163 removed outlier: 4.214A pdb=" N SER A 163 " --> pdb=" O SER A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.991A pdb=" N PHE A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.588A pdb=" N ASP B 90 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.077A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.676A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.620A pdb=" N PHE A 129 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A 175 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU A 131 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 149 Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 180 removed outlier: 6.796A pdb=" N CYS A 327 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N MET A 230 " --> pdb=" O CYS A 327 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY A 329 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA A 228 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 331 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP A 226 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N MET A 333 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA A 335 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N MET A 337 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 228 " --> pdb=" O MET A 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 248 removed outlier: 3.570A pdb=" N VAL A 316 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 256 through 259 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.943A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12 removed outlier: 4.035A pdb=" N TYR B 117 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 135 through 139 removed outlier: 5.425A pdb=" N ALA B 152 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 199 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLY B 154 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL B 197 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU B 156 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER B 195 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS B 158 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B 193 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 5.425A pdb=" N ALA B 152 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 199 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLY B 154 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL B 197 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU B 156 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER B 195 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS B 158 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B 193 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 166 through 169 Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.565A pdb=" N PHE C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.507A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.507A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 114 through 118 removed outlier: 5.160A pdb=" N SER C 131 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU C 181 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL C 133 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU C 179 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU C 135 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N SER C 177 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN C 137 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU C 175 " --> pdb=" O ASN C 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 153 through 154 188 hydrogen bonds defined for protein. 462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.66 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1787 1.34 - 1.46: 1567 1.46 - 1.59: 2596 1.59 - 1.71: 0 1.71 - 1.84: 51 Bond restraints: 6001 Sorted by residual: bond pdb=" C4 MAN E 3 " pdb=" C5 MAN E 3 " ideal model delta sigma weight residual 1.533 1.472 0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" CB VAL B 109 " pdb=" CG1 VAL B 109 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.36e+00 bond pdb=" C2 MAN E 3 " pdb=" C3 MAN E 3 " ideal model delta sigma weight residual 1.525 1.567 -0.042 2.00e-02 2.50e+03 4.42e+00 bond pdb=" C THR B 180 " pdb=" N PHE B 181 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.48e-02 4.57e+03 3.80e+00 bond pdb=" C1 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.399 1.437 -0.038 2.00e-02 2.50e+03 3.62e+00 ... (remaining 5996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 7690 1.95 - 3.90: 373 3.90 - 5.85: 52 5.85 - 7.79: 14 7.79 - 9.74: 8 Bond angle restraints: 8137 Sorted by residual: angle pdb=" N SER C 28 " pdb=" CA SER C 28 " pdb=" C SER C 28 " ideal model delta sigma weight residual 111.02 118.83 -7.81 1.25e+00 6.40e-01 3.91e+01 angle pdb=" C SER B 108 " pdb=" N VAL B 109 " pdb=" CA VAL B 109 " ideal model delta sigma weight residual 121.97 129.97 -8.00 1.80e+00 3.09e-01 1.98e+01 angle pdb=" N PRO A 122 " pdb=" CA PRO A 122 " pdb=" C PRO A 122 " ideal model delta sigma weight residual 111.22 116.42 -5.20 1.40e+00 5.10e-01 1.38e+01 angle pdb=" N SER C 30 " pdb=" CA SER C 30 " pdb=" C SER C 30 " ideal model delta sigma weight residual 110.80 118.69 -7.89 2.13e+00 2.20e-01 1.37e+01 angle pdb=" C ILE C 29 " pdb=" N SER C 30 " pdb=" CA SER C 30 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 ... (remaining 8132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3249 17.75 - 35.49: 307 35.49 - 53.24: 102 53.24 - 70.99: 31 70.99 - 88.73: 7 Dihedral angle restraints: 3696 sinusoidal: 1540 harmonic: 2156 Sorted by residual: dihedral pdb=" CA ILE C 29 " pdb=" C ILE C 29 " pdb=" N SER C 30 " pdb=" CA SER C 30 " ideal model delta harmonic sigma weight residual -180.00 -139.54 -40.46 0 5.00e+00 4.00e-02 6.55e+01 dihedral pdb=" CA GLY A 121 " pdb=" C GLY A 121 " pdb=" N PRO A 122 " pdb=" CA PRO A 122 " ideal model delta harmonic sigma weight residual -180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CB CYS A 274 " pdb=" SG CYS A 274 " pdb=" SG CYS A 305 " pdb=" CB CYS A 305 " ideal model delta sinusoidal sigma weight residual -86.00 -134.72 48.72 1 1.00e+01 1.00e-02 3.27e+01 ... (remaining 3693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 699 0.065 - 0.130: 174 0.130 - 0.195: 33 0.195 - 0.260: 2 0.260 - 0.324: 1 Chirality restraints: 909 Sorted by residual: chirality pdb=" C4 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" C5 NAG E 2 " pdb=" O4 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 33 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL B 109 " pdb=" CA VAL B 109 " pdb=" CG1 VAL B 109 " pdb=" CG2 VAL B 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 906 not shown) Planarity restraints: 1030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 13 " 0.047 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO B 14 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 181 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.52e+00 pdb=" N PRO A 182 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 132 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO A 133 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.036 5.00e-02 4.00e+02 ... (remaining 1027 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1335 2.78 - 3.31: 4578 3.31 - 3.84: 9616 3.84 - 4.37: 11100 4.37 - 4.90: 19621 Nonbonded interactions: 46250 Sorted by model distance: nonbonded pdb=" OE2 GLU B 6 " pdb=" OG SER B 119 " model vdw 2.255 3.040 nonbonded pdb=" O GLU A 293 " pdb=" OG SER A 299 " model vdw 2.288 3.040 nonbonded pdb=" OG SER A 45 " pdb=" OE2 GLU A 271 " model vdw 2.309 3.040 nonbonded pdb=" O SER A 253 " pdb=" OG SER A 253 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR C 36 " pdb=" OE1 GLN C 89 " model vdw 2.314 3.040 ... (remaining 46245 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: 0.420 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.660 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 6021 Z= 0.365 Angle : 1.034 12.561 8185 Z= 0.551 Chirality : 0.059 0.324 909 Planarity : 0.009 0.070 1028 Dihedral : 16.617 88.732 2288 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 12.50 % Allowed : 11.57 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.83 (0.28), residues: 748 helix: -2.81 (0.35), residues: 88 sheet: -1.05 (0.32), residues: 263 loop : -2.25 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 53 TYR 0.030 0.003 TYR C 91 PHE 0.030 0.004 PHE A 225 TRP 0.022 0.003 TRP A 141 HIS 0.012 0.002 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00830 ( 6001) covalent geometry : angle 1.01180 ( 8137) SS BOND : bond 0.00373 ( 12) SS BOND : angle 1.82546 ( 24) hydrogen bonds : bond 0.13505 ( 179) hydrogen bonds : angle 7.63287 ( 462) link_ALPHA1-3 : bond 0.00404 ( 2) link_ALPHA1-3 : angle 2.30289 ( 6) link_ALPHA1-4 : bond 0.00129 ( 1) link_ALPHA1-4 : angle 7.42474 ( 3) link_ALPHA1-6 : bond 0.00244 ( 1) link_ALPHA1-6 : angle 1.63530 ( 3) link_BETA1-4 : bond 0.00669 ( 2) link_BETA1-4 : angle 4.16837 ( 6) link_NAG-ASN : bond 0.00526 ( 2) link_NAG-ASN : angle 2.24512 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 104 time to evaluate : 0.132 Fit side-chains REVERT: A 73 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.6791 (tp40) REVERT: A 188 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: A 195 LYS cc_start: 0.6587 (tttp) cc_final: 0.6325 (pttt) REVERT: A 261 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: A 283 ASP cc_start: 0.8004 (p0) cc_final: 0.7677 (p0) REVERT: A 296 GLU cc_start: -0.0481 (OUTLIER) cc_final: -0.1084 (tt0) REVERT: A 340 ASN cc_start: 0.3630 (OUTLIER) cc_final: 0.3115 (p0) REVERT: B 22 CYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7156 (t) REVERT: B 110 HIS cc_start: 0.8649 (OUTLIER) cc_final: 0.7164 (t70) REVERT: C 2 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8507 (mm) REVERT: C 12 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7301 (p) REVERT: C 28 SER cc_start: 0.8156 (t) cc_final: 0.7434 (p) REVERT: C 70 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: C 108 ARG cc_start: 0.5296 (ptm160) cc_final: 0.5029 (ptm-80) REVERT: C 137 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6734 (m-40) REVERT: C 140 TYR cc_start: 0.6838 (t80) cc_final: 0.6297 (t80) REVERT: C 158 ASN cc_start: 0.6311 (OUTLIER) cc_final: 0.5398 (p0) REVERT: C 173 TYR cc_start: 0.7517 (m-80) cc_final: 0.7107 (m-80) outliers start: 81 outliers final: 44 residues processed: 169 average time/residue: 0.0514 time to fit residues: 11.8163 Evaluate side-chains 131 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 75 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 185 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 40 HIS A 64 HIS A 66 GLN A 234 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.184401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146729 restraints weight = 8159.252| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.27 r_work: 0.3610 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6021 Z= 0.123 Angle : 0.650 7.679 8185 Z= 0.338 Chirality : 0.045 0.214 909 Planarity : 0.006 0.050 1028 Dihedral : 11.418 62.658 1058 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.33 % Allowed : 17.59 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.98 (0.29), residues: 748 helix: -1.21 (0.50), residues: 83 sheet: -0.44 (0.34), residues: 250 loop : -1.94 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 304 TYR 0.018 0.001 TYR C 91 PHE 0.015 0.002 PHE B 137 TRP 0.014 0.001 TRP A 141 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6001) covalent geometry : angle 0.62856 ( 8137) SS BOND : bond 0.00521 ( 12) SS BOND : angle 2.24242 ( 24) hydrogen bonds : bond 0.03505 ( 179) hydrogen bonds : angle 6.10068 ( 462) link_ALPHA1-3 : bond 0.00568 ( 2) link_ALPHA1-3 : angle 1.97692 ( 6) link_ALPHA1-4 : bond 0.00623 ( 1) link_ALPHA1-4 : angle 4.00530 ( 3) link_ALPHA1-6 : bond 0.00908 ( 1) link_ALPHA1-6 : angle 1.85526 ( 3) link_BETA1-4 : bond 0.00190 ( 2) link_BETA1-4 : angle 2.60864 ( 6) link_NAG-ASN : bond 0.00125 ( 2) link_NAG-ASN : angle 0.83324 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 84 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6829 (tttp) cc_final: 0.6412 (pttt) REVERT: A 254 LYS cc_start: 0.7424 (mttt) cc_final: 0.6878 (ttpt) REVERT: A 283 ASP cc_start: 0.8150 (p0) cc_final: 0.7943 (p0) REVERT: A 296 GLU cc_start: 0.2678 (OUTLIER) cc_final: 0.0817 (tt0) REVERT: A 340 ASN cc_start: 0.3542 (OUTLIER) cc_final: 0.2822 (p0) REVERT: B 110 HIS cc_start: 0.8796 (OUTLIER) cc_final: 0.8029 (t70) REVERT: B 162 PRO cc_start: 0.6884 (Cg_endo) cc_final: 0.6633 (Cg_exo) REVERT: C 2 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8680 (mm) REVERT: C 70 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: C 105 GLU cc_start: 0.8374 (pt0) cc_final: 0.8084 (pt0) REVERT: C 137 ASN cc_start: 0.6757 (OUTLIER) cc_final: 0.6416 (m-40) REVERT: C 140 TYR cc_start: 0.7370 (t80) cc_final: 0.6514 (t80) REVERT: C 173 TYR cc_start: 0.8042 (m-80) cc_final: 0.7494 (m-80) outliers start: 41 outliers final: 23 residues processed: 117 average time/residue: 0.0545 time to fit residues: 8.4575 Evaluate side-chains 99 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS C 79 GLN C 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.178774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141954 restraints weight = 8076.316| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.17 r_work: 0.3553 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.007 0.051 6021 Z= 0.284 Angle : 0.778 8.185 8185 Z= 0.402 Chirality : 0.050 0.270 909 Planarity : 0.007 0.051 1028 Dihedral : 10.244 59.593 1007 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 7.56 % Allowed : 17.75 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.91 (0.30), residues: 748 helix: -1.04 (0.49), residues: 82 sheet: -0.41 (0.34), residues: 239 loop : -1.87 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.025 0.003 TYR C 91 PHE 0.020 0.003 PHE B 68 TRP 0.016 0.003 TRP A 141 HIS 0.010 0.002 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00673 ( 6001) covalent geometry : angle 0.75610 ( 8137) SS BOND : bond 0.00560 ( 12) SS BOND : angle 2.16400 ( 24) hydrogen bonds : bond 0.04342 ( 179) hydrogen bonds : angle 6.03158 ( 462) link_ALPHA1-3 : bond 0.00186 ( 2) link_ALPHA1-3 : angle 2.05006 ( 6) link_ALPHA1-4 : bond 0.00566 ( 1) link_ALPHA1-4 : angle 4.94679 ( 3) link_ALPHA1-6 : bond 0.00105 ( 1) link_ALPHA1-6 : angle 2.03682 ( 3) link_BETA1-4 : bond 0.00282 ( 2) link_BETA1-4 : angle 3.43023 ( 6) link_NAG-ASN : bond 0.00273 ( 2) link_NAG-ASN : angle 1.53228 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 80 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6894 (tttp) cc_final: 0.6544 (pttt) REVERT: A 296 GLU cc_start: 0.2387 (OUTLIER) cc_final: 0.1306 (tt0) REVERT: A 340 ASN cc_start: 0.3659 (OUTLIER) cc_final: 0.2841 (p0) REVERT: B 110 HIS cc_start: 0.8870 (OUTLIER) cc_final: 0.8090 (t70) REVERT: C 2 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.8840 (mm) REVERT: C 70 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: C 140 TYR cc_start: 0.7301 (t80) cc_final: 0.6370 (t80) REVERT: C 173 TYR cc_start: 0.7783 (m-80) cc_final: 0.7219 (m-80) outliers start: 49 outliers final: 31 residues processed: 119 average time/residue: 0.0663 time to fit residues: 10.2507 Evaluate side-chains 106 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.182809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146452 restraints weight = 8049.378| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.22 r_work: 0.3597 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6021 Z= 0.121 Angle : 0.615 6.362 8185 Z= 0.318 Chirality : 0.045 0.174 909 Planarity : 0.006 0.065 1028 Dihedral : 8.950 59.275 1001 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.71 % Allowed : 18.98 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.31), residues: 748 helix: -0.40 (0.53), residues: 83 sheet: -0.18 (0.35), residues: 242 loop : -1.67 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 108 TYR 0.019 0.001 TYR C 91 PHE 0.022 0.002 PHE B 137 TRP 0.012 0.001 TRP A 141 HIS 0.002 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6001) covalent geometry : angle 0.59621 ( 8137) SS BOND : bond 0.00309 ( 12) SS BOND : angle 1.73943 ( 24) hydrogen bonds : bond 0.02998 ( 179) hydrogen bonds : angle 5.52694 ( 462) link_ALPHA1-3 : bond 0.00363 ( 2) link_ALPHA1-3 : angle 1.86544 ( 6) link_ALPHA1-4 : bond 0.00558 ( 1) link_ALPHA1-4 : angle 3.94989 ( 3) link_ALPHA1-6 : bond 0.00357 ( 1) link_ALPHA1-6 : angle 1.58509 ( 3) link_BETA1-4 : bond 0.00247 ( 2) link_BETA1-4 : angle 2.97685 ( 6) link_NAG-ASN : bond 0.00035 ( 2) link_NAG-ASN : angle 0.80952 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 0.150 Fit side-chains REVERT: A 195 LYS cc_start: 0.6759 (tttp) cc_final: 0.6411 (pttt) REVERT: A 250 GLU cc_start: 0.5311 (mt-10) cc_final: 0.5075 (mt-10) REVERT: A 296 GLU cc_start: 0.1759 (OUTLIER) cc_final: 0.0856 (tt0) REVERT: A 340 ASN cc_start: 0.3512 (OUTLIER) cc_final: 0.2771 (p0) REVERT: B 110 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.8002 (t70) REVERT: B 134 PRO cc_start: 0.6678 (Cg_exo) cc_final: 0.6390 (Cg_endo) REVERT: C 2 ILE cc_start: 0.9124 (mm) cc_final: 0.8648 (mm) REVERT: C 70 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: C 173 TYR cc_start: 0.7724 (m-80) cc_final: 0.7425 (m-80) outliers start: 37 outliers final: 27 residues processed: 107 average time/residue: 0.0664 time to fit residues: 9.5259 Evaluate side-chains 103 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 4.9990 chunk 73 optimal weight: 0.0070 chunk 71 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 51 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.183858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.146800 restraints weight = 8217.511| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.26 r_work: 0.3613 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6021 Z= 0.105 Angle : 0.576 6.191 8185 Z= 0.296 Chirality : 0.044 0.171 909 Planarity : 0.006 0.063 1028 Dihedral : 8.047 57.653 996 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 6.48 % Allowed : 17.90 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.31), residues: 748 helix: 0.31 (0.58), residues: 83 sheet: 0.04 (0.36), residues: 240 loop : -1.54 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 108 TYR 0.016 0.001 TYR C 91 PHE 0.015 0.001 PHE B 137 TRP 0.011 0.001 TRP A 141 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6001) covalent geometry : angle 0.56027 ( 8137) SS BOND : bond 0.00450 ( 12) SS BOND : angle 1.40238 ( 24) hydrogen bonds : bond 0.02727 ( 179) hydrogen bonds : angle 5.23588 ( 462) link_ALPHA1-3 : bond 0.00325 ( 2) link_ALPHA1-3 : angle 1.70061 ( 6) link_ALPHA1-4 : bond 0.00665 ( 1) link_ALPHA1-4 : angle 3.76508 ( 3) link_ALPHA1-6 : bond 0.00383 ( 1) link_ALPHA1-6 : angle 1.60016 ( 3) link_BETA1-4 : bond 0.00261 ( 2) link_BETA1-4 : angle 2.82482 ( 6) link_NAG-ASN : bond 0.00095 ( 2) link_NAG-ASN : angle 0.68749 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 81 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6608 (tttp) cc_final: 0.6324 (pttt) REVERT: A 250 GLU cc_start: 0.5287 (mt-10) cc_final: 0.5072 (mt-10) REVERT: A 254 LYS cc_start: 0.7405 (mttt) cc_final: 0.6852 (ttpt) REVERT: A 296 GLU cc_start: 0.1832 (OUTLIER) cc_final: 0.1055 (tt0) REVERT: A 340 ASN cc_start: 0.3143 (OUTLIER) cc_final: 0.2493 (p0) REVERT: B 134 PRO cc_start: 0.6721 (Cg_exo) cc_final: 0.6484 (Cg_endo) REVERT: C 2 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8603 (mm) REVERT: C 70 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: C 173 TYR cc_start: 0.7608 (m-80) cc_final: 0.7400 (m-80) outliers start: 42 outliers final: 33 residues processed: 113 average time/residue: 0.0586 time to fit residues: 9.1350 Evaluate side-chains 109 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 185 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.0370 chunk 12 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.0010 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.184812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.148297 restraints weight = 8163.259| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.21 r_work: 0.3626 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6021 Z= 0.100 Angle : 0.563 6.209 8185 Z= 0.288 Chirality : 0.043 0.162 909 Planarity : 0.005 0.065 1028 Dihedral : 7.505 57.867 992 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.63 % Allowed : 20.06 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.31), residues: 748 helix: 0.67 (0.59), residues: 83 sheet: 0.07 (0.36), residues: 242 loop : -1.50 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 108 TYR 0.017 0.001 TYR C 140 PHE 0.011 0.001 PHE B 137 TRP 0.011 0.001 TRP A 141 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 6001) covalent geometry : angle 0.54860 ( 8137) SS BOND : bond 0.00287 ( 12) SS BOND : angle 1.18303 ( 24) hydrogen bonds : bond 0.02612 ( 179) hydrogen bonds : angle 5.06758 ( 462) link_ALPHA1-3 : bond 0.00303 ( 2) link_ALPHA1-3 : angle 1.68904 ( 6) link_ALPHA1-4 : bond 0.00635 ( 1) link_ALPHA1-4 : angle 3.68050 ( 3) link_ALPHA1-6 : bond 0.00425 ( 1) link_ALPHA1-6 : angle 1.55611 ( 3) link_BETA1-4 : bond 0.00274 ( 2) link_BETA1-4 : angle 2.72582 ( 6) link_NAG-ASN : bond 0.00115 ( 2) link_NAG-ASN : angle 0.62587 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.213 Fit side-chains REVERT: A 195 LYS cc_start: 0.6457 (tttp) cc_final: 0.6192 (pttt) REVERT: A 207 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6558 (mtmt) REVERT: A 254 LYS cc_start: 0.7467 (mttt) cc_final: 0.6886 (ttpt) REVERT: B 110 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.7629 (t-90) REVERT: B 134 PRO cc_start: 0.7062 (Cg_exo) cc_final: 0.6790 (Cg_endo) REVERT: C 2 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8578 (mm) REVERT: C 124 GLN cc_start: 0.4306 (OUTLIER) cc_final: 0.3872 (tp-100) outliers start: 30 outliers final: 23 residues processed: 103 average time/residue: 0.0569 time to fit residues: 7.9657 Evaluate side-chains 101 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 18 optimal weight: 0.0070 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.180457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143865 restraints weight = 8127.111| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.20 r_work: 0.3570 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6021 Z= 0.199 Angle : 0.665 7.746 8185 Z= 0.339 Chirality : 0.047 0.222 909 Planarity : 0.006 0.066 1028 Dihedral : 7.382 58.650 981 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.71 % Allowed : 19.91 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.31), residues: 748 helix: 0.32 (0.58), residues: 83 sheet: -0.06 (0.35), residues: 243 loop : -1.56 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 108 TYR 0.025 0.002 TYR C 140 PHE 0.016 0.002 PHE A 225 TRP 0.012 0.002 TRP A 141 HIS 0.007 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 6001) covalent geometry : angle 0.64658 ( 8137) SS BOND : bond 0.00417 ( 12) SS BOND : angle 1.63780 ( 24) hydrogen bonds : bond 0.03330 ( 179) hydrogen bonds : angle 5.33206 ( 462) link_ALPHA1-3 : bond 0.00136 ( 2) link_ALPHA1-3 : angle 1.96610 ( 6) link_ALPHA1-4 : bond 0.00547 ( 1) link_ALPHA1-4 : angle 4.34866 ( 3) link_ALPHA1-6 : bond 0.00281 ( 1) link_ALPHA1-6 : angle 1.77700 ( 3) link_BETA1-4 : bond 0.00265 ( 2) link_BETA1-4 : angle 3.13679 ( 6) link_NAG-ASN : bond 0.00281 ( 2) link_NAG-ASN : angle 1.26130 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6693 (mtmt) REVERT: A 240 MET cc_start: 0.6921 (mpp) cc_final: 0.6392 (mpp) REVERT: B 110 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.7790 (t-90) REVERT: B 135 SER cc_start: 0.5780 (OUTLIER) cc_final: 0.5483 (t) REVERT: C 2 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8681 (mm) REVERT: C 105 GLU cc_start: 0.8311 (pt0) cc_final: 0.8095 (pt0) outliers start: 37 outliers final: 26 residues processed: 104 average time/residue: 0.0527 time to fit residues: 7.5568 Evaluate side-chains 99 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 8 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.183610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146394 restraints weight = 8167.064| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.25 r_work: 0.3609 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6021 Z= 0.111 Angle : 0.594 6.359 8185 Z= 0.302 Chirality : 0.044 0.169 909 Planarity : 0.005 0.066 1028 Dihedral : 6.761 56.007 981 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.09 % Allowed : 20.06 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.32), residues: 748 helix: 0.58 (0.59), residues: 83 sheet: 0.12 (0.36), residues: 242 loop : -1.48 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 108 TYR 0.025 0.001 TYR C 140 PHE 0.016 0.001 PHE B 137 TRP 0.011 0.001 TRP A 141 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6001) covalent geometry : angle 0.57787 ( 8137) SS BOND : bond 0.00266 ( 12) SS BOND : angle 1.43682 ( 24) hydrogen bonds : bond 0.02742 ( 179) hydrogen bonds : angle 5.10135 ( 462) link_ALPHA1-3 : bond 0.00297 ( 2) link_ALPHA1-3 : angle 1.72961 ( 6) link_ALPHA1-4 : bond 0.00573 ( 1) link_ALPHA1-4 : angle 3.80258 ( 3) link_ALPHA1-6 : bond 0.00354 ( 1) link_ALPHA1-6 : angle 1.58884 ( 3) link_BETA1-4 : bond 0.00187 ( 2) link_BETA1-4 : angle 2.76963 ( 6) link_NAG-ASN : bond 0.00089 ( 2) link_NAG-ASN : angle 0.74299 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.128 Fit side-chains REVERT: A 106 MET cc_start: 0.8388 (mtp) cc_final: 0.7917 (mtt) REVERT: A 207 LYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6542 (mtmt) REVERT: A 240 MET cc_start: 0.6988 (mpp) cc_final: 0.6537 (mpp) REVERT: A 254 LYS cc_start: 0.7471 (mttt) cc_final: 0.6906 (ttpt) REVERT: B 134 PRO cc_start: 0.7209 (Cg_exo) cc_final: 0.6921 (Cg_endo) REVERT: B 135 SER cc_start: 0.5881 (OUTLIER) cc_final: 0.5596 (t) REVERT: C 2 ILE cc_start: 0.9076 (mm) cc_final: 0.8589 (mm) REVERT: C 105 GLU cc_start: 0.8227 (pt0) cc_final: 0.8005 (pt0) REVERT: C 124 GLN cc_start: 0.4449 (OUTLIER) cc_final: 0.3939 (tp-100) outliers start: 33 outliers final: 27 residues processed: 100 average time/residue: 0.0538 time to fit residues: 7.2664 Evaluate side-chains 102 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 185 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.182871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146116 restraints weight = 8207.710| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.22 r_work: 0.3606 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6021 Z= 0.133 Angle : 0.604 6.857 8185 Z= 0.308 Chirality : 0.044 0.182 909 Planarity : 0.005 0.067 1028 Dihedral : 6.592 53.613 980 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.25 % Allowed : 20.37 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.32), residues: 748 helix: 0.55 (0.58), residues: 83 sheet: 0.13 (0.36), residues: 242 loop : -1.43 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 108 TYR 0.023 0.002 TYR C 140 PHE 0.019 0.002 PHE B 137 TRP 0.012 0.001 TRP A 141 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6001) covalent geometry : angle 0.58856 ( 8137) SS BOND : bond 0.00318 ( 12) SS BOND : angle 1.31738 ( 24) hydrogen bonds : bond 0.02783 ( 179) hydrogen bonds : angle 5.15656 ( 462) link_ALPHA1-3 : bond 0.00201 ( 2) link_ALPHA1-3 : angle 1.77241 ( 6) link_ALPHA1-4 : bond 0.00552 ( 1) link_ALPHA1-4 : angle 3.87128 ( 3) link_ALPHA1-6 : bond 0.00331 ( 1) link_ALPHA1-6 : angle 1.64785 ( 3) link_BETA1-4 : bond 0.00196 ( 2) link_BETA1-4 : angle 2.89369 ( 6) link_NAG-ASN : bond 0.00114 ( 2) link_NAG-ASN : angle 0.87858 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.129 Fit side-chains REVERT: A 106 MET cc_start: 0.8374 (mtp) cc_final: 0.7909 (mtt) REVERT: A 207 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6617 (mtmt) REVERT: A 254 LYS cc_start: 0.7472 (mttt) cc_final: 0.6906 (ttpt) REVERT: B 134 PRO cc_start: 0.7189 (Cg_exo) cc_final: 0.6891 (Cg_endo) REVERT: B 135 SER cc_start: 0.5902 (OUTLIER) cc_final: 0.5627 (t) REVERT: C 2 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8576 (mm) REVERT: C 105 GLU cc_start: 0.8240 (pt0) cc_final: 0.8003 (pt0) REVERT: C 124 GLN cc_start: 0.4532 (OUTLIER) cc_final: 0.4000 (tp-100) outliers start: 34 outliers final: 29 residues processed: 98 average time/residue: 0.0579 time to fit residues: 7.6393 Evaluate side-chains 105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.0030 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.181473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145048 restraints weight = 8133.487| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.22 r_work: 0.3591 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6021 Z= 0.172 Angle : 0.645 7.356 8185 Z= 0.329 Chirality : 0.045 0.200 909 Planarity : 0.006 0.070 1028 Dihedral : 6.796 51.521 980 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.40 % Allowed : 20.06 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.32), residues: 748 helix: 0.26 (0.57), residues: 82 sheet: 0.04 (0.36), residues: 243 loop : -1.42 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 304 TYR 0.023 0.002 TYR C 140 PHE 0.017 0.002 PHE B 137 TRP 0.012 0.002 TRP A 141 HIS 0.006 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 6001) covalent geometry : angle 0.62552 ( 8137) SS BOND : bond 0.00436 ( 12) SS BOND : angle 1.89417 ( 24) hydrogen bonds : bond 0.03043 ( 179) hydrogen bonds : angle 5.29438 ( 462) link_ALPHA1-3 : bond 0.00149 ( 2) link_ALPHA1-3 : angle 1.85151 ( 6) link_ALPHA1-4 : bond 0.00529 ( 1) link_ALPHA1-4 : angle 4.04578 ( 3) link_ALPHA1-6 : bond 0.00258 ( 1) link_ALPHA1-6 : angle 1.68998 ( 3) link_BETA1-4 : bond 0.00142 ( 2) link_BETA1-4 : angle 3.00755 ( 6) link_NAG-ASN : bond 0.00179 ( 2) link_NAG-ASN : angle 1.02247 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.194 Fit side-chains REVERT: A 106 MET cc_start: 0.8371 (mtp) cc_final: 0.7942 (mtt) REVERT: A 207 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6668 (mtmt) REVERT: A 240 MET cc_start: 0.7110 (mpp) cc_final: 0.6622 (mpp) REVERT: B 110 HIS cc_start: 0.8796 (OUTLIER) cc_final: 0.7615 (t-90) REVERT: C 2 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8603 (mm) REVERT: C 105 GLU cc_start: 0.8264 (pt0) cc_final: 0.8006 (pt0) REVERT: C 124 GLN cc_start: 0.4636 (OUTLIER) cc_final: 0.4087 (tp-100) outliers start: 35 outliers final: 29 residues processed: 103 average time/residue: 0.0587 time to fit residues: 8.1470 Evaluate side-chains 108 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 73 optimal weight: 0.0870 chunk 41 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.183670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146935 restraints weight = 8124.565| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.23 r_work: 0.3621 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6021 Z= 0.113 Angle : 0.598 6.801 8185 Z= 0.304 Chirality : 0.043 0.169 909 Planarity : 0.005 0.068 1028 Dihedral : 6.277 49.143 980 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.78 % Allowed : 20.52 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.32), residues: 748 helix: 0.52 (0.59), residues: 82 sheet: 0.16 (0.37), residues: 242 loop : -1.36 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 304 TYR 0.020 0.001 TYR C 140 PHE 0.018 0.001 PHE B 137 TRP 0.011 0.001 TRP A 141 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6001) covalent geometry : angle 0.58141 ( 8137) SS BOND : bond 0.00354 ( 12) SS BOND : angle 1.50849 ( 24) hydrogen bonds : bond 0.02610 ( 179) hydrogen bonds : angle 5.08921 ( 462) link_ALPHA1-3 : bond 0.00295 ( 2) link_ALPHA1-3 : angle 1.72220 ( 6) link_ALPHA1-4 : bond 0.00559 ( 1) link_ALPHA1-4 : angle 3.75844 ( 3) link_ALPHA1-6 : bond 0.00436 ( 1) link_ALPHA1-6 : angle 1.59645 ( 3) link_BETA1-4 : bond 0.00241 ( 2) link_BETA1-4 : angle 2.76762 ( 6) link_NAG-ASN : bond 0.00092 ( 2) link_NAG-ASN : angle 0.78794 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1522.29 seconds wall clock time: 26 minutes 38.99 seconds (1598.99 seconds total)